Henry Hei Ning LAM
林熙寧
PhD in Chemical Engineering
Massachusetts Institute of Technology, 2005

Associate Head and Associate Professor
Department of Chemical and Biological Engineering



(852) 2358 7133
kehlam@ust.hk
Room 4561
Personal Web

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Google Scholar
dQTozYwAAAAJ

ORCID
0000-0001-7928-0364

ResearcherID
D-8629-2011

Scopus ID
35280410200




Research Interest Publications Projects Teaching Assignment RPG Supervision Space used




Research Interest

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Bioinformatics
Mass spectrometry
Metabolomics
Microbiomes and microbial communities
Proteomics



Publications

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All Years 164 2022 1 2021 11 2020 17 2019 6 2018 14 2017 6 2016 109

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2022 1

Proteomics and Transcriptomics Uncovers Key Processes for Elasnin Tolerance in Methicillin-Resistant Staphylococcus aureus
mSystems, v. 7, (1), January 2022, article number e01393-21
Sulaiman, Jordy Evan; Long, Lexin; Qian, Peiyuan; Lam, Henry H N Article

2021 11

Combinatory strategy using nanoscale proteomics and machine learning for T cell subtyping in peripheral blood of single multiple myeloma patients
Analytica Chimica Acta, v. 1173, August 2021, article number 338672
Ye, Xueting; Yang, Yun; Zhou, Jihao; Xu, Ling; Wu, Long; Huang, Peiwu; Feng, Chun; Ke, Peng; He, An; Li, Gongqiang; Li, Yuan; Li, Yangqiu; Lam, Hei Ning; Zhang, Xinyou; Tian, Ruijun Article
Comparative Proteomic Investigation Of Multiple Methicillin-Resistant Staphylococcus Aureus Strains Generated Through Adaptive Laboratory Evolution
iScience, v. 24, (9), 24 September 2021, article number 102950
Sulaiman, Jordy Evan; Long, Lexin; Wu, Long; Qian, Peiyuan; Lam, Hei Ning Article
Evolution of Bacterial Tolerance Under Antibiotic Treatment and Its Implications on the Development of Resistance
Frontiers in Microbiology, v. 12, 26 February 2021, article number 617412
Sulaiman, Jordy Evan; Lam, Hei Ning Article
Integrated Omics Reveals the Orchestrating Role of Calycosin in Danggui Buxue Tang, a Herbal Formula Containing Angelicae Sinensis Radix and Astragali Radix, in Inducing Osteoblastic Differentiation and Proliferation
Frontiers in Pharmacology, v. 12, June 2021, article number 670947
Kwan, Kin Leung; Wong, Tin Yan; Yu, Xiaodan; Dong, Ting Xia; Lam, Hei Ning; Tsim, Karl Wah Keung Article
Mass spectrometry-based multi-omics analysis reveals the thermogenetic regulation of herbal medicine in rat model of yeast-induced fever
Journal of Ethnopharmacology, v. 279, October 2021, article number 114382
Kwan, Kin Leung; Wong, Tin Yan; Wu, Qiyun; Dong, Ting Xia; Lam, Hei Ning; Tsim, Karl Wah Keung Article
Novel Daptomycin Tolerance and Resistance Mutations in Methicillin-Resistant Staphylococcus aureus from Adaptive Laboratory Evolution
mSphere, v. 6, (5), September 2021, article number e00692-21
Sulaiman, Jordy Evan; Lam, Hei Ning Article
Susceptibility to false discovery in biomarker research using liquid chromatography-high resolution mass spectrometry based untargeted metabolomics profiling
Clinical and Translational Medicine, v. 11, (6), June 2021, article number e469
Zhang, Pengwei; Ang, Irene L.; Lam, Melody M. T.; Wei, Rui; Lei, Kate M. K.; Zhou, Xingwang; Lam, Hei Ning; He, Qing-Yu; Poon, Terence C. W. Article
The osteogenic function of danggui buxue tang, a herbal decoction containing astragali radix and angelicae sinensis radix, is optimized by boiling the two herbs together: Signaling analyses revealed by systems biology
Processes, v. 9, (7), July 2021, article number 1119
Kwan, Kin Leung; Wong, Tin Yan; Yu, Xiaodan; Dong, Ting Xia; Lam, Hei Ning; Tsim, Karl Wah Keung Article
Universal Spectrum Identifier for mass spectra
Nature Methods, v. 18, (7), July 2021, p. 768-770
Deutsch, Eric W.; Perez-Riverol, Yasset; Carver, Jeremy; Kawano, Shin; Mendoza, Luis; Van Den Bossche, Tim; Gabriels, Ralf; Binz, Pierre-Alain; Pullman, Benjamin; Sun, Zhi; Shofstahl, Jim; Bittremieux, Wout; Mak, Tytus D.; Klein, Joshua; Zhu, Yunping; Lam, Hei Ning; Vizcaíno, Juan Antonio; Bandeira, Nuno Article
Comprehensive Proteomic Analysis of Tolerant and Resistant MRSA Strains Generated Through Laboratory Evolution
31st European Congress of Clinical Microbiology & Infectious Diseases (ECCMID 2021), Online, 9-12 July 2021
Sulaiman, Jordy Evan; Long, Lexin; Wu, Long; Qian, Peiyuan; Lam, Hei Ning Conference paper
Development of Tolerance and Resistance in MRSA Under Daptomycin Treatment and Differences in the Proteome Profile of the Evolved Strains
World Microbe Forum 2021, ASM Microbe 2021 and FEMS2021, Online, 20-24 June 2021
Sulaiman, Jordy Evan; Lam, Hei Ning Conference paper

2020 17

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery
Genomics, Proteomics and Bioinformatics, v. 18, (2), April 2020, p. 104-119
Lam, Hei Ning Article
In Vitro Salivary Protein Adsorption Profile on Titanium and Ceramic Surfaces and the Corresponding Putative Immunological Implications
International Journal of Molecular Sciences, v. 21, (9), May 2020, article number 3083
Wei, Chen-Xuan; Burrow, Michael Francis; Botelho, Michael George; Lam, Hei Ning; Leung, Wai Keung Article
Proteomic Analysis of Thioproline Misincorporation in Escherichia coli
Journal of Proteomics, v. 210, January 2020, article number 103541
Liu, Jingjing; Hao, Chunlin; Wu, Long; Madej, Dominik; Chan, Wan; Lam, Hei Ning Article
Proteomic Investigation of Tolerant Escherichia coli Populations from Cyclic Antibiotic Treatment
Journal of Proteome Research, v. 19, (2), February 2020, p. 900-913
Sulaiman, Jordy Evan; Lam, Hei Ning Article
Proteomic Study of the Survival and Resuscitation Mechanisms of Filamentous Persisters in an Evolved Escherichia coli Population from Cyclic Ampicillin Treatment
mSystems, v. 5, (4), August 2020, article number e00462-20
Sulaiman, Jordy Evan; Lam, Hei Ning Article
Proteomics Study of DNA-Protein Crosslinks in Methylmethanesulfonate and Fe²⁺-EDTA-Exposed Human Cells
Chemical Research in Toxicology, v. 33, (11), November 2020, p. 2739-2744
Ham, Yat Hing; Chan, Kwan Kit; Madej, Dominik; Lam, Hei Ning; Chan, Wan Article
Quantitative Proteomics Reveals UGA-Independent Misincorporation of Selenocysteine throughout the Escherichia coli Proteome
Journal of Proteome Research, v. 20, (1), January 2021, p. 212-221
Hao, Chunlin; Lam, Hei Ning Article
A real time spectral visualization tool for PSM validation
8th Asia-Oceania Mass Spectrometry Conference (AOMSC 2020), Macau, China, 5-7 January 2020
Wu, Long; Lam, Henry Hei Ning Conference paper
Common decoy distribution as a stable and simple alternative to target-decoy search strategy in tandem MS-based shotgun proteomics
8th Asia-Oceania Mass Spectrometry Conference (AOMSC 2020), Macau, China, 5-7 January 2020
Madej, Dominik; Lam, Henry Hei Ning Conference paper
Insights into the anti-cancer effect triggered by silver nanoparticles in cisplatin-resistant A549 lung cancer cells using quantitative proteomics
68th American Society for Mass Spectrometry Conference (ASMS Reboot 2020), Online, 1-12 June 2020
Wong, Tin Yan; Kwan, Kin Leung; Lam, Henry Hei Ning Conference paper
Insights into the anti-cancer effect triggered by silver nanoparticles in cisplatin-resistant A549 lung cancer cells using quantitative proteomics
8th Asia-Oceania Mass Spectrometry Conference (AOMSC 2020), Macau, China, 5-7 January 2020
Wong, Tin Yan; Lam, Henry Conference paper
Integrated omics dissection of the effect of natural product decoction on cultured osteoblasts
8th Asia-Oceania Mass Spectrometry Conference (AOMSC 2020), Macau, China, 5-7 January 2020
Kwan, Kin Leung; Tsim, Karl Wah Keung; Lam, Henry Conference paper
Multi-omics investigation of synergistic effects of traditional Chinese medicine herbal decoction on cultured osteoblasts
68th American Society for Mass Spectrometry Conference (ASMS Reboot 2020), Online, 1-12 June 2020
Kwan, Kin Leung; Wong, Tin Yan; Yu, Anna Xiaodan; Dong, Tingxia; Lam, Henry Hei Ning; Tsim, Karl Wah Keung Conference paper
Proteomics Reveal the Underlying Mechanisms of Filamentous Persisters during Ampicillin Treatment and Resuscitation
68th American Society for Mass Spectrometry Conference (ASMS Reboot 2020), Online, 1-12 June 2020
Sulaiman, Jordy Evan; Lam, Hei Ning Conference paper
Quality control of results from searchable spectral archive
68th American Society for Mass Spectrometry Conference (ASMS Reboot 2020), Online, 1-12 June 2020
Wu, Long; Lam, Henry Hei Ning Conference paper
Quantitative proteomics analysis of apramycin producer Streptomyces tenebrarius
8th Asia-Oceania Mass Spectrometry Conference (AOMSC 2020), Macau, China, 5-7 January 2020
Linardi, Darwin; Lam, Henry Conference paper
Quantitative proteomics analysis of the aminoglycoside producer Streptomyces tenebrarius
68th American Society for Mass Spectrometry Conference (ASMS Reboot 2020), Online, 1-6 June 2020
Linardi, Darwin; Pan, T.; Yu, Yi; Lam, Henry Hei Ning Conference paper

2019 6

Application of proteomics in studying bacterial persistence
Expert Review of Proteomics, v. 16, (3), March 2019, p. 227-239
Sulaiman, Jordy Evan; Lam, Hei Ning Article
Genomic and proteomic study of evolved Escherichia coli populations from cyclic antibiotic treatment exhibiting high persistence phenotype
29th European Congress of Clinical Microbiology & Infectious Diseases (ECCMID), Amsterdam, Netherlands, 13-16 April 2019
Sulaiman, Jordy Evan; Lam, Hei Ning Conference paper
Genomic and Proteomic Study of High Persistence Evolved Escherichia coli Populations from Cyclic Antibiotic Treatment
Hong Kong Society of Mass Spectrometry (HKSMS) Annual Conference, Hong Kong, 22 June 2019
Sulaiman, Jordy Evan; Lam, Hei Ning Conference paper
Mass spectrometry based omics technology to reveal the effect of herbal decoction in cultured osteoblasts
15th International Postgraduate Symposium on Chinese Medicine, IPSCM 2019 第15届国际研究生中医药研讨会, Hong Kong, 15-16 August 2019
Kwan, Kin Leung; Wong, Tin Yan; Yu, Xiaodan; Leung, Ka Wing; Dong, Tingxia; Lam, Hei Ning; Tsim, Karl Wah Keung Conference paper
Mass-Spectrometry-Based Omics Technology to Reveal the Effect of Herbal Decoction in Cultured Osteoblasts
67th ASMS Conference on Mass Spectrometry and Allied Topics, Atlanta, Georgia, 2-6 June 2019
Kwan, Kin Leung; Wong, Tin Yan; Yu, Xiaodan; Leung, Ka Wing; Dong, Tingxia; Lam, Hei Ning; Tsim, Karl Wah Keung Conference paper
Towards a better understanding of apramycin biosynthesis in Streptomyces tenebrarius through quantitative proteomics analysis
The 29th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID 2019), Amsterdam, Netherlands, 13-16 April 2019
Linardi, Darwin; Yu, Yi; Lam, Henry Conference paper

2018 14

A Comprehensive Proteomics Study on Edible Bird's Nest Using New Monoclonal Antibody Approach And Application In Quality Control
Journal of Food Composition And Analysis, v. 66, March 2018, p. 145-151
Wong, Chun Fai; Chan, Kar Lun Gallant; Wu, Long; Lam, Hei Ning; Yao, Ping; Dong, Tina T. X.; Tsim, Karl Wah Keung Article
ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data
Journal of Biomolecular Techniques : JBT, v. 29, (2), July 2018, p. 39-45
Lee, Joonyong; Choi, Hyungwon; Colangelo, Christopher M.; Davis, Darryl; Hoopmann, Michael R.; K?ll, Lukas; Lam, Henry H N; Payne, Samuel H.; Pérez-Riverol, Yasset; The, Matthew; Wilson, Ryan; Weintraub, Susan T.; Palmblad, Magnus Article
Expanding the Use of Spectral Libraries in Proteomics
Journal of Proteome Research, v. 17, (12), 7 December 2018, p. 4051-4060
Deutsch, Eric W.; Perez-Riverol, Yasset; Chalkley, Robert J.; Wilhelm, Mathias; Tate, Stephen; Sachsenberg, Timo; Walzer, Mathias; Kall, Lukas; Delanghe, Bernard; Boecker, Sebastian; Schymanski, Emma L.; Wilmes, Paul; Dorfer, Viktoria; Kuster, Bernhard; Volders, Pieter-Jan; Jehmlich, Nico; Vissers, Johannes P. C.; Wolan, Dennis W.; Wang, Ana Y.; Mendoza, Luis; Shofstahl, Jim; Dowsey, Andrew W.; Griss, Johannes; Salek, Reza M.; Neumann, Steffen; Binz, Pierre-Alain; Lam, Hei Ning; Vizcaino, Juan Antonio; Bandeira, Nuno; Rost, Hannes Article
Proteomic Analysis of Nucleus Pulposus Cell-derived Extracellular Matrix Niche and Its Effect on Phenotypic Alteration of Dermal Fibroblasts
Scientific Reports, v. 8, (1), December 2018, article number 1512
Yuan, Minting; Pai, Pei-Jing; Liu, Xiaofen; Lam, Hei Ning; Chan, Barbara P. Article
Specific Enrichment and Proteomics Analysis of Escherichia coli Persisters from Rifampin Pretreatment
Journal of Proteome Research, v. 17, (11), November 2018, p. 3984-3996
Sulaiman, Jordy Evan; Hao, Chunlin; Lam, Hei Ning Article
A metabolomic view on methicillin-resistant Staphylococcus aureus antibiotic resistance
66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, California, USA, 2-7 June 2018
Liu, Jingjing; Yuan, Zichen; Lam, Henry Hei Ning Conference paper
Building high-quality spectral library from massive collections of tandem mass spectra with machine learning
66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, California, USA, 2-7 June 2018
Wu, Long; Lam, Henry Hei Ning Conference paper
Deep Quantitative Proteomics Analysis of the Escherichia coli Persisters
In-depth analysis of bacterial persistence and resistance, article number O1140
Sulaiman, Jordy Evan; Hao, Chunlin; Lam, Hei Ning Conference paper
Development of metaproteomics workflow for functional profiling of gut microbiome
28th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID, 2018), Madrid, Spain, 21-24 April 2018
Hao, Chunlin; Linardi, darwin; Lam, Hei Ning Conference paper
Discrimination of Environmental E.coli strains through LC-MS/MS based Metabolomics
66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, CA, USA, 3-7 Jun 2018
Yuan, Zichen; Liu, Jingjing; Ng, Chun Ning; Henry lam Conference paper
Investigation of environmental-specific E. coli from marine sediment in different nutritional niches by shotgun proteomics
66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, California, USA, 2-7 June 2018
Ng, Chun Ning; Wu, Long; Lau, Chun Kwan Stanley; Lam, Henry Hei Ning Conference paper
Label-free Quantitative Proteomics Analysis of the E. coli Persisters
Hong Kong Society of Mass Spectrometry (HKSMS) Annual Conference, Hong Kong, 30 June 2018
Sulaiman, Jordy Evan; Lam, Hei Ning Conference paper
Quantitative proteomic analysis of aminoglycoside antibiotic producer Streptomyces tenebrarius
28th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID 2018), Madrid, Spain, 21-24 April 2018
Linardi, Darwin; Hao, Chunlin; Yu, Yi; Lam, Henry Hei Ning Conference paper
Spectral cluster refinement by DBSCAN clustering for proteomics data
66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, California, USA, 3-7 June 2018
Lee, Yik Yeung; To, Ka Po; Wu, Long; Lam, Hei Ning Conference paper

2017 6

ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments
Journal of Proteome Research, v. 16, (2), February 2017, p. 945-957
Choi, Meena; Eren Do?u, Zeynep Filiz; Colangelo, Christopher M.; Cottrell, John S.; Hoopmann, Michael R.; Kapp, Eugene A.; Kim, Sangtae; Lam, Henry H N; Neubert, Thomas A.; Palmblad, Magnus; Phinney, Brett; Weintraub, Susan T.; MacLean, Brendan X.; Vitek, Olga Article
Proteomics Standards Initiative: Fifteen years of progress and future work.
Journal of Proteome Research, v. 16, (12), 1 December 2017, p. 4288-4298
Deutsch, ew; Orchard, s; Binz, pa; Bittremieux, w; Eisenacher, m; Hermjakob, h; Kawano, s; Lam, Henry Hei Ning; Mayer, g; Menschaert, g; Perez-riverol, y; Salek, rm; Tabb, dl; Tenzer, s; Vizcaino, ja; Walzer, m; Jones, ar Article
Tandem mass spectral libraries of peptides and their roles in proteomics research
Mass Spectrometry Reviews, v. 36, (5), September 2017, p. 634-648
Shao, Wenguang; Lam, Henry Hei Ning Article
Building peptide spectra library by spectral clustering using Graphics Processing Units (GPUs)
65th Annual Conference of The American Society of Mass Spectrometry (ASMS), Indianapolis, IN, USA, 4-8 June, 2017
To, Ka Po; Lam, Henry Hei Ning Conference paper
Fast Similarity Measure of SWATH-MS by Cosine Similarity of Random Pairs
7th Asia-Oceania Mass Spectrometry Conference, Singapore, 10-13 December 2017
Li, Yan Chak; Wu, Long; Lam, Henry Hei Ning Conference paper
New Functionality for the Trans-Proteomic Pipeline: Tools for the Analysis of Proteomics Data
65th Annual Conference of the American Society of Mass Spectrometry (ASMS), Indianapolis, IN, USA (2017)., Indianapolis, IN, USA, 4-8, June, 2017
Mendoza, Luis; Shteynberg, David; Hoopmann, mr; Lam, Henry Hei Ning; Eng, jk; Deutsch, Eric; Moritz, rl Conference paper

