Faculty Profiles - LAM Henry Hei Ning | The Hong Kong University of Science and Technology

2024 2

On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation

Proteomics, March 2024, article number 2300398
Madej, Dominik; Lam, Hei Ning
Article

Targeted Protein O-GlcNAcylation Using Bifunctional Small Molecules

Journal of the American Chemical Society, v. 146, (14), April 2024, p. 9779-9789
Ma, Bowen; Khan, Khadija Shahed; Xu, Tongyang; Xeque Amada, Josefina; Guo, Zhihao; Huang, Yunpeng; Yan, Yu; Lam, Hei Ning; Cheng, Alfred Sze-Lok; Ng, Billy Wai-Lung
Article

2023 14

Comparative proteomic analysis reveals the different hepatotoxic mechanisms of human hepatocytes exposed to silver nanoparticles

Journal of Hazardous Materials, v. 445, March 2023, article number 130599
Wong, Tin Yan; Yan, Neng; Kwan, Kenneth Kin Leung; Pan, Yanrong; Liu, Jingjing; Xiao, Yao; Wu, Long; Lam, Henry Hei Ning
Article

Mechanistic Insight into the Inhibitory Activity of Elasnin-Based Coating against Early Marine Biofilms

Environmental Science and Technology, v. 57, (26), July 2023, p. 9515-9525
Long, Lexin; Xiao, Yao; Sulaiman, Jordy Evan; Luo, Fuqing; Tang, Jianwei; Huang, Yuqing; Wu, Chuanhai; Wu, Long; Wong, Wai Chuen; Chen, Feng; Lam, Hei Ning; Qian, Peiyuan
Article

Merging Full-Spectrum and Fragment Ion Intensity Predictions from Deep Learning for High-Quality Spectral Libraries

Journal of Proteome Research, v. 22, (12), December 2023, p. 3692-3702
Chan, Chak Ming Jerry; Lam, Hei Ning
Article

metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering

Microbiome, v. 11, (1), August 2023, article number 176
Hao, Chunlin; Elias, Joshua E.; Lee, Patrick K.H.; Lam, Hei Ning
Article

Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics

Journal of Proteome Research, v. 22, (4), April 2023, p. 1159-1171
Madej, Dominik; Lam, Hei Ning
Article

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

Journal of Proteome Research, v. 22, (2), February 2023, p. 287-301
Deutsch, Eric W; Vizcaíno, Juan Antonio; Jones, Andrew R.; Binz, Pierre-Alain; Lam, Hei Ning; Klein, Joshua; Bittremieux, Wout; Perez-Riverol, Yasset; Tabb, David L; Walzer, Mathias; Ricard-Blum, Sylvie; Hermjakob, Henning; Neumann, Steffen; Mak, Tytus D.; Kawano, Shin; Mendoza, Luis; Van Den Bossche, Tim; Gabriels, Ralf; Bandeira, Nuno; Carver, Jeremy; Pullman, Benjamin; Sun, Zhi; Hoffmann, Nil; Shofstahl, Jim; Zhu, Yunping; Licata, Luana; Quaglia, Federica; Tosatto, Silvio C. E.; Orchard, Sandra E
Article

Pterosin sesquiterpenoids from Pteris laeta Wall. ex Ettingsh. protect cells from glutamate excitotoxicity by modulating mitochondrial signals

Journal of Ethnopharmacology, v. 308, May 2023, article number 116308
Cheng, Aifang; Zhang, Yan; Sun, Jin; Huang, Duli; Sulaiman, Jordy Evan; Huang, Xin; Wu, Long; Ye, Wenkang; Wu, Chuanhai; Lam, Hei Ning; Shi, Yusheng; Qian, Peiyuan
Article

Spectroscape enables real-time query and visualization of a spectral archive in proteomics

Nature Communications, v. 14, (1), October 2023, article number 6267
Wu, Long; Hoque, Ayman; Lam, Hei Ning
Article

Merging full-spectrum and fragment ion intensity predictions from deep learning for high quality spectral libraries

Chan, Chak Ming Jerry; Lam, Henry Hei Ning
Conference paper

Proteomics Standards Initiative (PSI) proposed peak annotation format (mzPAF) and spectral library format (mzSpecLib) standards