2016 10

A Hybrid Retention Time Alignment Algorithm for SWATH-MS Data
Proteomics, v. 16, (15-16), August 2016, p. 2272-2283
Wu, Long; Amon, Sabine; Lam, Henry H N Article
Direct Glycan Structure Determination of Intact N-Linked Glycopeptides by Low-Energy Collision-Induced Dissociation Tandem Mass Spectrometry and Predicted Spectral Library Searching
Analytica Chimica Acta, v. 934, August 2016, p. 152-162
Pai, Peggy; Hu, Yingwei; Lam, Henry H N Article
Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
Cell, v. 166, (3), July 2016, p. 766-778
Kusebauch, Ulrike; Campbell, David S.; Deutsch, Eric W.; Chu, Caroline S.; Spicer, Douglas A.; Brusniak, Mi-Youn; Slagel, Joseph; Sun, Zhi; Stevens, Jeffrey; Grimes, Barbara; Shteynberg, David; Hoopmann, Michael R.; Blattmann, Peter; Ratushny, Alexander V.; Rinner, Oliver; Picotti, Paola; Carapito, Christine; Huang, Chung-Ying; Kapousouz, Meghan; Lam, Henry H N; Tran, Tommy; Demir, Emek; Aitchison, John D.; Sander, Chris; Hood, Leroy; Aebersold, Ruedi; Moritz, Robert L. Article
Proteomic response of methicillin-resistant S. aureus to a synergistic antibacterial drug combination: a novel erythromycin derivative and oxacillin
Scientific Reports, v. 6, January 2016, article number 19841
Liu, Xiaofen; Pai, Pei-Jin; Zhang, Weipeng; Hu, Yingwei; Dong, Xiaojing; Qian, Peiyuan; Chen, Daijie; Lam, Henry H N Article
Spectral Library Searching To Identify Cross-Linked Peptides
Journal of Proteome Research, v. 15, (5), May 2016, p. 1725-1731
Schweppe, Devin K.; Chavez, Juan D.; Navare, Arti T.; Wu, Xia; Ruiz, Bianca; Eng, Jimmy K.; Lam, Henry H N; Bruce, James E. Article
An Efficient and Accurate Feature-based Label-free Quantification Software Tool for SWATH MS Data
15th Human Proteome Organization World Congress in 2016 (HUPO 2016), Taipei, Taiwan, 18 - 22 September 2016
Wu, Long; Li, Yan Chak; Lam, Henry H.N. Conference paper
Meat Species Identification by Protein Profiling and Spectral Fingerprinting Using MALDI-TOF-MS
64th Annual Conference of the American Society of Mass Spectrometry and Allied Topics, SAN ANTONIO, TEXAS, June 5 - 9, 2016,
Lam, Henry H N; So, Man On Conference paper
Proteome-wide Quantitative Profiling of Mis-incorporation of Selenocysteine into Proteins by LC-MS Based Shotgun Proteomics
The 64th ASMS Annual Conference on Mass Spectrometry and Allied Topics, San Antonio, Texas, U.S, 5-9 June, 2016
Hao, Chunlin; Lam, Hei Ning Conference paper
Quality control of cooking oils by metabolic profiling and spectral fingerprinting
64th ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, Texas, US, 5-9 June 2016
Cheung, Chi Yuen; Lam, Henry H.N. Conference paper
The 2016 iPRG Study: Inferring Proteoforms From Bottom-up Proteomics Data
64th Annual Conference of the American Society of Mass Spectrometry and Allied Topics (ASMS 2016), San Antonio, TX, USA, 5-9 June 2016
Palmblad, Magnus; Lam, Henry H.N.; Choi, Hyungwon; Colangelo, Christopher; Davis, Darryl; Hoopmann, Michael; Kall, Lukas; Payne, Samuel; Perez-riversol, Yasset; Weintraub, Susan T. Conference paper

2015 6

A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation
Scientific Reports, v. 5, September 2015, article number 14337
Shao, Wenguang; Zhang, Min; Lam, Henry H N; Lau, Stanley C.K. Article
An open-source computational and data resource to analyze digital maps of immunopeptidomes
eLife, July 2015, article number e07661
Caron, Etienne; Espona, Lucia; Kowalewski, Daniel J.; Schuster, Heiko; Ternette, Nicola; Alpízar, Adán; Schittenhelm, Ralf B.; Ramarathinam, Sri H.; Arlehamn, Cecilia S. Lindestam; Koh, Ching Chiek; Gillet, Ludovic C.; Rabsteyn, Armin; Navarro, Pedro; Kim, Sangtae; Lam, Henry H.N.; Sturm, Theo; Marcilla, Miguel; Sette, Alessandro; Campbell, David S.; Deutsch, Eric W.; Moritz, Robert L.; Purcell, Anthony W.; Rammensee, Hans-Georg; Stevanovic, Stefan; Aebersold, Ruedi Article
Building high-quality assay libraries for targeted analysis of SWATH MS data
Nature Protocols, v. 10, (3), March 2015, p. 426-441
Schubert, Olga T.; Gillet, Ludovic C.; Collins, Ben C.; Navarro, Pedro; Rosenberger, George; Wolski, Witold E.; Lam, Henry H N; Amodei, Dario; Mallick, Parag; MacLean, Brendan; Aebersold, Ruedi Article
Fruit of Ziziphus jujuba (Jujube) at Two Stages of Maturity: Distinction by Metabolic Profiling and Biological Assessment
Journal of Agricultural and Food Chemistry, v. 63, (2), January 2015, p. 739-744
Chen, Jianping; Chan, Pui Hei; Lam, Candy Ting Wai; Li, Zhonggui; Lam, Kelly Yin Ching; Yao, Ping; Dong, Tina Ting Xia; Lin, Huangquan; Lam, Henry H N; Tsim, Karl Wah Keung Article
iPRG 2015: Differential abundance analysis in label-free quantitative proteomics
2015 Annual Conference of the American Society of Mass Spectrometry (ASMS), St. Louis, MO, USA, 2015
Kapp, E.; Lam, Henry H N; Phinney, B.; Cottrell, J.; Hoopmann, M.; Kim, S.; Neubert, T.; Palmblad, M.; Vitek, O.; Weintraub, S. Conference paper
New functionality for the Trans-Proteomic Pipeline: tools for analysis of proteomics data
2015 Annual Conference of the American Society for Mass Spectrometry (ASMS), St. Louis, MO, USA, 2015
Mendoza, L; Shteynberg, D; Slagel, J; Hoopmann, M; Lam, Henry H N; Eng, J; Deutsch, E; Moritz, R Conference paper

2014 16

A draft map of the human proteome
Nature, v. 509, (7502), 2014, p. 575-581
Kim, Minsik; Pinto, Sneha Maria Aria; Getnet, Derese; Nirujogi, Raja Sekhar Ekhar; Manda, Srikanth Srinivas Rinivas; Chaerkady, Raghothama; Madugundu, Anil Kumar; Kelkar, Dhanashree; Isserlin, Ruth; Jain, Shobhit; Thomas, Joji Kurian; Muthusamy, Babylakshmi; Leal-Rojas, Pamela; Kumar, Praveen; Sahasrabuddhe, Nandini; Balakrishnan, Lavanya; Advani, Jayshree; George, Bijesh; Renuse, Santosh; Selvan, Lakshmi Dhevi Nagarajha Nagarajha; Patil, Arun; Nanjappa, Vishalakshi; Radhakrishnan, Aneesha; Prasad, Samarjeet; Subbannayya, Tejaswini; Raju, Rajesh; Kumar, Manish Vijaya; Sreenivasamurthy, Sreelakshmi; Marimuthu, Arivusudar; Sathe, Gajanan; Chavan, Sandip; Datta, Keshava; Subbannayya, Yashwanth; Sahu, Apeksha; Yelamanchi, Soujanya; Jayaram, Savita; Rajagopalan, Pavithra; Sharma, Jyoti; Murthy, Krishna Ramachandra; Syed, Nazia; Goel, Renu; Khan, Aafaqueahmad; Ahmad, Sartaj Akhtar; Dey, Gourav; Mudgal, Keshav; Chatterjee, Aditi; Huang, Taichung; Zhong, Jun; Wu, Xinyan; Shaw, Patrick; Freed, Donald; Zahari, Muhammad Saddiq; Mukherjee, Kanchan Kumar; Shankar, Subramanian Ravi; Mahadevan, Anita; Lam, Henry H N; Mitchell, Christopher; Shankar, Susarla Krishna Rishna; Satishchandra, Parthasarathy; Schroeder, John; Sirdeshmukh, Ravi; Maitra, Anirban; Leach, Steven; Drake, Charles; Halushka, Marc Kenneth; Prasad, Thottethodi Subrahmanya Keshava; Hruban, Ralph; Kerr, Candace; Bader, Gary; Iacobuzio-Donahue, Christine; Gowda, Harsha; Pandey, Akhilesh Article
A High-resolution LC-MS-based Secondary Metabolite Fingerprint Database of Marine Bacteria
Scientific Reports, v. 4, 2014, article number 6537
Lu, Liang; Wang, Jijie; Xu, Ying; Wang, Kailing; Hu, Yingwei; Tian, Renmao; Yang, Bo; Lai, Qiliang; Li, Yongxin; Zhang, Weipeng; Shao, Zongze; Lam, Henry H N; Qian, Peiyuan Article
A repository of assays to quantify 10,000 human proteins by SWATH-MS
Scientific Data, v. 1, September 2014, article number 140031
Rosenberger, George; Koh, Ching Chiek; Guo, Tiannan; R?st, Hannes L.; Kouvonen, Petri; Collins, Ben C.; Heusel, Moritz; Liu, Yansheng; Caron, Etienne; Vichalkovski, Anton; Faini, Marco; Schubert, Olga T.; Faridi, Pouya; Ebhardt, H. Alexander; Matondo, Mariette; Lam, Henry H N; Bader, Samuel L.; Campbell, David S.; Deutsch, Eric W.; Moritz, Robert L.; Tate, Stephen; Aebersold, Ruedi Article
Hunting for Unexpected Post-Translational Modifications by Spectral Library Searching with Tier-Wise Scoring
Journal of Proteome Research, v. 13, (5), May 2014, p. 2262-2271
Ma, Chun Wai Manson; Lam, Henry H N Article
Label-Free Quantitative Proteomics Analysis of Antibiotic Response in Staphylococcus aureus to Oxacillin
Journal of Proteome Research, v. 13, (3), March 2014, p. 1223-1233
Liu, Xiaofen; Hu, Yingwei; Pai, Pei-Jin; Chen, Daijie; Lam, Henry H N Article
Metabonomic Analysis of Water Extracts from Different Angelica Roots by ¹H-Nuclear Magnetic Resonance Spectroscopy
Molecules, v. 19, (3), 2014, p. 3460-3470
Chan, Pui Hei Nicholas; Zhang, Wendy L.; Lau, Chungho; Cheung, Chi Yuen; Keun, Hector C.; Tsim, Karl Wah Keung; Lam, Henry H N Article
Proteome Informatics Research Group (iPRG)_2012: A Study on Detecting Modified Peptides in a Complex Mixture
Molecular & cellular proteomics, v. 13, (1), January 2014, p. 360-371
Chalkley, Robert J.; Bandeira, Nuno; Chambers, Matthew C.; Clauser, Karl R.; Cottrell, John S.; Deutsch, Eric W.; Kapp, Eugene A.; Lam, Henry H N; McDonald, W. Hayes; Neubert, Thomas A.; Sun, Rui-Xiang Article
Quality Control of Danggui Buxue Tang, a Traditional Chinese Medicine Decoction, by ¹H-NMR Metabolic Profiling
Evidence-Based Complementary and Alternative Medicine, v. 2014, 2014, article number 567893
Chan, Pui Hei; Zhang, Wendy L.; Cheung, Chi Yuen; Tsim, Karl W.K.; Lam, Henry Article
Tracking the Sources of Blood Meals of Parasitic Arthropods Using Shotgun Proteomics and Unidentified Tandem Mass Spectral Libraries
Nature protocols, v. 9, (4), April 2014, p. 842-850
Oender, Oezlem; Shao, Wenguang; Lam, Henry H N; Brisson, Dustin Article
A New N-linked Glycopeptide Identification Tool, for Large-scale Glycoproteomics Analysis by Spectral Library Searching
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, Maryland, USA, 15-19 June 2014
Hu, Yingwei; Pai, Peggy Pei Jing; Lam, Henry H N Conference paper
A Novel Shotgun Proteomics-based Microbial Source Tracking Method to Differentiate E. coli Isolates Pertaining to the Feces of Different Species of Warm-blooded Animals
American Society for Microbiology (ASM) 114th General Meeting, Boston, MA, USA, 17-20 May 2014
Shao, Wenguang; Zhang, Min; Lau, Stanley Chun Kwan; Lam, Henry H N Conference paper
A Shotgun Proteomics-based Method to Differentiate E. coli Strains for Microbial Source Tracking
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, MD, USA, 15-19 June 2014
Shao, Wenguang; Zhang, Min; Lau, Stanley Chun Kwan; Lam, Henry H N Conference paper
Erythromycin Resistance Study by Label-free Quantitative Proteomics Analysis in Methicillin-resistant Staphylococcus Aureus
12th National Antibiotic Conference, Chengdu, China, 2014
Liu, Xiaofen; Hu, Yingwei; Pai, Peggy; Chen, Daijie; Lam, Henry H N Conference paper
Label-free Quantitative Proteomics Study of the Synergistic Effect of Oxacillin and a Novel Erythromycin Derivative against Methicillin-resistant Staphylococcus Aureus
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, Maryland, USA, 15-19 June 2014
Liu, Xiaofen; Pai, Peggy Pei Jing; Hu, Yingwei; Chen, Daijie; Lam, Henry H N Conference paper
Quality Control of Cooking Oils by GC-MS Profiling and Spectral Fingerprinting
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, MD, USA, 15-19 June 2014
Chan, Pui Hei Nicholas; Zhu, Y.; Tsim, Karl Wah Keung; Lam, Henry H N Conference paper
Site-specific N-linked Glycoproteomics Analysis by Nano-LC Tandem Mass Spectrometry and Spectral Library Searching
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, Maryland, USA, 15-19 June 2014
Pai, Peggy Pei Jing; Hu, Yingwei; Lam, Henry H N Conference paper

2013 16

A Complete Mass-spectrometric Map of the Yeast Proteome Applied to Quantitative Trait Analysis
Nature, v. 494, (7436), February 2013, p. 266-270
Picott, P.; Clément-ziza, M.; Lam, Henry H N; Campbell, D.S.; Schmidt, A.; Deutsch, E.W.; R?st, H.; Sun, Z.; Rinner, O.; Reiter, L.; Shen, Q.; Michaelson, J.J.; Frei, A.; Alberti, S,; Kusebauch, U.; Wollscheid, B.; Moritz, R.L.; Beyer, A.; Aebersold, R. Article
Chemical changes of Angelicae Sinensis Radix and Chuanxiong Rhizoma by wine treatment: chemical profiling and marker selection by gas chromatography coupled with triple quadrupole mass spectrometry
Chinese Medicine (United Kingdom), v. 8, (1), June 2013, article number 12
Zhan, Janis Ya-Xian; Zhang, Wendy Li; Zheng, Ken Yu-zhong; Zhu, Kevin Yue; Chen, Jian-ping; Chan, Pui-Hei; Dong, Tina Ting-xia; Choi, Roy Chi-yan; Lam, Henry H N; Tsim, Karl Wah Keung; Lau, David Tai-wai Article
Denoising Peptide Tandem Mass Spectra for Spectral Libraries: A Bayesian Approach
Journal of Proteome Research, v. 12, (7), July 2013, p. 3223-3232
Shao, Wenguang; Lam, Henry H N Article
Expanding Tandem Mass Spectral Libraries of Phosphorylated Peptides: Advances and Applications
Journal of Proteome Research, v. 12, (12), December 2013, p. 5971-5977
Hu, Yingwei; Lam, Henry H N Article
Graph-based peak alignment algorithms for multiple liquid chromatography-mass spectrometry datasets
Bioinformatics, v. 29, (19), 2013, p. 2469-2476
Wang, Jijie; Lam, Henry H N Article
Identifying Sources of Tick Blood Meals Using Unidentified Tandem Mass Spectral Libraries
Nature Communications, v. 4, April 2013, article number 1746
Onder, O.; Shao, Wenguang; Kemps, B.; Lam, Henry H N; Brisson, D. Article
Refining similarity scoring to enable decoy-free validation in spectral library searching
Proteomics, v. 13, (22), November 2013, p. 3273-3283
Shao, Wenguang; Zhu, Kan; Lam, Henry H N Article
Stable Isotope Metabolic Labeling-based Quantitative Phosphoproteomic Analysis of Arabidopsis Mutants Reveals Ethyleneregulated Time-dependent Phosphoproteins and Putative Substrates of Constitutive Triple Response 1 Kinase
Molecular and Cellular Proteomics, v. 12, (12), December 2013, p. 3559-3582
Yang, Zhu; Guo, Guangyu; Zhang, Manyu; Liu, Ying Qi; Hu, Qin; Lam, Henry H N; Cheng, Han; Xue, Yu; Li, Jiayang; Li, Ning Article
A chemical fingerprint database of marine bacteria based on high-resolution LC-MS
61th Annual Conference of the American Society of Mass Spectrometry, Minneapolis, MN, USA, 9 - 13 June 2013
Lu, Liang; Wang, Jijie; Xu, Sharon Ying; Hu, Yingwei; Lam, Henry H N; Qian, Peiyuan Conference paper
Advances in spectral library searching for phosphorylated peptides
Gordon Research Conference:Posttranslational Modification Networks, Hong Kong, China, 2013
Hu, Yingwei; Lam, Henry H N Conference paper
Graph-based time alignment algorithms for LC-MS datasets with large retention-time drifts
61th Annual Conference of the American Society of Mass Spectrometry, Minneapolis, MN, USA, 9 - 13 June 2013
Wang, Jijie; Lam, Henry H N Conference paper
iPRG-2013 Proteome Informatics Research Group study: Using RNA-seq data to refine proteomic data analysis
Annual Conference of the American Society of Mass Spectrometry, Minneapolis, MN, USA, 2 - 5 March 2013
Chalkley, Robert; Bandeira, N.; Chambers, M.C.; Cottrell, J.S.; Deutsch, E.W.; Kapp, E.A.; Lam, Henry H N; Neubert, T.A.; Sun, R.X.; Vitek, O.; Weintraub, S.T. Conference paper
Optimization of MS/MS spectral library searching for high mass accuracy spectra of peptides
Annual Conference of the American Society of Mass Spectrometr, Minneapolis, MN, USA, 9 - 13 June 2013
Zhu, Kan; Shao, Wenguang; Hu, Yingwei; Lam, Henry H N Conference paper
Oxacillin Resistance Study on Methicillin Resistant and SusceptibleStaphylococcus aureus by Label free Quantitative
61st ASMS Conference on Mass Spectrometry and Allied Topics, Minneapolis, Minnesota, USA, 9 - 13 June 2013
Liu, Xiaofen; Hu, Yingwei; Pai, Peggy Pei Jing; Chen, Daijie; Lam, Hei Ning Conference paper
Site-specific N-linked glycosylation analysis by nano-LC tandem mass spectrometry coupled with a spectral library searching approach
The Human Proteome Organisation 12th Annual World Congress (HUPO 2013), Yokohama, Japan, 2013
Pai, Peggy Pei Jing; Hu, Yingwei; Lam, Henry H N Conference paper
Utilizing unidentified tandem mass spectral libraries for biological sample fingerprinting
Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Berlin, Germany, 21 - 23 July 2013
Shao, Wenguang; Lam, Henry H N Conference paper

2012 4

Metabonomic analysis of water extracts from Chinese and American ginsengs by H-1 nuclear magnetic resonance: identification of chemical profile for quality control
Chinese medicine, v. 7, November 2012, Article number 25
Chan, Pui Hei; Zheng, Ken Y.Z.; Tsim, Karl Wah Keung; Lam, Henry H N Article
Spectral library searching for peptide identification in proteomics
Statistics and Its Interface, v. 5, (1), 2012, p. 39-46
Lam, Henry H N Article
Expanding spectral libraries of phosphorylated peptides: Progress in coverage and accuracy
Human Proteome Organization (HUPO) 11th Annual World Congress, Boston, MA, USA, 2012
Hu, Yingwei; Lam, Henry H N Conference paper
Multi-resolution LC-MS images alignment using dynamic time warping and Kullback-Leibler distance
Proceedings - International Conference on Image Processing, ICIP, 2012, article number 6467201, p. 1681-1684
Wu, William K.H.; Chung, Albert Chi Shing; Lam, Henry H N Conference paper

2011 14

A semi-empirical approach for predicting unobserved peptide MS/MS spectra from spectral libraries
Proteomics, v. 11, (24), December 2011, p. 4702-4711
Hu, Yingwei; Li, Yunzi; Lam, Henry H N Article
Absolute quantification of microbial proteomes at different states by directed mass spectrometry
Molecular Systems Biology, v. 7, (510), July 2011, Article number 510
Schmidt, Alexander; Beck, Martin; Malmstroem, Johan; Lam, Henry H N; Claassen, Manfred; Campbell, David; Aebersold, Ruedi Article
Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics
Methods, v. 54, (4), August 2011, p. 424-431
Lam, Henry H N; Aebersold, Ruedi Article
Building and searching tandem mass spectral libraries for peptide identification
Molecular & cellular proteomics, v. 10, (12), December 2011
Lam, Henry H N Article
Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration
Journal of proteome research, v. 10, (6), June 2011, p. 2882-2888
Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry H N; Eng, Jimmy K.; Martin, Daniel B. Article
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
Molecular & cellular proteomics, v. 10, (12), December 2011, M111.007690
Shteynberg, David; Deutsch, Eric W.; Lam, Henry H N; Eng, Jimmy K.; Sun, Zhi; Tasman, Natalie; Mendoza, Luis; Moritz, Robert L.; Aebersold, Ruedi; Nesvizhskii, Alexey I. Article
Spectral archives: a vision for future proteomics data repositories
Nature Methods, v. 8, (7), July 2011, p. 546-548
Lam, Henry H N Article
Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis
Proteomics, v. 11, (6), March 2011, p. 1075-1085
Zhang, Xin; Li, Yunzi; Shao, Wenguang; Lam, Henry H N Article
1H-NMR metabonomics analysis of Danggui Buxue Tang effects in HEK293T kidney cell lines
China Human Proteome Organization (CNHUPO) 7th Annual Congress, Hangzhou, China, 2011
Chan, Pui Hei Nicholas; Tsim, Karl Wah Keung; Lam, Henry H N Conference paper
A novel de-noising method for spectral library in peptide identification from tandem mass spectrometry
China Human Proteome Organization (CNHUPO) 7th Annual Congress, Hangzhou, China, 2011
Shao, Wenguang; Lam, Henry H N Conference paper
Identification of peptides with single amino acid polymorphisms by using semi-empirical MS/MS spectral library
China Human Proteome Organization (CNHUPO) 7th Annual Congress, Hangzhou, China, 2011
Hu, Yingwei; Lam, Henry H N Conference paper
iPRG 2011: A study on the identification of electron transfer dissociation (ETD) mass spectra
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2011
Martens, L.; Askenazi, M.; Bandeira, N.; Chalkley, R.; Clauser, K.; Deutsch, E.; Lam, Henry H N; Mcdonald, W.; Neubert, T.; Rudnick, P. Conference paper
iProphet: Improved statistical validation of peptide and protein identifications in shotgun proteomics
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2011
Shteynberg, D.; Deutsch, E.; Lam, Henry H N; Fermin, D.; Sun, Z.; Tasman, N.; Mendoza, L.; Moritz, R.; Aebersold, R.; Nesvizhskii, A. Conference paper
RTCalc and RTCatalog: Open-source software tools for prediction and cataloging of sequence specific retentions of peptides on liquid chromatography systems
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2011
Shteynberg, D.; Deutsch, E.; Chu, C.; Kusebauch, U.; Stevens, J.; Sun, Z.; Swearingen, K.; Lam, Henry H N; Moritz, R. Conference paper

2010 10

A guided tour of the Trans-Proteomic Pipeline
Proteomics, v. 10, (6), March 2010, p. 1150-1159
Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Farrah, Terry; Lam, Henry H N; Tasman, Natalie; Sun, Zhi; Nilsson, Erik; Pratt, Brian; Prazen, Bryan; Eng, Jimmy K.; Martin, Daniel B.; Nesvizhskii, Alexey I.; Aebersold, Ruedi Article
A ubiquitin and ubiquitin-like protein spectral library
Proteomics, v. 10, (2), January 2010, p. 337-342
Srikumar, Tharan; Jeram, Stanley M.; Lam, Henry H N; Raught, Brian Article
Artificial Decoy Spectral Libraries for False Discovery Rate Estimation in Spectral Library Searching in Proteomics
Journal of proteome research, v. 9, (1), January 2010, p. 605-610
Lam, Henry H N; Deutsch, Eric W.; Aebersold, Ruedi Article
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast
Science Signaling, v. 3, (153), December 2010
Bodenmiller, B.; Wanka, S.; Kraft, C.; Urban, J.; Campbell, D.; Pedrioli, P.G.; Gerrits, B.; Picotti, P.; Lam, Henry H N; Vitek, O.; Brusniak, M.Y.; Roschitzki, B.; Zhang, C.; Shokat, K.M.; Schlapbach, R.; Colman-Lerner, A.; Nolan, G.P.; Nesvizhskii, A.I.; Peter, M.; Loewith, R.; Mering, C.V.; Aebersold, R. Article
Spectral Library Searching for Peptide Identification via Tandem MS
Methods in Molecular Biology, v. 604, 2010, p. 95-103
Lam, Henry H N; Aebersold, Ruedi Article
Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets
Proteomics, v. 10, (6), March 2010, p. 1190-1195
Deutsch, Eric W.; Shteynberg, David; Lam, Henry H N; Sun, Zhi; Eng, Jimmy K.; Carapito, Christine; von Haller, Priska D.; Tasman, Natalie; Mendoza, Luis; Farrah, Terry; Aebersold, Ruedi Article
Using spectral libraries for peptide identification from tandem mass spectrometry (MS/MS) data
Current protocols in protein science, v. Ch. 25, April 2010, Pages Unit 25.5
Lam, Henry H N; Aebersold, Ruedi Article
Spectral Library Searching for Peptide Identification via Tandem MS
Proteome Bioinformatics /Edited by Simon J. Hubbard, Andrew R. Jones. New York, NY: Humana Press; Springer, c2010, chapter 7, p. 95-103
Lam, Henry H N; Aebersold, Ruedi Book chapter
A semi-empirical approach to predict unobserved peptide MS/MS spectra from spectral libraries
The Human Proteome Organisation 9th Annual World Congress (HUPO 2010), Sydney, Australia, 2010
Hu, Yingwei; Lam, Henry H N Conference paper
New functionality for the Trans-Proteomic Pipeline: tools for analysis of proteomics data
US Human Proteome Organization 6th Annual Conference, Denver, CO, USA
Mendoza, L.; Shteynberg, D.; Slagel, J.; Holstein, C.; Tasman, N.; Pratt, B.; Lam, Henry H N; Eng, J.; Nesvizhskii, A.; Martin, D.; Deutsch, E.; Moritz, R.; Aebersold, R. Conference paper

2009 10

MaRiMba: A Software Application for Spectral Library-Based MRM Transition List Assembly
Journal of proteome research, v. 8, (10), October 2009, p. 4396-4405
Sherwood, Carly A.; Eastham, Ashley; Lee, Lik Wee; Peterson, Amelia; Eng, Jimmy K.; Shteynberg, David; Mendoza, Luis; Deutsch, Eric W.; Risler, Jenni; Tasman, Natalie; Aebersold, Ruedi; Lam, Henry H N; Martin, Daniel B. Article
A Bayesian approach to distinguish signal and noise peaks in peptide tandem mass spectra
Human Proteome Organization 6th Annual Conference, Toronto, Canada
Shao, Wenguang; Zhang, Xin; Lam, Henry H N Conference paper
A high quality human plasma proteome available in the PeptideAtlas
Annual Conference, American Society of Mass Spectrometry, Philadelphia, PA
Ferrah, T.; Deutsch, E.; Shteynberg, D.; Campbell, D.; Lam, Henry H N; Sun, Z.; Omenn, G.; Aebersold, R. Conference paper
A human plasma proteome in the PeptideAtlas with estimated protein concentrations
Human Proteome Organization 6th Annual Conference, Toronto, Canada
Farrah, T.; Deutsch, E.; Zhang, N.; Shteynberg, D.; Lam, Henry H N; Campbell, D.; Tasman, N.; Sun, Z.; Mendoza, L.; Omenn, G.; Aebersold, R. Conference paper
A systematic investigation on the improvement in sensitivity of spectral library searching over sequence database searching in proteomics
Annual Conference, American Society of Mass Spectrometry, Philadelphia, PA
Zhang, Xin; Shao, Wenguang; Lam, Henry H N Conference paper
Identification of Ub/Ubl chains in an integrated mass spectrometry/SpectraST/SUMmOn-based work-flow
Human Proteome Organization 6th Annual Conference, Toronto, Canada
Srikumar, T.; Jeram, S.; Pedrioli, P.; Lam, Henry H N; Raught, B. Conference paper
Identification of Ub/Ubl chains using an integrated mass spectrometry/SpectraST/SUMmOn-based work-flow
International Mass Spectrometry Conference, Bremen, Germany, 2009
Srikumar, T.; Jeram, S.; Pedrioli, P.; Lam, Henry H N; Raught, B. Conference paper
Improved support for targeted proteomics workflows in PeptideAtlas
Annual Conference, US Human Proteome Organization, San Diego, CA, USA
Campbell, D.; Deutsch, E.; Lam, Henry H N; Picotti, P.; Aebersold, R. Conference paper
New functionality for the Trans-Proteomic Pipeline: tools for the analysis of proteomics data
Annual Conference, American Society of Mass Spectrometry, Philadelphia, PA
Mendoza, L.; Shteynberg, D.; Tasman, N.; Pratt, B.; Eng, J.; Lam, Henry H N; Nesvizhskii, A.; Deutsch, E.; Aebersold, R. Conference paper
Quality control of ginseng by 1H NMR metabolic profiling
International Conference on Resource Development of Chinese Medicines from Northwestern China, Hong Kong, China, 2009
Chan, Pui Hei Nicholas; Choi, Chi Yan; Chan, Kar Lun Gallant; Tsim, Karl Wah Keung; Lam, Henry H N Conference paper

2008 11

A database of mass spectrometric assays for the yeast proteome
Nature Methods, v. 5, (11), 2008, p. 913-914
Picotti, Paola; Lam, Henry H N; Campbell, David; Deutsch, Eric W.; Mirzaei, Hamid; Ranish, Jeff; Domon, Bruno; Aebersold, Ruedi Article
Building consensus spectral libraries for peptide identification in proteomics
Nature Methods, v. 5, (10), October 2008, p. 873-875
Lam, Henry H N; Deutsch, Eric W.; Eddes, James S.; Eng, Jimmy K.; Stein, Stephen E.; Aebersold, Ruedi Article
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
Physiological genomics, v. 33, (1), March 2008, p. 18-25
Deutsch, E.W.; Lam, Henry H N; Aebersold, R. Article
PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
EMBO reports, v. 9, (5), May 2008, p. 429-434
Deutsch, E.W.; Lam, Henry H N; Aebersold, R. Article
PhosphoPep - A database of protein phosphorylation sites in model organisms
Nature Biotechnology, v. 26, (12), December 2008, p. 1339-1340
Bodenmiller, Bernd; Campbell, David; Gerrits, Bertran; Lam, Henry H N; Jovanovic, Marko; Picotti, Paola; Schlapbach, Ralph; Aebersold, Ruedi Article
Absolute protein quantification estimated by spectral counting using large datasets in PeptideAtlas
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2008
Zhang, N.; Deutsch, E.; Lam, Henry H N; Aebersold, R. Conference paper
iProphet: A new tool for combining PeptideProphet results from multiple search engines improves spectrum validation
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2008
Shteynberg, D.; Nesvizhskii, A.; Deutsch, E.; Lam, Henry H N; Aebersold, R. Conference paper
iProphet: improved validation of peptide identification in shotgun proteomics
World Congress, Human Proteome Organization, Amsterdam, the Netherlands
Shteynberg, D.; Deustch, E.; Lam, Henry H N; Aebersold, R.; Nesvizhskii, A. Conference paper
New developments for open-source shotgun proteomics analysis with the Trans-Proteomic Pipeline
World Congress, Human Proteome Organization, Amsterdam, the Netherlands
Mendoza, L.; Tasman, J.; Shteynberg, D.; Eddes, J.; Zhang, N.; Wong, C.; Pratt, B.; Lam, Henry H N; Eng, J.; Deutsch, E.; Aebersold, R. Conference paper
PeptideAtlas: Resource for target selection for emerging targeted proteomics workflows
US Human Proteome Organization (USHUPO) 4th Annual Conference, Bethesda, MD, USA, 2008
Deutsch, E.; Lam, Henry H N; Aebersold, R. Conference paper
The PeptideAtlas as a tool for targeted proteomics
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2008
Campbell, D.; Deutsch, E.; Lange, V.; Picotti, P.; King, N.; Letarte, S.; Lam, Henry H N; Zhang, N.; Aebersold, R. Conference paper

2007 5

Development and validation of a spectral library searching method for peptide identification from MS/MS
Proteomics, v. 7, (5), March 2007, p. 655-667
Lam, Henry H N; Deutsch, E.W.; Eddes, J.S.; Eng, J.K.; King, N.; Stein, S.E.; Aebersold, R. Article
PhosphoPep - A phosphoproteome resource for systems biology research in Drosophila Kc167 cells
Molecular Systems Biology, v. 3, January2007, article number 139
Bodenmiller, B.; Malmstrom, J.; Gerrits, B.; Campbell, D.; Lam, Henry H N; Schmidt, A.; Rinner, O.; Mueller, L.N.; Shannon, P.T.; Pedrioli, P.G.; Panse, C.; Lee, H.K.; Schlapbach, R.; Aebersold, R. Article
Development of a spectral library building tool and re-analysis of Human Plasma PeptideAtlas datasets using spectral searching
US Human Proteome Organization (USHUPO) 3rd Annual Conference, Seattle, WA, 2007
Lam, Henry H N; Deutsch, E.; Eddes, J.; Eng, J.; King, N.; Stein, S.; Aebersold, R. Conference paper
Encoding the observed human plasma proteome in spectral libraries
Human Proteome Organization (HUPO) 6th Annual World Congress, Seoul, Korea, 2007
Lam, Henry H N; Deutsch, E.; Shteynberg, D.; Zhang, N.; Stein, S.; Aebersold, R. Conference paper
Estimating false discovery rates in spectral searching using decoy spectral libraries
Human Proteome Organization (HUPO) 6th Annual World Congress, Seoul, Korea, 2007
Lam, Henry H N; Deutsch, E.; Eddes, J.; Aebersold, R. Conference paper

2006 4

Affinity-tagged green fluorescent protein (GFP) extraction from a clarified E-coli cell lysate using a two-phase aqueous micellar system
Biotechnology and bioengineering, v. 93, (5), April 2006, p. 998-1004
Mazzola, PG; Lam, Henry H N; Kavoosi, M.; Haynes, CA; Pessoa, A.; Penna, TCV; Wang, DIC; Blankschtein, D. Article
Annotation of the yeast Proteome with PeptideAtlas
American Society of Mass Spectrometry Annual Conference (ASMS), Seattle, WA, 2006
King, N.; Deutsch, E.; Eng, J.; Ranish, J.; Raught, B.; Eddes, J.; Nesvizhskii, A.; Mallick, P.; Martin, D.; Flory, M.; Lee, H.; Lam, Henry H N; Aebersold, R. Conference paper
SpectraST: An open-source MS/MS spectra-matching search tool for targeted proteomics
American Society of Mass Spectrometry Annual Conference (ASMS), Seattle, WA, 2006
Lam, Henry H N; Deutsch, E.; Eddes, J.; Eng, J.; King, N.; Yang, S.; Roth, J.; Kilpatrick, L.; Neta, P.; Stein, S.; Aebersold, R. Conference paper
The PeptideAtlas Project
International Symposium of the Institute for Systems Biology, Seattle, WA, 2006
Deutsch, E.; Eddes, J.; Eng, J.; King, N.; Lam, Henry H N; Campbell, D.; Loevenich, S.; Mallick, P.; Martin, D.; Mendoza, L.; Nesvizhiskii, A.; Ranish, J.; Raught, B.; Shteynberg, D.; Tasman, J.; Zhang, N.; Vitek, O.; Aebersold, R. Conference paper

2005 1

Affinity-enhanced protein partitioning in decyl beta-D-glucopyranoside two-phase aqueous micellar systems
Biotechnology and bioengineering, v. 89, (4), February 2005, p. 381-392
Lam, Henry H N; Kavoosi, M.; Haynes, CA; Wang, DIC; Blankschtein, D. Article

2004 1

Affinity-enhanced protein partitioning in decyl beta-D-glucopyranoside two-phase aqueous micellar systems
American Institute of Chemical Engineers (AIChE) Annual Meeting, Austin, TX, 2004
Lam, Henry H N; Kavoosi, M.; Haynes, C.A.; Wang, D.I.C.; Blankschtein, D. Conference paper

2003 1

Glucose-6-phosphate dehydrogenase partitioning in two-phase aqueous mixed (nonionic/cationic) micellar systems
Biotechnology and bioengineering, v. 82, (4), May 2003, p. 445-456
Rangel-Yagui, CO; Lam, Henry H N; Kamei, DT; Wang, DIC; Pessoa, A.; Blankstein, D. Article


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Article 1

Proteomics and Transcriptomics Uncovers Key Processes for Elasnin Tolerance in Methicillin-Resistant Staphylococcus aureus
mSystems, v. 7, (1), January 2022, article number e01393-21
Sulaiman, Jordy Evan; Long, Lexin; Qian, Peiyuan; Lam, Henry H N