Lam, Henry Hei Ning; Mak, Tytus; Klein, Joshua A.; Bittremieux, Wout; Gabriels, Ralf; Perez-riverol, Yasset; Van den bossche, Tim; Jones, Andrew R.; Binz, Pierre-Alain; Kawano, Shin; Mendoza, Luis; Bandeira, Nuno; Carver, Jeremy; Pullman, Benjamin; Sun, Zhi; Hoffmann, Nils; Shofstahl, Jim; Zhu, Yunping; Heche, Helge; Deutsch, Eric W.; Vizcaino, Juan-Antonio
Conference paper

Rescuing unidentified spectra using self-correcting spectral archival methods in proteomics

Hoque, Ayman; Wu, Long; Lam, Henry Hei Ning
Conference paper

Self-contained validation by partition as a way of verifying FDR estimates in proteomics

Madej, Dominik; Lam, Hei Ning
Conference paper

Spectroscape: validating PSMs by real-time visualization of their neighborhoods with an interactive web interface

Wu, Long; Hoque, Ayman; Lam, Henry Hei Ning
Conference paper

The Pitfalls of Using Entrapments for Validation of False Discovery Rate Estimation in Proteomics

Madej, Dominik; Lam, Hei Ning
Conference paper

2022 15

Antibody stabilization for thermally accelerated deep immunostaining

Nature Methods, v. 19, (9), September 2022, p. 1137-1146
Lai, Hei Ming; Tang, Yumi; Lau, Zachary Y. H.; Campbell, Robert A. A.; Yau, Juno C. N.; Chan, Caleb C. Y.; Chan, Danny C. W.; Wong, Tin Yan; Wong, Harriet K. T.; Yan, Leo. Y. C.; Wu, William K. K.; Wong, Sunny H.; Kwok, Ka-Wai; Wing, Yun-Kwok; Lam, Henry Hei Ning; Ng, Ho-Keung; Mrsic-Flogel, Thomas D.; Mok, Vincent C. T.; Chan, Jason Y. K.; Ko, Ho
Article

Common Decoy Distributions Simplify False Discovery Rate Estimation in Shotgun Proteomics

Journal of Proteome Research, v. 21, (2), February 2022, p. 339-348
Madej, Dominik; Wu, Long; Lam, Hei Ning
Article

Elasnin Effectively Eradicates Daptomycin-Resistant Methicillin-Resistant Staphylococcus aureus Biofilms

Microbiology Spectrum, v. 10, (1), 23 February 2022, article number e02320-21
Sulaiman, Jordy Evan; Long, Lexin; Qian, Peiyuan; Lam, Hei Ning
Article

Fluorescent Imaging and Sorting of High-Lipid-Content Strains of Green Algae by Using an Aggregation-Induced Emission Luminogen

ACS Nano, v. 16, (9), 27 September 2022, p. 14973-14981
Liu, Haixiang; Yan, Neng; Wong, Tin Yan; Lam, Hei Ning; Lam, Wing Yip; Kwok, Tsz Kin; Sun, Jianwei; Tang, Benzhong
Article

Fritted Tip Capillary Column with Negligible Dead Volume Facilitated Ultrasensitive and Deep Proteomics

Analytica Chimica Acta, v. 1201, April 2022, article number 339615
Yang, Yun; Su, Yiran; Wang, Xi; Gao, Weina; Lu, Xue; Lam, Hei Ning; Tian, Ruijun
Article

Fully integrated on-line strategy for highly sensitive proteome profiling of 10-500 mammalian cells

Analyst, v. 148, (1), November 2022, p. 120-127
Yang, Yun; Sun, Suhong; He, Shunji; Liu, Chengmin; Fu, Changying; Tang, Min; Liu, Chao; Sun, Ying; Lam, Hei Ning; Liu, Zhiyong; Tian, Ruijun
Article

Mode of action of elasnin as biofilm formation eradicator of methicillin-resistant Staphylococcus aureus

Frontiers in Microbiology, v. 13, August 2022, article number 967845
Long, Lexin; Sulaiman, Jordy Evan; Xiao, Yao; Cheng, Aifang; Wang, Ruojun; Malit, Jessie James Limlingan; Wong, Wai Chuen; Liu, Wenchao; Li, Yong-Xin; Chen, Feng; Lam, Hei Ning; Qian, Peiyuan
Article