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Article 9

Combinatory strategy using nanoscale proteomics and machine learning for T cell subtyping in peripheral blood of single multiple myeloma patients
Analytica Chimica Acta, v. 1173, August 2021, article number 338672
Ye, Xueting; Yang, Yun; Zhou, Jihao; Xu, Ling; Wu, Long; Huang, Peiwu; Feng, Chun; Ke, Peng; He, An; Li, Gongqiang; Li, Yuan; Li, Yangqiu; Lam, Hei Ning; Zhang, Xinyou; Tian, Ruijun
Comparative Proteomic Investigation Of Multiple Methicillin-Resistant Staphylococcus Aureus Strains Generated Through Adaptive Laboratory Evolution
iScience, v. 24, (9), 24 September 2021, article number 102950
Sulaiman, Jordy Evan; Long, Lexin; Wu, Long; Qian, Peiyuan; Lam, Hei Ning
Evolution of Bacterial Tolerance Under Antibiotic Treatment and Its Implications on the Development of Resistance
Frontiers in Microbiology, v. 12, 26 February 2021, article number 617412
Sulaiman, Jordy Evan; Lam, Hei Ning
Integrated Omics Reveals the Orchestrating Role of Calycosin in Danggui Buxue Tang, a Herbal Formula Containing Angelicae Sinensis Radix and Astragali Radix, in Inducing Osteoblastic Differentiation and Proliferation
Frontiers in Pharmacology, v. 12, June 2021, article number 670947
Kwan, Kin Leung; Wong, Tin Yan; Yu, Xiaodan; Dong, Ting Xia; Lam, Hei Ning; Tsim, Karl Wah Keung
Mass spectrometry-based multi-omics analysis reveals the thermogenetic regulation of herbal medicine in rat model of yeast-induced fever
Journal of Ethnopharmacology, v. 279, October 2021, article number 114382
Kwan, Kin Leung; Wong, Tin Yan; Wu, Qiyun; Dong, Ting Xia; Lam, Hei Ning; Tsim, Karl Wah Keung
Novel Daptomycin Tolerance and Resistance Mutations in Methicillin-Resistant Staphylococcus aureus from Adaptive Laboratory Evolution
mSphere, v. 6, (5), September 2021, article number e00692-21
Sulaiman, Jordy Evan; Lam, Hei Ning
Susceptibility to false discovery in biomarker research using liquid chromatography-high resolution mass spectrometry based untargeted metabolomics profiling
Clinical and Translational Medicine, v. 11, (6), June 2021, article number e469
Zhang, Pengwei; Ang, Irene L.; Lam, Melody M. T.; Wei, Rui; Lei, Kate M. K.; Zhou, Xingwang; Lam, Hei Ning; He, Qing-Yu; Poon, Terence C. W.
The osteogenic function of danggui buxue tang, a herbal decoction containing astragali radix and angelicae sinensis radix, is optimized by boiling the two herbs together: Signaling analyses revealed by systems biology
Processes, v. 9, (7), July 2021, article number 1119
Kwan, Kin Leung; Wong, Tin Yan; Yu, Xiaodan; Dong, Ting Xia; Lam, Hei Ning; Tsim, Karl Wah Keung
Universal Spectrum Identifier for mass spectra
Nature Methods, v. 18, (7), July 2021, p. 768-770
Deutsch, Eric W.; Perez-Riverol, Yasset; Carver, Jeremy; Kawano, Shin; Mendoza, Luis; Van Den Bossche, Tim; Gabriels, Ralf; Binz, Pierre-Alain; Pullman, Benjamin; Sun, Zhi; Shofstahl, Jim; Bittremieux, Wout; Mak, Tytus D.; Klein, Joshua; Zhu, Yunping; Lam, Hei Ning; Vizcaíno, Juan Antonio; Bandeira, Nuno

Conference paper 2

Comprehensive Proteomic Analysis of Tolerant and Resistant MRSA Strains Generated Through Laboratory Evolution
31st European Congress of Clinical Microbiology & Infectious Diseases (ECCMID 2021), Online, 9-12 July 2021
Sulaiman, Jordy Evan; Long, Lexin; Wu, Long; Qian, Peiyuan; Lam, Hei Ning
Development of Tolerance and Resistance in MRSA Under Daptomycin Treatment and Differences in the Proteome Profile of the Evolved Strains
World Microbe Forum 2021, ASM Microbe 2021 and FEMS2021, Online, 20-24 June 2021
Sulaiman, Jordy Evan; Lam, Hei Ning


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Article 7

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery
Genomics, Proteomics and Bioinformatics, v. 18, (2), April 2020, p. 104-119
Lam, Hei Ning
In Vitro Salivary Protein Adsorption Profile on Titanium and Ceramic Surfaces and the Corresponding Putative Immunological Implications
International Journal of Molecular Sciences, v. 21, (9), May 2020, article number 3083
Wei, Chen-Xuan; Burrow, Michael Francis; Botelho, Michael George; Lam, Hei Ning; Leung, Wai Keung
Proteomic Analysis of Thioproline Misincorporation in Escherichia coli
Journal of Proteomics, v. 210, January 2020, article number 103541
Liu, Jingjing; Hao, Chunlin; Wu, Long; Madej, Dominik; Chan, Wan; Lam, Hei Ning
Proteomic Investigation of Tolerant Escherichia coli Populations from Cyclic Antibiotic Treatment
Journal of Proteome Research, v. 19, (2), February 2020, p. 900-913
Sulaiman, Jordy Evan; Lam, Hei Ning
Proteomic Study of the Survival and Resuscitation Mechanisms of Filamentous Persisters in an Evolved Escherichia coli Population from Cyclic Ampicillin Treatment
mSystems, v. 5, (4), August 2020, article number e00462-20
Sulaiman, Jordy Evan; Lam, Hei Ning
Proteomics Study of DNA-Protein Crosslinks in Methylmethanesulfonate and Fe²⁺-EDTA-Exposed Human Cells
Chemical Research in Toxicology, v. 33, (11), November 2020, p. 2739-2744
Ham, Yat Hing; Chan, Kwan Kit; Madej, Dominik; Lam, Hei Ning; Chan, Wan
Quantitative Proteomics Reveals UGA-Independent Misincorporation of Selenocysteine throughout the Escherichia coli Proteome
Journal of Proteome Research, v. 20, (1), January 2021, p. 212-221
Hao, Chunlin; Lam, Hei Ning

Conference paper 10

A real time spectral visualization tool for PSM validation
8th Asia-Oceania Mass Spectrometry Conference (AOMSC 2020), Macau, China, 5-7 January 2020
Wu, Long; Lam, Henry Hei Ning
Common decoy distribution as a stable and simple alternative to target-decoy search strategy in tandem MS-based shotgun proteomics
8th Asia-Oceania Mass Spectrometry Conference (AOMSC 2020), Macau, China, 5-7 January 2020
Madej, Dominik; Lam, Henry Hei Ning
Insights into the anti-cancer effect triggered by silver nanoparticles in cisplatin-resistant A549 lung cancer cells using quantitative proteomics
68th American Society for Mass Spectrometry Conference (ASMS Reboot 2020), Online, 1-12 June 2020
Wong, Tin Yan; Kwan, Kin Leung; Lam, Henry Hei Ning
Insights into the anti-cancer effect triggered by silver nanoparticles in cisplatin-resistant A549 lung cancer cells using quantitative proteomics
8th Asia-Oceania Mass Spectrometry Conference (AOMSC 2020), Macau, China, 5-7 January 2020
Wong, Tin Yan; Lam, Henry
Integrated omics dissection of the effect of natural product decoction on cultured osteoblasts
8th Asia-Oceania Mass Spectrometry Conference (AOMSC 2020), Macau, China, 5-7 January 2020
Kwan, Kin Leung; Tsim, Karl Wah Keung; Lam, Henry
Multi-omics investigation of synergistic effects of traditional Chinese medicine herbal decoction on cultured osteoblasts
68th American Society for Mass Spectrometry Conference (ASMS Reboot 2020), Online, 1-12 June 2020
Kwan, Kin Leung; Wong, Tin Yan; Yu, Anna Xiaodan; Dong, Tingxia; Lam, Henry Hei Ning; Tsim, Karl Wah Keung
Proteomics Reveal the Underlying Mechanisms of Filamentous Persisters during Ampicillin Treatment and Resuscitation
68th American Society for Mass Spectrometry Conference (ASMS Reboot 2020), Online, 1-12 June 2020
Sulaiman, Jordy Evan; Lam, Hei Ning
Quality control of results from searchable spectral archive
68th American Society for Mass Spectrometry Conference (ASMS Reboot 2020), Online, 1-12 June 2020
Wu, Long; Lam, Henry Hei Ning
Quantitative proteomics analysis of apramycin producer Streptomyces tenebrarius
8th Asia-Oceania Mass Spectrometry Conference (AOMSC 2020), Macau, China, 5-7 January 2020
Linardi, Darwin; Lam, Henry
Quantitative proteomics analysis of the aminoglycoside producer Streptomyces tenebrarius
68th American Society for Mass Spectrometry Conference (ASMS Reboot 2020), Online, 1-6 June 2020
Linardi, Darwin; Pan, T.; Yu, Yi; Lam, Henry Hei Ning


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Article 1

Application of proteomics in studying bacterial persistence
Expert Review of Proteomics, v. 16, (3), March 2019, p. 227-239
Sulaiman, Jordy Evan; Lam, Hei Ning

Conference paper 5

Genomic and proteomic study of evolved Escherichia coli populations from cyclic antibiotic treatment exhibiting high persistence phenotype
29th European Congress of Clinical Microbiology & Infectious Diseases (ECCMID), Amsterdam, Netherlands, 13-16 April 2019
Sulaiman, Jordy Evan; Lam, Hei Ning
Genomic and Proteomic Study of High Persistence Evolved Escherichia coli Populations from Cyclic Antibiotic Treatment
Hong Kong Society of Mass Spectrometry (HKSMS) Annual Conference, Hong Kong, 22 June 2019
Sulaiman, Jordy Evan; Lam, Hei Ning
Mass spectrometry based omics technology to reveal the effect of herbal decoction in cultured osteoblasts
15th International Postgraduate Symposium on Chinese Medicine, IPSCM 2019 第15届国际研究生中医药研讨会, Hong Kong, 15-16 August 2019
Kwan, Kin Leung; Wong, Tin Yan; Yu, Xiaodan; Leung, Ka Wing; Dong, Tingxia; Lam, Hei Ning; Tsim, Karl Wah Keung
Mass-Spectrometry-Based Omics Technology to Reveal the Effect of Herbal Decoction in Cultured Osteoblasts
67th ASMS Conference on Mass Spectrometry and Allied Topics, Atlanta, Georgia, 2-6 June 2019
Kwan, Kin Leung; Wong, Tin Yan; Yu, Xiaodan; Leung, Ka Wing; Dong, Tingxia; Lam, Hei Ning; Tsim, Karl Wah Keung
Towards a better understanding of apramycin biosynthesis in Streptomyces tenebrarius through quantitative proteomics analysis
The 29th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID 2019), Amsterdam, Netherlands, 13-16 April 2019
Linardi, Darwin; Yu, Yi; Lam, Henry


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Article 5

A Comprehensive Proteomics Study on Edible Bird's Nest Using New Monoclonal Antibody Approach And Application In Quality Control
Journal of Food Composition And Analysis, v. 66, March 2018, p. 145-151
Wong, Chun Fai; Chan, Kar Lun Gallant; Wu, Long; Lam, Hei Ning; Yao, Ping; Dong, Tina T. X.; Tsim, Karl Wah Keung
ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data
Journal of Biomolecular Techniques : JBT, v. 29, (2), July 2018, p. 39-45
Lee, Joonyong; Choi, Hyungwon; Colangelo, Christopher M.; Davis, Darryl; Hoopmann, Michael R.; K?ll, Lukas; Lam, Henry H N; Payne, Samuel H.; Pérez-Riverol, Yasset; The, Matthew; Wilson, Ryan; Weintraub, Susan T.; Palmblad, Magnus
Expanding the Use of Spectral Libraries in Proteomics
Journal of Proteome Research, v. 17, (12), 7 December 2018, p. 4051-4060
Deutsch, Eric W.; Perez-Riverol, Yasset; Chalkley, Robert J.; Wilhelm, Mathias; Tate, Stephen; Sachsenberg, Timo; Walzer, Mathias; Kall, Lukas; Delanghe, Bernard; Boecker, Sebastian; Schymanski, Emma L.; Wilmes, Paul; Dorfer, Viktoria; Kuster, Bernhard; Volders, Pieter-Jan; Jehmlich, Nico; Vissers, Johannes P. C.; Wolan, Dennis W.; Wang, Ana Y.; Mendoza, Luis; Shofstahl, Jim; Dowsey, Andrew W.; Griss, Johannes; Salek, Reza M.; Neumann, Steffen; Binz, Pierre-Alain; Lam, Hei Ning; Vizcaino, Juan Antonio; Bandeira, Nuno; Rost, Hannes
Proteomic Analysis of Nucleus Pulposus Cell-derived Extracellular Matrix Niche and Its Effect on Phenotypic Alteration of Dermal Fibroblasts
Scientific Reports, v. 8, (1), December 2018, article number 1512
Yuan, Minting; Pai, Pei-Jing; Liu, Xiaofen; Lam, Hei Ning; Chan, Barbara P.
Specific Enrichment and Proteomics Analysis of Escherichia coli Persisters from Rifampin Pretreatment
Journal of Proteome Research, v. 17, (11), November 2018, p. 3984-3996
Sulaiman, Jordy Evan; Hao, Chunlin; Lam, Hei Ning

Conference paper 9

A metabolomic view on methicillin-resistant Staphylococcus aureus antibiotic resistance
66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, California, USA, 2-7 June 2018
Liu, Jingjing; Yuan, Zichen; Lam, Henry Hei Ning
Building high-quality spectral library from massive collections of tandem mass spectra with machine learning
66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, California, USA, 2-7 June 2018
Wu, Long; Lam, Henry Hei Ning
Deep Quantitative Proteomics Analysis of the Escherichia coli Persisters
In-depth analysis of bacterial persistence and resistance, article number O1140
Sulaiman, Jordy Evan; Hao, Chunlin; Lam, Hei Ning
Development of metaproteomics workflow for functional profiling of gut microbiome
28th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID, 2018), Madrid, Spain, 21-24 April 2018
Hao, Chunlin; Linardi, darwin; Lam, Hei Ning
Discrimination of Environmental E.coli strains through LC-MS/MS based Metabolomics
66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, CA, USA, 3-7 Jun 2018
Yuan, Zichen; Liu, Jingjing; Ng, Chun Ning; Henry lam
Investigation of environmental-specific E. coli from marine sediment in different nutritional niches by shotgun proteomics
66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, California, USA, 2-7 June 2018
Ng, Chun Ning; Wu, Long; Lau, Chun Kwan Stanley; Lam, Henry Hei Ning
Label-free Quantitative Proteomics Analysis of the E. coli Persisters
Hong Kong Society of Mass Spectrometry (HKSMS) Annual Conference, Hong Kong, 30 June 2018
Sulaiman, Jordy Evan; Lam, Hei Ning
Quantitative proteomic analysis of aminoglycoside antibiotic producer Streptomyces tenebrarius
28th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID 2018), Madrid, Spain, 21-24 April 2018
Linardi, Darwin; Hao, Chunlin; Yu, Yi; Lam, Henry Hei Ning
Spectral cluster refinement by DBSCAN clustering for proteomics data
66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, California, USA, 3-7 June 2018
Lee, Yik Yeung; To, Ka Po; Wu, Long; Lam, Hei Ning


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Article 3

ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments
Journal of Proteome Research, v. 16, (2), February 2017, p. 945-957
Choi, Meena; Eren Do?u, Zeynep Filiz; Colangelo, Christopher M.; Cottrell, John S.; Hoopmann, Michael R.; Kapp, Eugene A.; Kim, Sangtae; Lam, Henry H N; Neubert, Thomas A.; Palmblad, Magnus; Phinney, Brett; Weintraub, Susan T.; MacLean, Brendan X.; Vitek, Olga
Proteomics Standards Initiative: Fifteen years of progress and future work.
Journal of Proteome Research, v. 16, (12), 1 December 2017, p. 4288-4298
Deutsch, ew; Orchard, s; Binz, pa; Bittremieux, w; Eisenacher, m; Hermjakob, h; Kawano, s; Lam, Henry Hei Ning; Mayer, g; Menschaert, g; Perez-riverol, y; Salek, rm; Tabb, dl; Tenzer, s; Vizcaino, ja; Walzer, m; Jones, ar
Tandem mass spectral libraries of peptides and their roles in proteomics research
Mass Spectrometry Reviews, v. 36, (5), September 2017, p. 634-648
Shao, Wenguang; Lam, Henry Hei Ning

Conference paper 3

Building peptide spectra library by spectral clustering using Graphics Processing Units (GPUs)
65th Annual Conference of The American Society of Mass Spectrometry (ASMS), Indianapolis, IN, USA, 4-8 June, 2017
To, Ka Po; Lam, Henry Hei Ning
Fast Similarity Measure of SWATH-MS by Cosine Similarity of Random Pairs
7th Asia-Oceania Mass Spectrometry Conference, Singapore, 10-13 December 2017
Li, Yan Chak; Wu, Long; Lam, Henry Hei Ning
New Functionality for the Trans-Proteomic Pipeline: Tools for the Analysis of Proteomics Data
65th Annual Conference of the American Society of Mass Spectrometry (ASMS), Indianapolis, IN, USA (2017)., Indianapolis, IN, USA, 4-8, June, 2017
Mendoza, Luis; Shteynberg, David; Hoopmann, mr; Lam, Henry Hei Ning; Eng, jk; Deutsch, Eric; Moritz, rl


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Article 5

A Hybrid Retention Time Alignment Algorithm for SWATH-MS Data
Proteomics, v. 16, (15-16), August 2016, p. 2272-2283
Wu, Long; Amon, Sabine; Lam, Henry H N
Direct Glycan Structure Determination of Intact N-Linked Glycopeptides by Low-Energy Collision-Induced Dissociation Tandem Mass Spectrometry and Predicted Spectral Library Searching
Analytica Chimica Acta, v. 934, August 2016, p. 152-162
Pai, Peggy; Hu, Yingwei; Lam, Henry H N
Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
Cell, v. 166, (3), July 2016, p. 766-778
Kusebauch, Ulrike; Campbell, David S.; Deutsch, Eric W.; Chu, Caroline S.; Spicer, Douglas A.; Brusniak, Mi-Youn; Slagel, Joseph; Sun, Zhi; Stevens, Jeffrey; Grimes, Barbara; Shteynberg, David; Hoopmann, Michael R.; Blattmann, Peter; Ratushny, Alexander V.; Rinner, Oliver; Picotti, Paola; Carapito, Christine; Huang, Chung-Ying; Kapousouz, Meghan; Lam, Henry H N; Tran, Tommy; Demir, Emek; Aitchison, John D.; Sander, Chris; Hood, Leroy; Aebersold, Ruedi; Moritz, Robert L.
Proteomic response of methicillin-resistant S. aureus to a synergistic antibacterial drug combination: a novel erythromycin derivative and oxacillin
Scientific Reports, v. 6, January 2016, article number 19841
Liu, Xiaofen; Pai, Pei-Jin; Zhang, Weipeng; Hu, Yingwei; Dong, Xiaojing; Qian, Peiyuan; Chen, Daijie; Lam, Henry H N
Spectral Library Searching To Identify Cross-Linked Peptides
Journal of Proteome Research, v. 15, (5), May 2016, p. 1725-1731
Schweppe, Devin K.; Chavez, Juan D.; Navare, Arti T.; Wu, Xia; Ruiz, Bianca; Eng, Jimmy K.; Lam, Henry H N; Bruce, James E.

Conference paper 5

An Efficient and Accurate Feature-based Label-free Quantification Software Tool for SWATH MS Data
15th Human Proteome Organization World Congress in 2016 (HUPO 2016), Taipei, Taiwan, 18 - 22 September 2016
Wu, Long; Li, Yan Chak; Lam, Henry H.N.
Meat Species Identification by Protein Profiling and Spectral Fingerprinting Using MALDI-TOF-MS
64th Annual Conference of the American Society of Mass Spectrometry and Allied Topics, SAN ANTONIO, TEXAS, June 5 - 9, 2016,
Lam, Henry H N; So, Man On
Proteome-wide Quantitative Profiling of Mis-incorporation of Selenocysteine into Proteins by LC-MS Based Shotgun Proteomics
The 64th ASMS Annual Conference on Mass Spectrometry and Allied Topics, San Antonio, Texas, U.S, 5-9 June, 2016
Hao, Chunlin; Lam, Hei Ning
Quality control of cooking oils by metabolic profiling and spectral fingerprinting
64th ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, Texas, US, 5-9 June 2016
Cheung, Chi Yuen; Lam, Henry H.N.
The 2016 iPRG Study: Inferring Proteoforms From Bottom-up Proteomics Data
64th Annual Conference of the American Society of Mass Spectrometry and Allied Topics (ASMS 2016), San Antonio, TX, USA, 5-9 June 2016
Palmblad, Magnus; Lam, Henry H.N.; Choi, Hyungwon; Colangelo, Christopher; Davis, Darryl; Hoopmann, Michael; Kall, Lukas; Payne, Samuel; Perez-riversol, Yasset; Weintraub, Susan T.