Mutation in the Two-Component System Regulator YycH Leads to Daptomycin Tolerance in Methicillin-Resistant Staphylococcus aureus upon Evolution with a Population Bottleneck

Microbiology Spectrum, v. 10, (4), August 2022, article number e01687-22, p. 13
Sulaiman, Jordy Evan; Wu, Long; Lam, Hei Ning
Article

Nontargeted Metabolomics Reveals Differences in the Metabolite Profiling among Methicillin-Resistant and Methicillin-Susceptible Staphylococcus Aureus in Response to Antibiotics

Molecular Omics, v.18, (10), 19 September 2022, p. 948-956
Liu, Jingjing; Qi, Mingyang; Yuan, Zichen; Wong, Tin Yan; Song, Xiaofeng; Lam, Henry Hei Ning
Article

Proteome Profiling of Evolved Methicillin-Resistant Staphylococcus aureus Strains with Distinct Daptomycin Tolerance and Resistance Phenotypes

Frontiers in Microbiology, v.13, 4 August 2022, article number 970146
Sulaiman, Jordy Evan; Long, Lexin; Qian, Peiyuan; Lam, Hei Ning
Article

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

Proteomics in Antibiotic Resistance and Tolerance Research: Mapping the Resistome and the Tolerome of Bacterial Pathogens

Proteomics, v. 22, (8), April 2022, article number 2100409
Sulaiman, Jordy Evan; Lam, Hei Ning
Article

Proteomining-based elucidation of natural product biosynthetic pathways in Streptomyces

Frontiers in Microbiology, v. 13, 11 July 2022, article number 913756
Linardi, Darwin; She, Weiyi; Zhang, Qian; Yu, Yi; Qian, Peiyuan; Lam, Hei Ning
Article

Lower-order statistics facilitate decoy-free FDR control in shotgun proteomics

Madej, Dominik; Lam, Henry Hei Ning
Conference paper

Order Statistics Provides a Theoretical Basis for Decoy-free FDR Control in Mass Spectrometry-based Proteomics

Madej, Dominik; Lam, Hei Ning
Conference paper

2021 14

Boosting Cyanobacteria Growth by Fivefold with Aggregation-Induced Emission Luminogens: Toward the Development of a Biofactory

ACS Sustainable Chemistry and Engineering, v. 9, (45), November 2021, p. 15258-15266
Liu, Haixiang; Bai, Haotian; Yan, Neng; Wong, Tin Yan; Dang, Dongfeng; Ni, Jen-Shyang; Lam, Wing Yip; Lam, Hei Ning; Kwok, Tsz Kin; Wang, Wen-Xiong; Tang, Benzhong
Article

ClusterSheep: A Graphics Processing Unit-Accelerated Software Tool for Large-Scale Clustering of Tandem Mass Spectra from Shotgun Proteomics

Journal of Proteome Research, v. 20, (12), December 2021, p. 5359-5367
To, Paul Ka Po; Wu, Long; Chan, Chak Ming; Hoque, Ayman; Lam, Henry Hei Ning
Article

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

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

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

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

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

A real time spectral visualization tool for PSM validation

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

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

Wong, Tin Yan; Lam, Henry
Conference paper

Insights into the anti-cancer effect triggered by silver nanoparticles in cisplatin-resistant A549 lung cancer cells using quantitative proteomics

Wong, Tin Yan; Kwan, Kin Leung; Lam, Henry Hei Ning
Conference paper

Integrated omics dissection of the effect of natural product decoction on cultured osteoblasts

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

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

Sulaiman, Jordy Evan; Lam, Hei Ning
Conference paper

Quality control of results from searchable spectral archive

Wu, Long; Lam, Henry Hei Ning
Conference paper

Quantitative proteomics analysis of apramycin producer Streptomyces tenebrarius

Linardi, Darwin; Lam, Henry
Conference paper

Quantitative proteomics analysis of the aminoglycoside producer Streptomyces tenebrarius

Linardi, Darwin; Pan, T.; Yu, Yi; Lam, Henry Hei Ning
Conference paper

Time-Course Proteome Profiling of Filamentous β-lactam Persisters during Antibiotic Treatment and Resuscitation