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Article 4

A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation
Scientific Reports, v. 5, September 2015, article number 14337
Shao, Wenguang; Zhang, Min; Lam, Henry H N; Lau, Stanley C.K.
An open-source computational and data resource to analyze digital maps of immunopeptidomes
eLife, July 2015, article number e07661
Caron, Etienne; Espona, Lucia; Kowalewski, Daniel J.; Schuster, Heiko; Ternette, Nicola; Alpízar, Adán; Schittenhelm, Ralf B.; Ramarathinam, Sri H.; Arlehamn, Cecilia S. Lindestam; Koh, Ching Chiek; Gillet, Ludovic C.; Rabsteyn, Armin; Navarro, Pedro; Kim, Sangtae; Lam, Henry H.N.; Sturm, Theo; Marcilla, Miguel; Sette, Alessandro; Campbell, David S.; Deutsch, Eric W.; Moritz, Robert L.; Purcell, Anthony W.; Rammensee, Hans-Georg; Stevanovic, Stefan; Aebersold, Ruedi
Building high-quality assay libraries for targeted analysis of SWATH MS data
Nature Protocols, v. 10, (3), March 2015, p. 426-441
Schubert, Olga T.; Gillet, Ludovic C.; Collins, Ben C.; Navarro, Pedro; Rosenberger, George; Wolski, Witold E.; Lam, Henry H N; Amodei, Dario; Mallick, Parag; MacLean, Brendan; Aebersold, Ruedi
Fruit of Ziziphus jujuba (Jujube) at Two Stages of Maturity: Distinction by Metabolic Profiling and Biological Assessment
Journal of Agricultural and Food Chemistry, v. 63, (2), January 2015, p. 739-744
Chen, Jianping; Chan, Pui Hei; Lam, Candy Ting Wai; Li, Zhonggui; Lam, Kelly Yin Ching; Yao, Ping; Dong, Tina Ting Xia; Lin, Huangquan; Lam, Henry H N; Tsim, Karl Wah Keung

Conference paper 2

iPRG 2015: Differential abundance analysis in label-free quantitative proteomics
2015 Annual Conference of the American Society of Mass Spectrometry (ASMS), St. Louis, MO, USA, 2015
Kapp, E.; Lam, Henry H N; Phinney, B.; Cottrell, J.; Hoopmann, M.; Kim, S.; Neubert, T.; Palmblad, M.; Vitek, O.; Weintraub, S.
New functionality for the Trans-Proteomic Pipeline: tools for analysis of proteomics data
2015 Annual Conference of the American Society for Mass Spectrometry (ASMS), St. Louis, MO, USA, 2015
Mendoza, L; Shteynberg, D; Slagel, J; Hoopmann, M; Lam, Henry H N; Eng, J; Deutsch, E; Moritz, R


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Article 9

A draft map of the human proteome
Nature, v. 509, (7502), 2014, p. 575-581
Kim, Minsik; Pinto, Sneha Maria Aria; Getnet, Derese; Nirujogi, Raja Sekhar Ekhar; Manda, Srikanth Srinivas Rinivas; Chaerkady, Raghothama; Madugundu, Anil Kumar; Kelkar, Dhanashree; Isserlin, Ruth; Jain, Shobhit; Thomas, Joji Kurian; Muthusamy, Babylakshmi; Leal-Rojas, Pamela; Kumar, Praveen; Sahasrabuddhe, Nandini; Balakrishnan, Lavanya; Advani, Jayshree; George, Bijesh; Renuse, Santosh; Selvan, Lakshmi Dhevi Nagarajha Nagarajha; Patil, Arun; Nanjappa, Vishalakshi; Radhakrishnan, Aneesha; Prasad, Samarjeet; Subbannayya, Tejaswini; Raju, Rajesh; Kumar, Manish Vijaya; Sreenivasamurthy, Sreelakshmi; Marimuthu, Arivusudar; Sathe, Gajanan; Chavan, Sandip; Datta, Keshava; Subbannayya, Yashwanth; Sahu, Apeksha; Yelamanchi, Soujanya; Jayaram, Savita; Rajagopalan, Pavithra; Sharma, Jyoti; Murthy, Krishna Ramachandra; Syed, Nazia; Goel, Renu; Khan, Aafaqueahmad; Ahmad, Sartaj Akhtar; Dey, Gourav; Mudgal, Keshav; Chatterjee, Aditi; Huang, Taichung; Zhong, Jun; Wu, Xinyan; Shaw, Patrick; Freed, Donald; Zahari, Muhammad Saddiq; Mukherjee, Kanchan Kumar; Shankar, Subramanian Ravi; Mahadevan, Anita; Lam, Henry H N; Mitchell, Christopher; Shankar, Susarla Krishna Rishna; Satishchandra, Parthasarathy; Schroeder, John; Sirdeshmukh, Ravi; Maitra, Anirban; Leach, Steven; Drake, Charles; Halushka, Marc Kenneth; Prasad, Thottethodi Subrahmanya Keshava; Hruban, Ralph; Kerr, Candace; Bader, Gary; Iacobuzio-Donahue, Christine; Gowda, Harsha; Pandey, Akhilesh
A High-resolution LC-MS-based Secondary Metabolite Fingerprint Database of Marine Bacteria
Scientific Reports, v. 4, 2014, article number 6537
Lu, Liang; Wang, Jijie; Xu, Ying; Wang, Kailing; Hu, Yingwei; Tian, Renmao; Yang, Bo; Lai, Qiliang; Li, Yongxin; Zhang, Weipeng; Shao, Zongze; Lam, Henry H N; Qian, Peiyuan
A repository of assays to quantify 10,000 human proteins by SWATH-MS
Scientific Data, v. 1, September 2014, article number 140031
Rosenberger, George; Koh, Ching Chiek; Guo, Tiannan; R?st, Hannes L.; Kouvonen, Petri; Collins, Ben C.; Heusel, Moritz; Liu, Yansheng; Caron, Etienne; Vichalkovski, Anton; Faini, Marco; Schubert, Olga T.; Faridi, Pouya; Ebhardt, H. Alexander; Matondo, Mariette; Lam, Henry H N; Bader, Samuel L.; Campbell, David S.; Deutsch, Eric W.; Moritz, Robert L.; Tate, Stephen; Aebersold, Ruedi
Hunting for Unexpected Post-Translational Modifications by Spectral Library Searching with Tier-Wise Scoring
Journal of Proteome Research, v. 13, (5), May 2014, p. 2262-2271
Ma, Chun Wai Manson; Lam, Henry H N
Label-Free Quantitative Proteomics Analysis of Antibiotic Response in Staphylococcus aureus to Oxacillin
Journal of Proteome Research, v. 13, (3), March 2014, p. 1223-1233
Liu, Xiaofen; Hu, Yingwei; Pai, Pei-Jin; Chen, Daijie; Lam, Henry H N
Metabonomic Analysis of Water Extracts from Different Angelica Roots by ¹H-Nuclear Magnetic Resonance Spectroscopy
Molecules, v. 19, (3), 2014, p. 3460-3470
Chan, Pui Hei Nicholas; Zhang, Wendy L.; Lau, Chungho; Cheung, Chi Yuen; Keun, Hector C.; Tsim, Karl Wah Keung; Lam, Henry H N
Proteome Informatics Research Group (iPRG)_2012: A Study on Detecting Modified Peptides in a Complex Mixture
Molecular & cellular proteomics, v. 13, (1), January 2014, p. 360-371
Chalkley, Robert J.; Bandeira, Nuno; Chambers, Matthew C.; Clauser, Karl R.; Cottrell, John S.; Deutsch, Eric W.; Kapp, Eugene A.; Lam, Henry H N; McDonald, W. Hayes; Neubert, Thomas A.; Sun, Rui-Xiang
Quality Control of Danggui Buxue Tang, a Traditional Chinese Medicine Decoction, by ¹H-NMR Metabolic Profiling
Evidence-Based Complementary and Alternative Medicine, v. 2014, 2014, article number 567893
Chan, Pui Hei; Zhang, Wendy L.; Cheung, Chi Yuen; Tsim, Karl W.K.; Lam, Henry
Tracking the Sources of Blood Meals of Parasitic Arthropods Using Shotgun Proteomics and Unidentified Tandem Mass Spectral Libraries
Nature protocols, v. 9, (4), April 2014, p. 842-850
Oender, Oezlem; Shao, Wenguang; Lam, Henry H N; Brisson, Dustin

Conference paper 7

A New N-linked Glycopeptide Identification Tool, for Large-scale Glycoproteomics Analysis by Spectral Library Searching
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, Maryland, USA, 15-19 June 2014
Hu, Yingwei; Pai, Peggy Pei Jing; Lam, Henry H N
A Novel Shotgun Proteomics-based Microbial Source Tracking Method to Differentiate E. coli Isolates Pertaining to the Feces of Different Species of Warm-blooded Animals
American Society for Microbiology (ASM) 114th General Meeting, Boston, MA, USA, 17-20 May 2014
Shao, Wenguang; Zhang, Min; Lau, Stanley Chun Kwan; Lam, Henry H N
A Shotgun Proteomics-based Method to Differentiate E. coli Strains for Microbial Source Tracking
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, MD, USA, 15-19 June 2014
Shao, Wenguang; Zhang, Min; Lau, Stanley Chun Kwan; Lam, Henry H N
Erythromycin Resistance Study by Label-free Quantitative Proteomics Analysis in Methicillin-resistant Staphylococcus Aureus
12th National Antibiotic Conference, Chengdu, China, 2014
Liu, Xiaofen; Hu, Yingwei; Pai, Peggy; Chen, Daijie; Lam, Henry H N
Label-free Quantitative Proteomics Study of the Synergistic Effect of Oxacillin and a Novel Erythromycin Derivative against Methicillin-resistant Staphylococcus Aureus
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, Maryland, USA, 15-19 June 2014
Liu, Xiaofen; Pai, Peggy Pei Jing; Hu, Yingwei; Chen, Daijie; Lam, Henry H N
Quality Control of Cooking Oils by GC-MS Profiling and Spectral Fingerprinting
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, MD, USA, 15-19 June 2014
Chan, Pui Hei Nicholas; Zhu, Y.; Tsim, Karl Wah Keung; Lam, Henry H N
Site-specific N-linked Glycoproteomics Analysis by Nano-LC Tandem Mass Spectrometry and Spectral Library Searching
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, Maryland, USA, 15-19 June 2014
Pai, Peggy Pei Jing; Hu, Yingwei; Lam, Henry H N


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Article 8

A Complete Mass-spectrometric Map of the Yeast Proteome Applied to Quantitative Trait Analysis
Nature, v. 494, (7436), February 2013, p. 266-270
Picott, P.; Clément-ziza, M.; Lam, Henry H N; Campbell, D.S.; Schmidt, A.; Deutsch, E.W.; R?st, H.; Sun, Z.; Rinner, O.; Reiter, L.; Shen, Q.; Michaelson, J.J.; Frei, A.; Alberti, S,; Kusebauch, U.; Wollscheid, B.; Moritz, R.L.; Beyer, A.; Aebersold, R.
Chemical changes of Angelicae Sinensis Radix and Chuanxiong Rhizoma by wine treatment: chemical profiling and marker selection by gas chromatography coupled with triple quadrupole mass spectrometry
Chinese Medicine (United Kingdom), v. 8, (1), June 2013, article number 12
Zhan, Janis Ya-Xian; Zhang, Wendy Li; Zheng, Ken Yu-zhong; Zhu, Kevin Yue; Chen, Jian-ping; Chan, Pui-Hei; Dong, Tina Ting-xia; Choi, Roy Chi-yan; Lam, Henry H N; Tsim, Karl Wah Keung; Lau, David Tai-wai
Denoising Peptide Tandem Mass Spectra for Spectral Libraries: A Bayesian Approach
Journal of Proteome Research, v. 12, (7), July 2013, p. 3223-3232
Shao, Wenguang; Lam, Henry H N
Expanding Tandem Mass Spectral Libraries of Phosphorylated Peptides: Advances and Applications
Journal of Proteome Research, v. 12, (12), December 2013, p. 5971-5977
Hu, Yingwei; Lam, Henry H N
Graph-based peak alignment algorithms for multiple liquid chromatography-mass spectrometry datasets
Bioinformatics, v. 29, (19), 2013, p. 2469-2476
Wang, Jijie; Lam, Henry H N
Identifying Sources of Tick Blood Meals Using Unidentified Tandem Mass Spectral Libraries
Nature Communications, v. 4, April 2013, article number 1746
Onder, O.; Shao, Wenguang; Kemps, B.; Lam, Henry H N; Brisson, D.
Refining similarity scoring to enable decoy-free validation in spectral library searching
Proteomics, v. 13, (22), November 2013, p. 3273-3283
Shao, Wenguang; Zhu, Kan; Lam, Henry H N
Stable Isotope Metabolic Labeling-based Quantitative Phosphoproteomic Analysis of Arabidopsis Mutants Reveals Ethyleneregulated Time-dependent Phosphoproteins and Putative Substrates of Constitutive Triple Response 1 Kinase
Molecular and Cellular Proteomics, v. 12, (12), December 2013, p. 3559-3582
Yang, Zhu; Guo, Guangyu; Zhang, Manyu; Liu, Ying Qi; Hu, Qin; Lam, Henry H N; Cheng, Han; Xue, Yu; Li, Jiayang; Li, Ning

Conference paper 8

A chemical fingerprint database of marine bacteria based on high-resolution LC-MS
61th Annual Conference of the American Society of Mass Spectrometry, Minneapolis, MN, USA, 9 - 13 June 2013
Lu, Liang; Wang, Jijie; Xu, Sharon Ying; Hu, Yingwei; Lam, Henry H N; Qian, Peiyuan
Advances in spectral library searching for phosphorylated peptides
Gordon Research Conference:Posttranslational Modification Networks, Hong Kong, China, 2013
Hu, Yingwei; Lam, Henry H N
Graph-based time alignment algorithms for LC-MS datasets with large retention-time drifts
61th Annual Conference of the American Society of Mass Spectrometry, Minneapolis, MN, USA, 9 - 13 June 2013
Wang, Jijie; Lam, Henry H N
iPRG-2013 Proteome Informatics Research Group study: Using RNA-seq data to refine proteomic data analysis
Annual Conference of the American Society of Mass Spectrometry, Minneapolis, MN, USA, 2 - 5 March 2013
Chalkley, Robert; Bandeira, N.; Chambers, M.C.; Cottrell, J.S.; Deutsch, E.W.; Kapp, E.A.; Lam, Henry H N; Neubert, T.A.; Sun, R.X.; Vitek, O.; Weintraub, S.T.
Optimization of MS/MS spectral library searching for high mass accuracy spectra of peptides
Annual Conference of the American Society of Mass Spectrometr, Minneapolis, MN, USA, 9 - 13 June 2013
Zhu, Kan; Shao, Wenguang; Hu, Yingwei; Lam, Henry H N
Oxacillin Resistance Study on Methicillin Resistant and SusceptibleStaphylococcus aureus by Label free Quantitative
61st ASMS Conference on Mass Spectrometry and Allied Topics, Minneapolis, Minnesota, USA, 9 - 13 June 2013
Liu, Xiaofen; Hu, Yingwei; Pai, Peggy Pei Jing; Chen, Daijie; Lam, Hei Ning
Site-specific N-linked glycosylation analysis by nano-LC tandem mass spectrometry coupled with a spectral library searching approach
The Human Proteome Organisation 12th Annual World Congress (HUPO 2013), Yokohama, Japan, 2013
Pai, Peggy Pei Jing; Hu, Yingwei; Lam, Henry H N
Utilizing unidentified tandem mass spectral libraries for biological sample fingerprinting
Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Berlin, Germany, 21 - 23 July 2013
Shao, Wenguang; Lam, Henry H N


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Article 2

Metabonomic analysis of water extracts from Chinese and American ginsengs by H-1 nuclear magnetic resonance: identification of chemical profile for quality control
Chinese medicine, v. 7, November 2012, Article number 25
Chan, Pui Hei; Zheng, Ken Y.Z.; Tsim, Karl Wah Keung; Lam, Henry H N
Spectral library searching for peptide identification in proteomics
Statistics and Its Interface, v. 5, (1), 2012, p. 39-46
Lam, Henry H N

Conference paper 2

Expanding spectral libraries of phosphorylated peptides: Progress in coverage and accuracy
Human Proteome Organization (HUPO) 11th Annual World Congress, Boston, MA, USA, 2012
Hu, Yingwei; Lam, Henry H N
Multi-resolution LC-MS images alignment using dynamic time warping and Kullback-Leibler distance
Proceedings - International Conference on Image Processing, ICIP, 2012, article number 6467201, p. 1681-1684
Wu, William K.H.; Chung, Albert Chi Shing; Lam, Henry H N


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Article 8

A semi-empirical approach for predicting unobserved peptide MS/MS spectra from spectral libraries
Proteomics, v. 11, (24), December 2011, p. 4702-4711
Hu, Yingwei; Li, Yunzi; Lam, Henry H N
Absolute quantification of microbial proteomes at different states by directed mass spectrometry
Molecular Systems Biology, v. 7, (510), July 2011, Article number 510
Schmidt, Alexander; Beck, Martin; Malmstroem, Johan; Lam, Henry H N; Claassen, Manfred; Campbell, David; Aebersold, Ruedi
Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics
Methods, v. 54, (4), August 2011, p. 424-431
Lam, Henry H N; Aebersold, Ruedi
Building and searching tandem mass spectral libraries for peptide identification
Molecular & cellular proteomics, v. 10, (12), December 2011
Lam, Henry H N
Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration
Journal of proteome research, v. 10, (6), June 2011, p. 2882-2888
Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry H N; Eng, Jimmy K.; Martin, Daniel B.
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
Molecular & cellular proteomics, v. 10, (12), December 2011, M111.007690
Shteynberg, David; Deutsch, Eric W.; Lam, Henry H N; Eng, Jimmy K.; Sun, Zhi; Tasman, Natalie; Mendoza, Luis; Moritz, Robert L.; Aebersold, Ruedi; Nesvizhskii, Alexey I.
Spectral archives: a vision for future proteomics data repositories
Nature Methods, v. 8, (7), July 2011, p. 546-548
Lam, Henry H N
Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis
Proteomics, v. 11, (6), March 2011, p. 1075-1085
Zhang, Xin; Li, Yunzi; Shao, Wenguang; Lam, Henry H N

Conference paper 6

1H-NMR metabonomics analysis of Danggui Buxue Tang effects in HEK293T kidney cell lines
China Human Proteome Organization (CNHUPO) 7th Annual Congress, Hangzhou, China, 2011
Chan, Pui Hei Nicholas; Tsim, Karl Wah Keung; Lam, Henry H N
A novel de-noising method for spectral library in peptide identification from tandem mass spectrometry
China Human Proteome Organization (CNHUPO) 7th Annual Congress, Hangzhou, China, 2011
Shao, Wenguang; Lam, Henry H N
Identification of peptides with single amino acid polymorphisms by using semi-empirical MS/MS spectral library
China Human Proteome Organization (CNHUPO) 7th Annual Congress, Hangzhou, China, 2011
Hu, Yingwei; Lam, Henry H N
iPRG 2011: A study on the identification of electron transfer dissociation (ETD) mass spectra
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2011
Martens, L.; Askenazi, M.; Bandeira, N.; Chalkley, R.; Clauser, K.; Deutsch, E.; Lam, Henry H N; Mcdonald, W.; Neubert, T.; Rudnick, P.
iProphet: Improved statistical validation of peptide and protein identifications in shotgun proteomics
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2011
Shteynberg, D.; Deutsch, E.; Lam, Henry H N; Fermin, D.; Sun, Z.; Tasman, N.; Mendoza, L.; Moritz, R.; Aebersold, R.; Nesvizhskii, A.
RTCalc and RTCatalog: Open-source software tools for prediction and cataloging of sequence specific retentions of peptides on liquid chromatography systems
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2011
Shteynberg, D.; Deutsch, E.; Chu, C.; Kusebauch, U.; Stevens, J.; Sun, Z.; Swearingen, K.; Lam, Henry H N; Moritz, R.


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Article 7

A guided tour of the Trans-Proteomic Pipeline
Proteomics, v. 10, (6), March 2010, p. 1150-1159
Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Farrah, Terry; Lam, Henry H N; Tasman, Natalie; Sun, Zhi; Nilsson, Erik; Pratt, Brian; Prazen, Bryan; Eng, Jimmy K.; Martin, Daniel B.; Nesvizhskii, Alexey I.; Aebersold, Ruedi
A ubiquitin and ubiquitin-like protein spectral library
Proteomics, v. 10, (2), January 2010, p. 337-342
Srikumar, Tharan; Jeram, Stanley M.; Lam, Henry H N; Raught, Brian
Artificial Decoy Spectral Libraries for False Discovery Rate Estimation in Spectral Library Searching in Proteomics
Journal of proteome research, v. 9, (1), January 2010, p. 605-610
Lam, Henry H N; Deutsch, Eric W.; Aebersold, Ruedi
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast
Science Signaling, v. 3, (153), December 2010
Bodenmiller, B.; Wanka, S.; Kraft, C.; Urban, J.; Campbell, D.; Pedrioli, P.G.; Gerrits, B.; Picotti, P.; Lam, Henry H N; Vitek, O.; Brusniak, M.Y.; Roschitzki, B.; Zhang, C.; Shokat, K.M.; Schlapbach, R.; Colman-Lerner, A.; Nolan, G.P.; Nesvizhskii, A.I.; Peter, M.; Loewith, R.; Mering, C.V.; Aebersold, R.
Spectral Library Searching for Peptide Identification via Tandem MS
Methods in Molecular Biology, v. 604, 2010, p. 95-103
Lam, Henry H N; Aebersold, Ruedi
Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets
Proteomics, v. 10, (6), March 2010, p. 1190-1195
Deutsch, Eric W.; Shteynberg, David; Lam, Henry H N; Sun, Zhi; Eng, Jimmy K.; Carapito, Christine; von Haller, Priska D.; Tasman, Natalie; Mendoza, Luis; Farrah, Terry; Aebersold, Ruedi
Using spectral libraries for peptide identification from tandem mass spectrometry (MS/MS) data
Current protocols in protein science, v. Ch. 25, April 2010, Pages Unit 25.5
Lam, Henry H N; Aebersold, Ruedi

Book chapter 1

Spectral Library Searching for Peptide Identification via Tandem MS
Proteome Bioinformatics /Edited by Simon J. Hubbard, Andrew R. Jones. New York, NY: Humana Press; Springer, c2010, chapter 7, p. 95-103
Lam, Henry H N; Aebersold, Ruedi

Conference paper 2

A semi-empirical approach to predict unobserved peptide MS/MS spectra from spectral libraries
The Human Proteome Organisation 9th Annual World Congress (HUPO 2010), Sydney, Australia, 2010
Hu, Yingwei; Lam, Henry H N
New functionality for the Trans-Proteomic Pipeline: tools for analysis of proteomics data
US Human Proteome Organization 6th Annual Conference, Denver, CO, USA
Mendoza, L.; Shteynberg, D.; Slagel, J.; Holstein, C.; Tasman, N.; Pratt, B.; Lam, Henry H N; Eng, J.; Nesvizhskii, A.; Martin, D.; Deutsch, E.; Moritz, R.; Aebersold, R.


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Article 1

MaRiMba: A Software Application for Spectral Library-Based MRM Transition List Assembly
Journal of proteome research, v. 8, (10), October 2009, p. 4396-4405
Sherwood, Carly A.; Eastham, Ashley; Lee, Lik Wee; Peterson, Amelia; Eng, Jimmy K.; Shteynberg, David; Mendoza, Luis; Deutsch, Eric W.; Risler, Jenni; Tasman, Natalie; Aebersold, Ruedi; Lam, Henry H N; Martin, Daniel B.

Conference paper 9

A Bayesian approach to distinguish signal and noise peaks in peptide tandem mass spectra
Human Proteome Organization 6th Annual Conference, Toronto, Canada
Shao, Wenguang; Zhang, Xin; Lam, Henry H N
A high quality human plasma proteome available in the PeptideAtlas
Annual Conference, American Society of Mass Spectrometry, Philadelphia, PA
Ferrah, T.; Deutsch, E.; Shteynberg, D.; Campbell, D.; Lam, Henry H N; Sun, Z.; Omenn, G.; Aebersold, R.
A human plasma proteome in the PeptideAtlas with estimated protein concentrations
Human Proteome Organization 6th Annual Conference, Toronto, Canada
Farrah, T.; Deutsch, E.; Zhang, N.; Shteynberg, D.; Lam, Henry H N; Campbell, D.; Tasman, N.; Sun, Z.; Mendoza, L.; Omenn, G.; Aebersold, R.
A systematic investigation on the improvement in sensitivity of spectral library searching over sequence database searching in proteomics
Annual Conference, American Society of Mass Spectrometry, Philadelphia, PA
Zhang, Xin; Shao, Wenguang; Lam, Henry H N
Identification of Ub/Ubl chains in an integrated mass spectrometry/SpectraST/SUMmOn-based work-flow
Human Proteome Organization 6th Annual Conference, Toronto, Canada
Srikumar, T.; Jeram, S.; Pedrioli, P.; Lam, Henry H N; Raught, B.
Identification of Ub/Ubl chains using an integrated mass spectrometry/SpectraST/SUMmOn-based work-flow
International Mass Spectrometry Conference, Bremen, Germany, 2009
Srikumar, T.; Jeram, S.; Pedrioli, P.; Lam, Henry H N; Raught, B.
Improved support for targeted proteomics workflows in PeptideAtlas
Annual Conference, US Human Proteome Organization, San Diego, CA, USA
Campbell, D.; Deutsch, E.; Lam, Henry H N; Picotti, P.; Aebersold, R.
New functionality for the Trans-Proteomic Pipeline: tools for the analysis of proteomics data
Annual Conference, American Society of Mass Spectrometry, Philadelphia, PA
Mendoza, L.; Shteynberg, D.; Tasman, N.; Pratt, B.; Eng, J.; Lam, Henry H N; Nesvizhskii, A.; Deutsch, E.; Aebersold, R.
Quality control of ginseng by 1H NMR metabolic profiling
International Conference on Resource Development of Chinese Medicines from Northwestern China, Hong Kong, China, 2009
Chan, Pui Hei Nicholas; Choi, Chi Yan; Chan, Kar Lun Gallant; Tsim, Karl Wah Keung; Lam, Henry H N


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Article 5

A database of mass spectrometric assays for the yeast proteome
Nature Methods, v. 5, (11), 2008, p. 913-914
Picotti, Paola; Lam, Henry H N; Campbell, David; Deutsch, Eric W.; Mirzaei, Hamid; Ranish, Jeff; Domon, Bruno; Aebersold, Ruedi
Building consensus spectral libraries for peptide identification in proteomics
Nature Methods, v. 5, (10), October 2008, p. 873-875
Lam, Henry H N; Deutsch, Eric W.; Eddes, James S.; Eng, Jimmy K.; Stein, Stephen E.; Aebersold, Ruedi
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
Physiological genomics, v. 33, (1), March 2008, p. 18-25
Deutsch, E.W.; Lam, Henry H N; Aebersold, R.
PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
EMBO reports, v. 9, (5), May 2008, p. 429-434
Deutsch, E.W.; Lam, Henry H N; Aebersold, R.
PhosphoPep - A database of protein phosphorylation sites in model organisms
Nature Biotechnology, v. 26, (12), December 2008, p. 1339-1340
Bodenmiller, Bernd; Campbell, David; Gerrits, Bertran; Lam, Henry H N; Jovanovic, Marko; Picotti, Paola; Schlapbach, Ralph; Aebersold, Ruedi

Conference paper 6

Absolute protein quantification estimated by spectral counting using large datasets in PeptideAtlas
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2008
Zhang, N.; Deutsch, E.; Lam, Henry H N; Aebersold, R.
iProphet: A new tool for combining PeptideProphet results from multiple search engines improves spectrum validation
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2008
Shteynberg, D.; Nesvizhskii, A.; Deutsch, E.; Lam, Henry H N; Aebersold, R.
iProphet: improved validation of peptide identification in shotgun proteomics
World Congress, Human Proteome Organization, Amsterdam, the Netherlands
Shteynberg, D.; Deustch, E.; Lam, Henry H N; Aebersold, R.; Nesvizhskii, A.
New developments for open-source shotgun proteomics analysis with the Trans-Proteomic Pipeline
World Congress, Human Proteome Organization, Amsterdam, the Netherlands
Mendoza, L.; Tasman, J.; Shteynberg, D.; Eddes, J.; Zhang, N.; Wong, C.; Pratt, B.; Lam, Henry H N; Eng, J.; Deutsch, E.; Aebersold, R.
PeptideAtlas: Resource for target selection for emerging targeted proteomics workflows
US Human Proteome Organization (USHUPO) 4th Annual Conference, Bethesda, MD, USA, 2008
Deutsch, E.; Lam, Henry H N; Aebersold, R.
The PeptideAtlas as a tool for targeted proteomics
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2008
Campbell, D.; Deutsch, E.; Lange, V.; Picotti, P.; King, N.; Letarte, S.; Lam, Henry H N; Zhang, N.; Aebersold, R.


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Article 2

Development and validation of a spectral library searching method for peptide identification from MS/MS
Proteomics, v. 7, (5), March 2007, p. 655-667
Lam, Henry H N; Deutsch, E.W.; Eddes, J.S.; Eng, J.K.; King, N.; Stein, S.E.; Aebersold, R.
PhosphoPep - A phosphoproteome resource for systems biology research in Drosophila Kc167 cells
Molecular Systems Biology, v. 3, January2007, article number 139
Bodenmiller, B.; Malmstrom, J.; Gerrits, B.; Campbell, D.; Lam, Henry H N; Schmidt, A.; Rinner, O.; Mueller, L.N.; Shannon, P.T.; Pedrioli, P.G.; Panse, C.; Lee, H.K.; Schlapbach, R.; Aebersold, R.

Conference paper 3

Development of a spectral library building tool and re-analysis of Human Plasma PeptideAtlas datasets using spectral searching
US Human Proteome Organization (USHUPO) 3rd Annual Conference, Seattle, WA, 2007
Lam, Henry H N; Deutsch, E.; Eddes, J.; Eng, J.; King, N.; Stein, S.; Aebersold, R.
Encoding the observed human plasma proteome in spectral libraries
Human Proteome Organization (HUPO) 6th Annual World Congress, Seoul, Korea, 2007
Lam, Henry H N; Deutsch, E.; Shteynberg, D.; Zhang, N.; Stein, S.; Aebersold, R.
Estimating false discovery rates in spectral searching using decoy spectral libraries
Human Proteome Organization (HUPO) 6th Annual World Congress, Seoul, Korea, 2007
Lam, Henry H N; Deutsch, E.; Eddes, J.; Aebersold, R.


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Article 1

Affinity-tagged green fluorescent protein (GFP) extraction from a clarified E-coli cell lysate using a two-phase aqueous micellar system
Biotechnology and bioengineering, v. 93, (5), April 2006, p. 998-1004
Mazzola, PG; Lam, Henry H N; Kavoosi, M.; Haynes, CA; Pessoa, A.; Penna, TCV; Wang, DIC; Blankschtein, D.

Conference paper 3

Annotation of the yeast Proteome with PeptideAtlas
American Society of Mass Spectrometry Annual Conference (ASMS), Seattle, WA, 2006
King, N.; Deutsch, E.; Eng, J.; Ranish, J.; Raught, B.; Eddes, J.; Nesvizhskii, A.; Mallick, P.; Martin, D.; Flory, M.; Lee, H.; Lam, Henry H N; Aebersold, R.
SpectraST: An open-source MS/MS spectra-matching search tool for targeted proteomics
American Society of Mass Spectrometry Annual Conference (ASMS), Seattle, WA, 2006
Lam, Henry H N; Deutsch, E.; Eddes, J.; Eng, J.; King, N.; Yang, S.; Roth, J.; Kilpatrick, L.; Neta, P.; Stein, S.; Aebersold, R.
The PeptideAtlas Project
International Symposium of the Institute for Systems Biology, Seattle, WA, 2006
Deutsch, E.; Eddes, J.; Eng, J.; King, N.; Lam, Henry H N; Campbell, D.; Loevenich, S.; Mallick, P.; Martin, D.; Mendoza, L.; Nesvizhiskii, A.; Ranish, J.; Raught, B.; Shteynberg, D.; Tasman, J.; Zhang, N.; Vitek, O.; Aebersold, R.


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Article 1

Affinity-enhanced protein partitioning in decyl beta-D-glucopyranoside two-phase aqueous micellar systems
Biotechnology and bioengineering, v. 89, (4), February 2005, p. 381-392
Lam, Henry H N; Kavoosi, M.; Haynes, CA; Wang, DIC; Blankschtein, D.


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Conference paper 1

Affinity-enhanced protein partitioning in decyl beta-D-glucopyranoside two-phase aqueous micellar systems
American Institute of Chemical Engineers (AIChE) Annual Meeting, Austin, TX, 2004
Lam, Henry H N; Kavoosi, M.; Haynes, C.A.; Wang, D.I.C.; Blankschtein, D.


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Article 1

Glucose-6-phosphate dehydrogenase partitioning in two-phase aqueous mixed (nonionic/cationic) micellar systems
Biotechnology and bioengineering, v. 82, (4), May 2003, p. 445-456
Rangel-Yagui, CO; Lam, Henry H N; Kamei, DT; Wang, DIC; Pessoa, A.; Blankstein, D.


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2016 10

A Hybrid Retention Time Alignment Algorithm for SWATH-MS Data
Proteomics, v. 16, (15-16), August 2016, p. 2272-2283
Wu, Long; Amon, Sabine; Lam, Henry H N Article
Direct Glycan Structure Determination of Intact N-Linked Glycopeptides by Low-Energy Collision-Induced Dissociation Tandem Mass Spectrometry and Predicted Spectral Library Searching
Analytica Chimica Acta, v. 934, August 2016, p. 152-162
Pai, Peggy; Hu, Yingwei; Lam, Henry H N Article
Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
Cell, v. 166, (3), July 2016, p. 766-778
Kusebauch, Ulrike; Campbell, David S.; Deutsch, Eric W.; Chu, Caroline S.; Spicer, Douglas A.; Brusniak, Mi-Youn; Slagel, Joseph; Sun, Zhi; Stevens, Jeffrey; Grimes, Barbara; Shteynberg, David; Hoopmann, Michael R.; Blattmann, Peter; Ratushny, Alexander V.; Rinner, Oliver; Picotti, Paola; Carapito, Christine; Huang, Chung-Ying; Kapousouz, Meghan; Lam, Henry H N; Tran, Tommy; Demir, Emek; Aitchison, John D.; Sander, Chris; Hood, Leroy; Aebersold, Ruedi; Moritz, Robert L. Article
Proteomic response of methicillin-resistant S. aureus to a synergistic antibacterial drug combination: a novel erythromycin derivative and oxacillin
Scientific Reports, v. 6, January 2016, article number 19841
Liu, Xiaofen; Pai, Pei-Jin; Zhang, Weipeng; Hu, Yingwei; Dong, Xiaojing; Qian, Peiyuan; Chen, Daijie; Lam, Henry H N Article
Spectral Library Searching To Identify Cross-Linked Peptides
Journal of Proteome Research, v. 15, (5), May 2016, p. 1725-1731
Schweppe, Devin K.; Chavez, Juan D.; Navare, Arti T.; Wu, Xia; Ruiz, Bianca; Eng, Jimmy K.; Lam, Henry H N; Bruce, James E. Article
An Efficient and Accurate Feature-based Label-free Quantification Software Tool for SWATH MS Data
15th Human Proteome Organization World Congress in 2016 (HUPO 2016), Taipei, Taiwan, 18 - 22 September 2016
Wu, Long; Li, Yan Chak; Lam, Henry H.N. Conference paper
Meat Species Identification by Protein Profiling and Spectral Fingerprinting Using MALDI-TOF-MS
64th Annual Conference of the American Society of Mass Spectrometry and Allied Topics, SAN ANTONIO, TEXAS, June 5 - 9, 2016,
Lam, Henry H N; So, Man On Conference paper
Proteome-wide Quantitative Profiling of Mis-incorporation of Selenocysteine into Proteins by LC-MS Based Shotgun Proteomics
The 64th ASMS Annual Conference on Mass Spectrometry and Allied Topics, San Antonio, Texas, U.S, 5-9 June, 2016
Hao, Chunlin; Lam, Hei Ning Conference paper
Quality control of cooking oils by metabolic profiling and spectral fingerprinting
64th ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, Texas, US, 5-9 June 2016
Cheung, Chi Yuen; Lam, Henry H.N. Conference paper
The 2016 iPRG Study: Inferring Proteoforms From Bottom-up Proteomics Data
64th Annual Conference of the American Society of Mass Spectrometry and Allied Topics (ASMS 2016), San Antonio, TX, USA, 5-9 June 2016
Palmblad, Magnus; Lam, Henry H.N.; Choi, Hyungwon; Colangelo, Christopher; Davis, Darryl; Hoopmann, Michael; Kall, Lukas; Payne, Samuel; Perez-riversol, Yasset; Weintraub, Susan T. Conference paper

2015 6

A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation
Scientific Reports, v. 5, September 2015, article number 14337
Shao, Wenguang; Zhang, Min; Lam, Henry H N; Lau, Stanley C.K. Article
An open-source computational and data resource to analyze digital maps of immunopeptidomes
eLife, July 2015, article number e07661
Caron, Etienne; Espona, Lucia; Kowalewski, Daniel J.; Schuster, Heiko; Ternette, Nicola; Alpízar, Adán; Schittenhelm, Ralf B.; Ramarathinam, Sri H.; Arlehamn, Cecilia S. Lindestam; Koh, Ching Chiek; Gillet, Ludovic C.; Rabsteyn, Armin; Navarro, Pedro; Kim, Sangtae; Lam, Henry H.N.; Sturm, Theo; Marcilla, Miguel; Sette, Alessandro; Campbell, David S.; Deutsch, Eric W.; Moritz, Robert L.; Purcell, Anthony W.; Rammensee, Hans-Georg; Stevanovic, Stefan; Aebersold, Ruedi Article
Building high-quality assay libraries for targeted analysis of SWATH MS data
Nature Protocols, v. 10, (3), March 2015, p. 426-441
Schubert, Olga T.; Gillet, Ludovic C.; Collins, Ben C.; Navarro, Pedro; Rosenberger, George; Wolski, Witold E.; Lam, Henry H N; Amodei, Dario; Mallick, Parag; MacLean, Brendan; Aebersold, Ruedi Article
Fruit of Ziziphus jujuba (Jujube) at Two Stages of Maturity: Distinction by Metabolic Profiling and Biological Assessment
Journal of Agricultural and Food Chemistry, v. 63, (2), January 2015, p. 739-744
Chen, Jianping; Chan, Pui Hei; Lam, Candy Ting Wai; Li, Zhonggui; Lam, Kelly Yin Ching; Yao, Ping; Dong, Tina Ting Xia; Lin, Huangquan; Lam, Henry H N; Tsim, Karl Wah Keung Article
iPRG 2015: Differential abundance analysis in label-free quantitative proteomics
2015 Annual Conference of the American Society of Mass Spectrometry (ASMS), St. Louis, MO, USA, 2015
Kapp, E.; Lam, Henry H N; Phinney, B.; Cottrell, J.; Hoopmann, M.; Kim, S.; Neubert, T.; Palmblad, M.; Vitek, O.; Weintraub, S. Conference paper
New functionality for the Trans-Proteomic Pipeline: tools for analysis of proteomics data
2015 Annual Conference of the American Society for Mass Spectrometry (ASMS), St. Louis, MO, USA, 2015
Mendoza, L; Shteynberg, D; Slagel, J; Hoopmann, M; Lam, Henry H N; Eng, J; Deutsch, E; Moritz, R Conference paper

2014 16

A draft map of the human proteome
Nature, v. 509, (7502), 2014, p. 575-581
Kim, Minsik; Pinto, Sneha Maria Aria; Getnet, Derese; Nirujogi, Raja Sekhar Ekhar; Manda, Srikanth Srinivas Rinivas; Chaerkady, Raghothama; Madugundu, Anil Kumar; Kelkar, Dhanashree; Isserlin, Ruth; Jain, Shobhit; Thomas, Joji Kurian; Muthusamy, Babylakshmi; Leal-Rojas, Pamela; Kumar, Praveen; Sahasrabuddhe, Nandini; Balakrishnan, Lavanya; Advani, Jayshree; George, Bijesh; Renuse, Santosh; Selvan, Lakshmi Dhevi Nagarajha Nagarajha; Patil, Arun; Nanjappa, Vishalakshi; Radhakrishnan, Aneesha; Prasad, Samarjeet; Subbannayya, Tejaswini; Raju, Rajesh; Kumar, Manish Vijaya; Sreenivasamurthy, Sreelakshmi; Marimuthu, Arivusudar; Sathe, Gajanan; Chavan, Sandip; Datta, Keshava; Subbannayya, Yashwanth; Sahu, Apeksha; Yelamanchi, Soujanya; Jayaram, Savita; Rajagopalan, Pavithra; Sharma, Jyoti; Murthy, Krishna Ramachandra; Syed, Nazia; Goel, Renu; Khan, Aafaqueahmad; Ahmad, Sartaj Akhtar; Dey, Gourav; Mudgal, Keshav; Chatterjee, Aditi; Huang, Taichung; Zhong, Jun; Wu, Xinyan; Shaw, Patrick; Freed, Donald; Zahari, Muhammad Saddiq; Mukherjee, Kanchan Kumar; Shankar, Subramanian Ravi; Mahadevan, Anita; Lam, Henry H N; Mitchell, Christopher; Shankar, Susarla Krishna Rishna; Satishchandra, Parthasarathy; Schroeder, John; Sirdeshmukh, Ravi; Maitra, Anirban; Leach, Steven; Drake, Charles; Halushka, Marc Kenneth; Prasad, Thottethodi Subrahmanya Keshava; Hruban, Ralph; Kerr, Candace; Bader, Gary; Iacobuzio-Donahue, Christine; Gowda, Harsha; Pandey, Akhilesh Article
A High-resolution LC-MS-based Secondary Metabolite Fingerprint Database of Marine Bacteria
Scientific Reports, v. 4, 2014, article number 6537
Lu, Liang; Wang, Jijie; Xu, Ying; Wang, Kailing; Hu, Yingwei; Tian, Renmao; Yang, Bo; Lai, Qiliang; Li, Yongxin; Zhang, Weipeng; Shao, Zongze; Lam, Henry H N; Qian, Peiyuan Article
A repository of assays to quantify 10,000 human proteins by SWATH-MS
Scientific Data, v. 1, September 2014, article number 140031
Rosenberger, George; Koh, Ching Chiek; Guo, Tiannan; R?st, Hannes L.; Kouvonen, Petri; Collins, Ben C.; Heusel, Moritz; Liu, Yansheng; Caron, Etienne; Vichalkovski, Anton; Faini, Marco; Schubert, Olga T.; Faridi, Pouya; Ebhardt, H. Alexander; Matondo, Mariette; Lam, Henry H N; Bader, Samuel L.; Campbell, David S.; Deutsch, Eric W.; Moritz, Robert L.; Tate, Stephen; Aebersold, Ruedi Article
Hunting for Unexpected Post-Translational Modifications by Spectral Library Searching with Tier-Wise Scoring
Journal of Proteome Research, v. 13, (5), May 2014, p. 2262-2271
Ma, Chun Wai Manson; Lam, Henry H N Article
Label-Free Quantitative Proteomics Analysis of Antibiotic Response in Staphylococcus aureus to Oxacillin
Journal of Proteome Research, v. 13, (3), March 2014, p. 1223-1233
Liu, Xiaofen; Hu, Yingwei; Pai, Pei-Jin; Chen, Daijie; Lam, Henry H N Article
Metabonomic Analysis of Water Extracts from Different Angelica Roots by ¹H-Nuclear Magnetic Resonance Spectroscopy
Molecules, v. 19, (3), 2014, p. 3460-3470
Chan, Pui Hei Nicholas; Zhang, Wendy L.; Lau, Chungho; Cheung, Chi Yuen; Keun, Hector C.; Tsim, Karl Wah Keung; Lam, Henry H N Article
Proteome Informatics Research Group (iPRG)_2012: A Study on Detecting Modified Peptides in a Complex Mixture
Molecular & cellular proteomics, v. 13, (1), January 2014, p. 360-371
Chalkley, Robert J.; Bandeira, Nuno; Chambers, Matthew C.; Clauser, Karl R.; Cottrell, John S.; Deutsch, Eric W.; Kapp, Eugene A.; Lam, Henry H N; McDonald, W. Hayes; Neubert, Thomas A.; Sun, Rui-Xiang Article
Quality Control of Danggui Buxue Tang, a Traditional Chinese Medicine Decoction, by ¹H-NMR Metabolic Profiling
Evidence-Based Complementary and Alternative Medicine, v. 2014, 2014, article number 567893
Chan, Pui Hei; Zhang, Wendy L.; Cheung, Chi Yuen; Tsim, Karl W.K.; Lam, Henry Article
Tracking the Sources of Blood Meals of Parasitic Arthropods Using Shotgun Proteomics and Unidentified Tandem Mass Spectral Libraries
Nature protocols, v. 9, (4), April 2014, p. 842-850
Oender, Oezlem; Shao, Wenguang; Lam, Henry H N; Brisson, Dustin Article
A New N-linked Glycopeptide Identification Tool, for Large-scale Glycoproteomics Analysis by Spectral Library Searching
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, Maryland, USA, 15-19 June 2014
Hu, Yingwei; Pai, Peggy Pei Jing; Lam, Henry H N Conference paper
A Novel Shotgun Proteomics-based Microbial Source Tracking Method to Differentiate E. coli Isolates Pertaining to the Feces of Different Species of Warm-blooded Animals
American Society for Microbiology (ASM) 114th General Meeting, Boston, MA, USA, 17-20 May 2014
Shao, Wenguang; Zhang, Min; Lau, Stanley Chun Kwan; Lam, Henry H N Conference paper
A Shotgun Proteomics-based Method to Differentiate E. coli Strains for Microbial Source Tracking
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, MD, USA, 15-19 June 2014
Shao, Wenguang; Zhang, Min; Lau, Stanley Chun Kwan; Lam, Henry H N Conference paper
Erythromycin Resistance Study by Label-free Quantitative Proteomics Analysis in Methicillin-resistant Staphylococcus Aureus
12th National Antibiotic Conference, Chengdu, China, 2014
Liu, Xiaofen; Hu, Yingwei; Pai, Peggy; Chen, Daijie; Lam, Henry H N Conference paper
Label-free Quantitative Proteomics Study of the Synergistic Effect of Oxacillin and a Novel Erythromycin Derivative against Methicillin-resistant Staphylococcus Aureus
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, Maryland, USA, 15-19 June 2014
Liu, Xiaofen; Pai, Peggy Pei Jing; Hu, Yingwei; Chen, Daijie; Lam, Henry H N Conference paper
Quality Control of Cooking Oils by GC-MS Profiling and Spectral Fingerprinting
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, MD, USA, 15-19 June 2014
Chan, Pui Hei Nicholas; Zhu, Y.; Tsim, Karl Wah Keung; Lam, Henry H N Conference paper
Site-specific N-linked Glycoproteomics Analysis by Nano-LC Tandem Mass Spectrometry and Spectral Library Searching
62nd ASMS Conference on Mass Spectrometry and Allied Topics 2014, Baltimore, Maryland, USA, 15-19 June 2014
Pai, Peggy Pei Jing; Hu, Yingwei; Lam, Henry H N Conference paper

2013 16

A Complete Mass-spectrometric Map of the Yeast Proteome Applied to Quantitative Trait Analysis
Nature, v. 494, (7436), February 2013, p. 266-270
Picott, P.; Clément-ziza, M.; Lam, Henry H N; Campbell, D.S.; Schmidt, A.; Deutsch, E.W.; R?st, H.; Sun, Z.; Rinner, O.; Reiter, L.; Shen, Q.; Michaelson, J.J.; Frei, A.; Alberti, S,; Kusebauch, U.; Wollscheid, B.; Moritz, R.L.; Beyer, A.; Aebersold, R. Article
Chemical changes of Angelicae Sinensis Radix and Chuanxiong Rhizoma by wine treatment: chemical profiling and marker selection by gas chromatography coupled with triple quadrupole mass spectrometry
Chinese Medicine (United Kingdom), v. 8, (1), June 2013, article number 12
Zhan, Janis Ya-Xian; Zhang, Wendy Li; Zheng, Ken Yu-zhong; Zhu, Kevin Yue; Chen, Jian-ping; Chan, Pui-Hei; Dong, Tina Ting-xia; Choi, Roy Chi-yan; Lam, Henry H N; Tsim, Karl Wah Keung; Lau, David Tai-wai Article
Denoising Peptide Tandem Mass Spectra for Spectral Libraries: A Bayesian Approach
Journal of Proteome Research, v. 12, (7), July 2013, p. 3223-3232
Shao, Wenguang; Lam, Henry H N Article
Expanding Tandem Mass Spectral Libraries of Phosphorylated Peptides: Advances and Applications
Journal of Proteome Research, v. 12, (12), December 2013, p. 5971-5977
Hu, Yingwei; Lam, Henry H N Article
Graph-based peak alignment algorithms for multiple liquid chromatography-mass spectrometry datasets
Bioinformatics, v. 29, (19), 2013, p. 2469-2476
Wang, Jijie; Lam, Henry H N Article
Identifying Sources of Tick Blood Meals Using Unidentified Tandem Mass Spectral Libraries
Nature Communications, v. 4, April 2013, article number 1746
Onder, O.; Shao, Wenguang; Kemps, B.; Lam, Henry H N; Brisson, D. Article
Refining similarity scoring to enable decoy-free validation in spectral library searching
Proteomics, v. 13, (22), November 2013, p. 3273-3283
Shao, Wenguang; Zhu, Kan; Lam, Henry H N Article
Stable Isotope Metabolic Labeling-based Quantitative Phosphoproteomic Analysis of Arabidopsis Mutants Reveals Ethyleneregulated Time-dependent Phosphoproteins and Putative Substrates of Constitutive Triple Response 1 Kinase
Molecular and Cellular Proteomics, v. 12, (12), December 2013, p. 3559-3582
Yang, Zhu; Guo, Guangyu; Zhang, Manyu; Liu, Ying Qi; Hu, Qin; Lam, Henry H N; Cheng, Han; Xue, Yu; Li, Jiayang; Li, Ning Article
A chemical fingerprint database of marine bacteria based on high-resolution LC-MS
61th Annual Conference of the American Society of Mass Spectrometry, Minneapolis, MN, USA, 9 - 13 June 2013
Lu, Liang; Wang, Jijie; Xu, Sharon Ying; Hu, Yingwei; Lam, Henry H N; Qian, Peiyuan Conference paper
Advances in spectral library searching for phosphorylated peptides
Gordon Research Conference:Posttranslational Modification Networks, Hong Kong, China, 2013
Hu, Yingwei; Lam, Henry H N Conference paper
Graph-based time alignment algorithms for LC-MS datasets with large retention-time drifts
61th Annual Conference of the American Society of Mass Spectrometry, Minneapolis, MN, USA, 9 - 13 June 2013
Wang, Jijie; Lam, Henry H N Conference paper
iPRG-2013 Proteome Informatics Research Group study: Using RNA-seq data to refine proteomic data analysis
Annual Conference of the American Society of Mass Spectrometry, Minneapolis, MN, USA, 2 - 5 March 2013
Chalkley, Robert; Bandeira, N.; Chambers, M.C.; Cottrell, J.S.; Deutsch, E.W.; Kapp, E.A.; Lam, Henry H N; Neubert, T.A.; Sun, R.X.; Vitek, O.; Weintraub, S.T. Conference paper
Optimization of MS/MS spectral library searching for high mass accuracy spectra of peptides
Annual Conference of the American Society of Mass Spectrometr, Minneapolis, MN, USA, 9 - 13 June 2013
Zhu, Kan; Shao, Wenguang; Hu, Yingwei; Lam, Henry H N Conference paper
Oxacillin Resistance Study on Methicillin Resistant and SusceptibleStaphylococcus aureus by Label free Quantitative
61st ASMS Conference on Mass Spectrometry and Allied Topics, Minneapolis, Minnesota, USA, 9 - 13 June 2013
Liu, Xiaofen; Hu, Yingwei; Pai, Peggy Pei Jing; Chen, Daijie; Lam, Hei Ning Conference paper
Site-specific N-linked glycosylation analysis by nano-LC tandem mass spectrometry coupled with a spectral library searching approach
The Human Proteome Organisation 12th Annual World Congress (HUPO 2013), Yokohama, Japan, 2013
Pai, Peggy Pei Jing; Hu, Yingwei; Lam, Henry H N Conference paper
Utilizing unidentified tandem mass spectral libraries for biological sample fingerprinting
Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Berlin, Germany, 21 - 23 July 2013
Shao, Wenguang; Lam, Henry H N Conference paper

2012 4

Metabonomic analysis of water extracts from Chinese and American ginsengs by H-1 nuclear magnetic resonance: identification of chemical profile for quality control
Chinese medicine, v. 7, November 2012, Article number 25
Chan, Pui Hei; Zheng, Ken Y.Z.; Tsim, Karl Wah Keung; Lam, Henry H N Article
Spectral library searching for peptide identification in proteomics
Statistics and Its Interface, v. 5, (1), 2012, p. 39-46
Lam, Henry H N Article
Expanding spectral libraries of phosphorylated peptides: Progress in coverage and accuracy
Human Proteome Organization (HUPO) 11th Annual World Congress, Boston, MA, USA, 2012
Hu, Yingwei; Lam, Henry H N Conference paper
Multi-resolution LC-MS images alignment using dynamic time warping and Kullback-Leibler distance
Proceedings - International Conference on Image Processing, ICIP, 2012, article number 6467201, p. 1681-1684
Wu, William K.H.; Chung, Albert Chi Shing; Lam, Henry H N Conference paper

2011 14

A semi-empirical approach for predicting unobserved peptide MS/MS spectra from spectral libraries
Proteomics, v. 11, (24), December 2011, p. 4702-4711
Hu, Yingwei; Li, Yunzi; Lam, Henry H N Article
Absolute quantification of microbial proteomes at different states by directed mass spectrometry
Molecular Systems Biology, v. 7, (510), July 2011, Article number 510
Schmidt, Alexander; Beck, Martin; Malmstroem, Johan; Lam, Henry H N; Claassen, Manfred; Campbell, David; Aebersold, Ruedi Article
Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics
Methods, v. 54, (4), August 2011, p. 424-431
Lam, Henry H N; Aebersold, Ruedi Article
Building and searching tandem mass spectral libraries for peptide identification
Molecular & cellular proteomics, v. 10, (12), December 2011
Lam, Henry H N Article
Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration
Journal of proteome research, v. 10, (6), June 2011, p. 2882-2888
Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry H N; Eng, Jimmy K.; Martin, Daniel B. Article
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
Molecular & cellular proteomics, v. 10, (12), December 2011, M111.007690
Shteynberg, David; Deutsch, Eric W.; Lam, Henry H N; Eng, Jimmy K.; Sun, Zhi; Tasman, Natalie; Mendoza, Luis; Moritz, Robert L.; Aebersold, Ruedi; Nesvizhskii, Alexey I. Article
Spectral archives: a vision for future proteomics data repositories
Nature Methods, v. 8, (7), July 2011, p. 546-548
Lam, Henry H N Article
Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis
Proteomics, v. 11, (6), March 2011, p. 1075-1085
Zhang, Xin; Li, Yunzi; Shao, Wenguang; Lam, Henry H N Article
1H-NMR metabonomics analysis of Danggui Buxue Tang effects in HEK293T kidney cell lines
China Human Proteome Organization (CNHUPO) 7th Annual Congress, Hangzhou, China, 2011
Chan, Pui Hei Nicholas; Tsim, Karl Wah Keung; Lam, Henry H N Conference paper
A novel de-noising method for spectral library in peptide identification from tandem mass spectrometry
China Human Proteome Organization (CNHUPO) 7th Annual Congress, Hangzhou, China, 2011
Shao, Wenguang; Lam, Henry H N Conference paper
Identification of peptides with single amino acid polymorphisms by using semi-empirical MS/MS spectral library
China Human Proteome Organization (CNHUPO) 7th Annual Congress, Hangzhou, China, 2011
Hu, Yingwei; Lam, Henry H N Conference paper
iPRG 2011: A study on the identification of electron transfer dissociation (ETD) mass spectra
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2011
Martens, L.; Askenazi, M.; Bandeira, N.; Chalkley, R.; Clauser, K.; Deutsch, E.; Lam, Henry H N; Mcdonald, W.; Neubert, T.; Rudnick, P. Conference paper
iProphet: Improved statistical validation of peptide and protein identifications in shotgun proteomics
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2011
Shteynberg, D.; Deutsch, E.; Lam, Henry H N; Fermin, D.; Sun, Z.; Tasman, N.; Mendoza, L.; Moritz, R.; Aebersold, R.; Nesvizhskii, A. Conference paper
RTCalc and RTCatalog: Open-source software tools for prediction and cataloging of sequence specific retentions of peptides on liquid chromatography systems
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2011
Shteynberg, D.; Deutsch, E.; Chu, C.; Kusebauch, U.; Stevens, J.; Sun, Z.; Swearingen, K.; Lam, Henry H N; Moritz, R. Conference paper

2010 10

A guided tour of the Trans-Proteomic Pipeline
Proteomics, v. 10, (6), March 2010, p. 1150-1159
Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Farrah, Terry; Lam, Henry H N; Tasman, Natalie; Sun, Zhi; Nilsson, Erik; Pratt, Brian; Prazen, Bryan; Eng, Jimmy K.; Martin, Daniel B.; Nesvizhskii, Alexey I.; Aebersold, Ruedi Article
A ubiquitin and ubiquitin-like protein spectral library
Proteomics, v. 10, (2), January 2010, p. 337-342
Srikumar, Tharan; Jeram, Stanley M.; Lam, Henry H N; Raught, Brian Article
Artificial Decoy Spectral Libraries for False Discovery Rate Estimation in Spectral Library Searching in Proteomics
Journal of proteome research, v. 9, (1), January 2010, p. 605-610
Lam, Henry H N; Deutsch, Eric W.; Aebersold, Ruedi Article
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast
Science Signaling, v. 3, (153), December 2010
Bodenmiller, B.; Wanka, S.; Kraft, C.; Urban, J.; Campbell, D.; Pedrioli, P.G.; Gerrits, B.; Picotti, P.; Lam, Henry H N; Vitek, O.; Brusniak, M.Y.; Roschitzki, B.; Zhang, C.; Shokat, K.M.; Schlapbach, R.; Colman-Lerner, A.; Nolan, G.P.; Nesvizhskii, A.I.; Peter, M.; Loewith, R.; Mering, C.V.; Aebersold, R. Article
Spectral Library Searching for Peptide Identification via Tandem MS
Methods in Molecular Biology, v. 604, 2010, p. 95-103
Lam, Henry H N; Aebersold, Ruedi Article
Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets
Proteomics, v. 10, (6), March 2010, p. 1190-1195
Deutsch, Eric W.; Shteynberg, David; Lam, Henry H N; Sun, Zhi; Eng, Jimmy K.; Carapito, Christine; von Haller, Priska D.; Tasman, Natalie; Mendoza, Luis; Farrah, Terry; Aebersold, Ruedi Article
Using spectral libraries for peptide identification from tandem mass spectrometry (MS/MS) data
Current protocols in protein science, v. Ch. 25, April 2010, Pages Unit 25.5
Lam, Henry H N; Aebersold, Ruedi Article
Spectral Library Searching for Peptide Identification via Tandem MS
Proteome Bioinformatics /Edited by Simon J. Hubbard, Andrew R. Jones. New York, NY: Humana Press; Springer, c2010, chapter 7, p. 95-103
Lam, Henry H N; Aebersold, Ruedi Book chapter
A semi-empirical approach to predict unobserved peptide MS/MS spectra from spectral libraries
The Human Proteome Organisation 9th Annual World Congress (HUPO 2010), Sydney, Australia, 2010
Hu, Yingwei; Lam, Henry H N Conference paper
New functionality for the Trans-Proteomic Pipeline: tools for analysis of proteomics data
US Human Proteome Organization 6th Annual Conference, Denver, CO, USA
Mendoza, L.; Shteynberg, D.; Slagel, J.; Holstein, C.; Tasman, N.; Pratt, B.; Lam, Henry H N; Eng, J.; Nesvizhskii, A.; Martin, D.; Deutsch, E.; Moritz, R.; Aebersold, R. Conference paper

2009 10

MaRiMba: A Software Application for Spectral Library-Based MRM Transition List Assembly
Journal of proteome research, v. 8, (10), October 2009, p. 4396-4405
Sherwood, Carly A.; Eastham, Ashley; Lee, Lik Wee; Peterson, Amelia; Eng, Jimmy K.; Shteynberg, David; Mendoza, Luis; Deutsch, Eric W.; Risler, Jenni; Tasman, Natalie; Aebersold, Ruedi; Lam, Henry H N; Martin, Daniel B. Article
A Bayesian approach to distinguish signal and noise peaks in peptide tandem mass spectra
Human Proteome Organization 6th Annual Conference, Toronto, Canada
Shao, Wenguang; Zhang, Xin; Lam, Henry H N Conference paper
A high quality human plasma proteome available in the PeptideAtlas
Annual Conference, American Society of Mass Spectrometry, Philadelphia, PA
Ferrah, T.; Deutsch, E.; Shteynberg, D.; Campbell, D.; Lam, Henry H N; Sun, Z.; Omenn, G.; Aebersold, R. Conference paper
A human plasma proteome in the PeptideAtlas with estimated protein concentrations
Human Proteome Organization 6th Annual Conference, Toronto, Canada
Farrah, T.; Deutsch, E.; Zhang, N.; Shteynberg, D.; Lam, Henry H N; Campbell, D.; Tasman, N.; Sun, Z.; Mendoza, L.; Omenn, G.; Aebersold, R. Conference paper
A systematic investigation on the improvement in sensitivity of spectral library searching over sequence database searching in proteomics
Annual Conference, American Society of Mass Spectrometry, Philadelphia, PA
Zhang, Xin; Shao, Wenguang; Lam, Henry H N Conference paper
Identification of Ub/Ubl chains in an integrated mass spectrometry/SpectraST/SUMmOn-based work-flow
Human Proteome Organization 6th Annual Conference, Toronto, Canada
Srikumar, T.; Jeram, S.; Pedrioli, P.; Lam, Henry H N; Raught, B. Conference paper
Identification of Ub/Ubl chains using an integrated mass spectrometry/SpectraST/SUMmOn-based work-flow
International Mass Spectrometry Conference, Bremen, Germany, 2009
Srikumar, T.; Jeram, S.; Pedrioli, P.; Lam, Henry H N; Raught, B. Conference paper
Improved support for targeted proteomics workflows in PeptideAtlas
Annual Conference, US Human Proteome Organization, San Diego, CA, USA
Campbell, D.; Deutsch, E.; Lam, Henry H N; Picotti, P.; Aebersold, R. Conference paper
New functionality for the Trans-Proteomic Pipeline: tools for the analysis of proteomics data
Annual Conference, American Society of Mass Spectrometry, Philadelphia, PA
Mendoza, L.; Shteynberg, D.; Tasman, N.; Pratt, B.; Eng, J.; Lam, Henry H N; Nesvizhskii, A.; Deutsch, E.; Aebersold, R. Conference paper
Quality control of ginseng by 1H NMR metabolic profiling
International Conference on Resource Development of Chinese Medicines from Northwestern China, Hong Kong, China, 2009
Chan, Pui Hei Nicholas; Choi, Chi Yan; Chan, Kar Lun Gallant; Tsim, Karl Wah Keung; Lam, Henry H N Conference paper

2008 11

A database of mass spectrometric assays for the yeast proteome
Nature Methods, v. 5, (11), 2008, p. 913-914
Picotti, Paola; Lam, Henry H N; Campbell, David; Deutsch, Eric W.; Mirzaei, Hamid; Ranish, Jeff; Domon, Bruno; Aebersold, Ruedi Article
Building consensus spectral libraries for peptide identification in proteomics
Nature Methods, v. 5, (10), October 2008, p. 873-875
Lam, Henry H N; Deutsch, Eric W.; Eddes, James S.; Eng, Jimmy K.; Stein, Stephen E.; Aebersold, Ruedi Article
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
Physiological genomics, v. 33, (1), March 2008, p. 18-25
Deutsch, E.W.; Lam, Henry H N; Aebersold, R. Article
PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
EMBO reports, v. 9, (5), May 2008, p. 429-434
Deutsch, E.W.; Lam, Henry H N; Aebersold, R. Article
PhosphoPep - A database of protein phosphorylation sites in model organisms
Nature Biotechnology, v. 26, (12), December 2008, p. 1339-1340
Bodenmiller, Bernd; Campbell, David; Gerrits, Bertran; Lam, Henry H N; Jovanovic, Marko; Picotti, Paola; Schlapbach, Ralph; Aebersold, Ruedi Article
Absolute protein quantification estimated by spectral counting using large datasets in PeptideAtlas
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2008
Zhang, N.; Deutsch, E.; Lam, Henry H N; Aebersold, R. Conference paper
iProphet: A new tool for combining PeptideProphet results from multiple search engines improves spectrum validation
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2008
Shteynberg, D.; Nesvizhskii, A.; Deutsch, E.; Lam, Henry H N; Aebersold, R. Conference paper
iProphet: improved validation of peptide identification in shotgun proteomics
World Congress, Human Proteome Organization, Amsterdam, the Netherlands
Shteynberg, D.; Deustch, E.; Lam, Henry H N; Aebersold, R.; Nesvizhskii, A. Conference paper
New developments for open-source shotgun proteomics analysis with the Trans-Proteomic Pipeline
World Congress, Human Proteome Organization, Amsterdam, the Netherlands
Mendoza, L.; Tasman, J.; Shteynberg, D.; Eddes, J.; Zhang, N.; Wong, C.; Pratt, B.; Lam, Henry H N; Eng, J.; Deutsch, E.; Aebersold, R. Conference paper
PeptideAtlas: Resource for target selection for emerging targeted proteomics workflows
US Human Proteome Organization (USHUPO) 4th Annual Conference, Bethesda, MD, USA, 2008
Deutsch, E.; Lam, Henry H N; Aebersold, R. Conference paper
The PeptideAtlas as a tool for targeted proteomics
Annual Conference of the American Society of Mass Spectrometry (ASMS), Denver, CO, USA, 2008
Campbell, D.; Deutsch, E.; Lange, V.; Picotti, P.; King, N.; Letarte, S.; Lam, Henry H N; Zhang, N.; Aebersold, R. Conference paper

2007 5

Development and validation of a spectral library searching method for peptide identification from MS/MS
Proteomics, v. 7, (5), March 2007, p. 655-667
Lam, Henry H N; Deutsch, E.W.; Eddes, J.S.; Eng, J.K.; King, N.; Stein, S.E.; Aebersold, R. Article
PhosphoPep - A phosphoproteome resource for systems biology research in Drosophila Kc167 cells
Molecular Systems Biology, v. 3, January2007, article number 139
Bodenmiller, B.; Malmstrom, J.; Gerrits, B.; Campbell, D.; Lam, Henry H N; Schmidt, A.; Rinner, O.; Mueller, L.N.; Shannon, P.T.; Pedrioli, P.G.; Panse, C.; Lee, H.K.; Schlapbach, R.; Aebersold, R. Article
Development of a spectral library building tool and re-analysis of Human Plasma PeptideAtlas datasets using spectral searching
US Human Proteome Organization (USHUPO) 3rd Annual Conference, Seattle, WA, 2007
Lam, Henry H N; Deutsch, E.; Eddes, J.; Eng, J.; King, N.; Stein, S.; Aebersold, R. Conference paper
Encoding the observed human plasma proteome in spectral libraries
Human Proteome Organization (HUPO) 6th Annual World Congress, Seoul, Korea, 2007
Lam, Henry H N; Deutsch, E.; Shteynberg, D.; Zhang, N.; Stein, S.; Aebersold, R. Conference paper
Estimating false discovery rates in spectral searching using decoy spectral libraries
Human Proteome Organization (HUPO) 6th Annual World Congress, Seoul, Korea, 2007
Lam, Henry H N; Deutsch, E.; Eddes, J.; Aebersold, R. Conference paper

2006 4

Affinity-tagged green fluorescent protein (GFP) extraction from a clarified E-coli cell lysate using a two-phase aqueous micellar system
Biotechnology and bioengineering, v. 93, (5), April 2006, p. 998-1004
Mazzola, PG; Lam, Henry H N; Kavoosi, M.; Haynes, CA; Pessoa, A.; Penna, TCV; Wang, DIC; Blankschtein, D. Article
Annotation of the yeast Proteome with PeptideAtlas
American Society of Mass Spectrometry Annual Conference (ASMS), Seattle, WA, 2006
King, N.; Deutsch, E.; Eng, J.; Ranish, J.; Raught, B.; Eddes, J.; Nesvizhskii, A.; Mallick, P.; Martin, D.; Flory, M.; Lee, H.; Lam, Henry H N; Aebersold, R. Conference paper
SpectraST: An open-source MS/MS spectra-matching search tool for targeted proteomics
American Society of Mass Spectrometry Annual Conference (ASMS), Seattle, WA, 2006
Lam, Henry H N; Deutsch, E.; Eddes, J.; Eng, J.; King, N.; Yang, S.; Roth, J.; Kilpatrick, L.; Neta, P.; Stein, S.; Aebersold, R. Conference paper
The PeptideAtlas Project
International Symposium of the Institute for Systems Biology, Seattle, WA, 2006
Deutsch, E.; Eddes, J.; Eng, J.; King, N.; Lam, Henry H N; Campbell, D.; Loevenich, S.; Mallick, P.; Martin, D.; Mendoza, L.; Nesvizhiskii, A.; Ranish, J.; Raught, B.; Shteynberg, D.; Tasman, J.; Zhang, N.; Vitek, O.; Aebersold, R. Conference paper

2005 1

Affinity-enhanced protein partitioning in decyl beta-D-glucopyranoside two-phase aqueous micellar systems
Biotechnology and bioengineering, v. 89, (4), February 2005, p. 381-392
Lam, Henry H N; Kavoosi, M.; Haynes, CA; Wang, DIC; Blankschtein, D. Article

2004 1

Affinity-enhanced protein partitioning in decyl beta-D-glucopyranoside two-phase aqueous micellar systems
American Institute of Chemical Engineers (AIChE) Annual Meeting, Austin, TX, 2004
Lam, Henry H N; Kavoosi, M.; Haynes, C.A.; Wang, D.I.C.; Blankschtein, D. Conference paper

2003 1

Glucose-6-phosphate dehydrogenase partitioning in two-phase aqueous mixed (nonionic/cationic) micellar systems
Biotechnology and bioengineering, v. 82, (4), May 2003, p. 445-456
Rangel-Yagui, CO; Lam, Henry H N; Kamei, DT; Wang, DIC; Pessoa, A.; Blankstein, D. Article






Teaching Assignment

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2021-22 Winter 0 2021-22 Fall 9 2020-21 Summer 1 2020-21 Spring 2 2020-21 Winter 0 2020-21 Fall 5

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BIEN2310 Modeling for Chemical and Biological Engineering
BIEN2990 Academic and Professional Development I
BIEN4920 Bioengineering Capstone Design
BIEN4930 Bioengineering Thesis Research
BIEN4940 Bioengineering Industrial Project
BIEN4990 Academic and Professional Development II
CENG1010 Academic and Professional Development I
CENG2310 Modeling for Chemical and Biological Engineering
CENG4020 Academic and Professional Development II


UROP1000 Undergraduate Research Opportunities


CENG2210 Chemical and Biological Engineering Thermodynamics
CENG4930 Chemical Engineering Thesis Research


BIEN2310 Modeling for Chemical and Biological Engineering
BIEN2990 Academic and Professional Development I
CENG1010 Academic and Professional Development I
CENG2310 Modeling for Chemical and Biological Engineering
SCIE4500 IRE Research Project II


No Teaching Assignments


No Teaching Assignments






Research Postgraduate (RPG) Supervision From January 2019 to December 2022 (As of 30 January 2022)

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All Supervisions Current RPGs Graduated RPGs

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Current RPGs

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Doctor of Philosophy HOQUE, Ayman
Bioengineering( 2021 - )

MADEJ, Dominik
Chemical and Biomolecular Engineering( 2020 - )

SULAIMAN, Jordy Evan
Chemical and Biomolecular Engineering( 2019 - )

YAN, Kai Qi
Chemical and Biomolecular Engineering( 2019 - )

LINARDI, Darwin
Chemical and Biomolecular Engineering( 2018 - )

WONG, Tin Yan
Chemical and Biomolecular Engineering( 2017 - )

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Master of Philosophy CHAN, Chak Ming Jerry
Chemical and Biomolecular Engineering( 2021 - )

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Graduated RPGs

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Doctor of Philosophy HAO, Chunlin
Bioengineering( Completed in 2021 )

YANG, Yun
Chemical and Biomolecular Engineering( Completed in 2021 )

KWAN, Kin Leung (co-supervision)
Life Science( Completed in 2020 )

MUSHTAQ, Faheem
Chemical and Biomolecular Engineering( Completed in 2020 )

WU, Long
Bioengineering( Completed in 2020 )

GAO, Tianpeng
Chemical and Biomolecular Engineering( Completed in 2019 )

LI, Quan
Chemical and Biomolecular Engineering( Completed in 2019 )

LIM, Khak Ho
Chemical and Biomolecular Engineering( Completed in 2019 )

ZHANG, Xiang
Chemical and Biomolecular Engineering( Completed in 2019 )

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Master of Philosophy MADEJ, Dominik
Chemical and Biomolecular Engineering( Completed in 2020 )

SULAIMAN, Jordy Evan
Chemical and Biomolecular Engineering( Completed in 2019 )

TANG, Jiayu
Chemical and Biomolecular Engineering( Completed in 2019 )

ZHANG, Shouchi
Chemical and Biomolecular Engineering( Completed in 2019 )









ProjectsFrom January 2020 to December 2022

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All Projects 12 Leading Projects 10 Participating Projects 2

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Proteomic investigation of evolved antibiotic tolerance in Staphylococcus aureus mutant strains from adaptive laboratory evolution


人工適應進化生成的具抗生素耐受性的金黃色葡萄球菌突變株之蛋白質組學研究 Leading


RGC - General Research Fund


Project Team (HKUST)
LAM Henry Hei Ning (Lead)


2021 -




Data Storage and Retrieval using Peptides and Tandem Mass Spectrometry Sequencing


多肽及串聯質譜測序用於數據儲存及讀取 Participating


Research Impact Fund


Project Team (HKUST)
LAM Henry Hei Ning


2020 -




Development of a spectral archive search engine for peptide identification in proteomics


用於蛋白組學中肽鑑定的質譜檔案搜索引擎之開發 Leading


RGC - General Research Fund


Project Team (HKUST)
LAM Henry Hei Ning (Lead)


2020 -




Research & Development of Traditional Chinese Medicine Classics formula——Data Platform Establishing


經典名方作用機理、物質基準和二次開發研究——數據平臺的建立 Participating


Nanhai People's Government of Foshan


Project Team (HKUST)
TSIM Karl Wah Keung (Lead)
CHAN Simon Wan
LAM Henry Hei Ning
WANG Yang


2020 -




Building tandem mass spectral libraries for proteomics in the Big Data Era


在大數據時代中建立蛋白質組學所用之串聯質譜庫 Leading


RGC - General Research Fund


Project Team (HKUST)
LAM Henry Hei Ning (Lead)


2017 - 2021




General research on product and process design Leading


ClearWaterBay Technology Limited


Project Team (HKUST)
LAM Henry Hei Ning (Lead)


2014 - 2021




Extending State-of-the-Art Proteomic Data Analysis Methods to the Analysis of Intact Glycopeptides Leading


RGC - Direct Allocation Grant


Project Team (HKUST)
LAM Henry Hei Ning (Lead)


2011 - 2020




Research on battery materials for electric vehicles, fabrication of organic solar cells, coating technologies and renewable biofuels Leading


CN Innovations Holdings Limited


Project Team (HKUST)
LAM Henry Hei Ning (Lead)


2010 -




Extracting useful information from existing public proteomic data to expand our knowledge of the proteome and to improve data analysis methods Leading


RGC - Direct Allocation Grant


Project Team (HKUST)
LAM Henry Hei Ning (Lead)


2008 - 2020




Research on crystallization and solids processing, including integrated manufacturing technologies for nanomaterials Leading


Mitsubishi Chemical Research Corporation


Project Team (HKUST)
LAM Henry Hei Ning (Lead)


2006 - 2021




Crystallization and solids processing, including integrated manufacturing technologies for nanomaterials Leading


Mitsubishi Chemical Corporation


Project Team (HKUST)
LAM Henry Hei Ning (Lead)


2004 -




Solid products and processes Leading


Mitsubishi Chemical Corporation


Project Team (HKUST)
LAM Henry Hei Ning (Lead)


2002 -