Sulaiman, Jordy Evan; Lam, 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

Sulaiman, Jordy Evan; Lam, Hei Ning
Conference paper

Genomic and Proteomic Study of High Persistence Evolved Escherichia coli Populations from Cyclic Antibiotic Treatment

Sulaiman, Jordy Evan; Lam, Hei Ning
Conference paper

Mass spectrometry based omics technology to reveal the effect of herbal decoction in cultured osteoblasts

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

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

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.; Käll, 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

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

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

Hao, Chunlin; Linardi, darwin; Lam, Hei Ning
Conference paper

Discrimination of Environmental E.coli strains through LC-MS/MS based Metabolomics

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

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

Sulaiman, Jordy Evan; Lam, Hei Ning
Conference paper

Quantitative proteomic analysis of aminoglycoside antibiotic producer Streptomyces tenebrarius

Linardi, Darwin; Hao, Chunlin; Yu, Yi; Lam, Henry Hei Ning
Conference paper

Spectral cluster refinement by DBSCAN clustering for proteomics data

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 Doǧu, 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)

To, Ka Po; Lam, Henry Hei Ning
Conference paper

Fast Similarity Measure of SWATH-MS by Cosine Similarity of Random Pairs

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

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, Hei Ning
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, Hei Ning
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, Hei Ning; 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, Hei Ning; Bruce, James E.
Article

An Efficient and Accurate Feature-based Label-free Quantification Software Tool for SWATH MS Data

Wu, Long; Li, Yan Chak; Lam, Henry H.N.
Conference paper

Meat Species Identification by Protein Profiling and Spectral Fingerprinting Using MALDI-TOF-MS

Lam, Hei Ning; So, Man On
Conference paper

Proteome-wide Quantitative Profiling of Mis-incorporation of Selenocysteine into Proteins by LC-MS Based Shotgun Proteomics

Hao, Chunlin; Lam, Hei Ning
Conference paper

Quality control of cooking oils by metabolic profiling and spectral fingerprinting

Cheung, Chi Yuen; Lam, Henry H. N.
Conference paper

The 2016 iPRG Study: Inferring Proteoforms From Bottom-up Proteomics Data

Palmblad, Magnus; Lam, Hei Ning; 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

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

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; Röst, 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

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

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

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

Liu, Xiaofen; Hu, Yingwei; Pai, Peggy; Chen, Daijie; Lam, Henry Hei Ning
Conference paper

Label-free Quantitative Proteomics Study of the Synergistic Effect of Oxacillin and a Novel Erythromycin Derivative against Methicillin-resistant Staphylococcus Aureus

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

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

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.; Röst, 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

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

Hu, Yingwei; Lam, Henry H N
Conference paper

Graph-based time alignment algorithms for LC-MS datasets with large retention-time drifts

Wang, Jijie; Lam, Henry H N
Conference paper

iPRG-2013 Proteome Informatics Research Group study: Using RNA-seq data to refine proteomic data analysis

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

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

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

Pai, Peggy Pei Jing; Hu, Yingwei; Lam, Henry H N
Conference paper

Utilizing unidentified tandem mass spectral libraries for biological sample fingerprinting

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

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, Hei Ning
Article

1H-NMR metabonomics analysis of Danggui Buxue Tang effects in HEK293T kidney cell lines

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

Shao, Wenguang; Lam, Henry H N
Conference paper

Identification of peptides with single amino acid polymorphisms by using semi-empirical MS/MS spectral library

Hu, Yingwei; Lam, Henry H N
Conference paper

iPRG 2011: A study on the identification of electron transfer dissociation (ETD) mass spectra

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

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

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

Hu, Yingwei; Lam, Henry H N
Conference paper

New functionality for the Trans-Proteomic Pipeline: tools for analysis of proteomics data

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

Shao, Wenguang; Zhang, Xin; Lam, Henry H N
Conference paper

A high quality human plasma proteome available in the PeptideAtlas

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

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

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

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

Srikumar, T.; Jeram, S.; Pedrioli, P.; Lam, Henry H N; Raught, B.
Conference paper

Improved support for targeted proteomics workflows in PeptideAtlas

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

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

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

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

Shteynberg, D.; Nesvizhskii, A.; Deutsch, E.; Lam, Henry H N; Aebersold, R.
Conference paper

iProphet: improved validation of peptide identification in shotgun proteomics

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

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

Deutsch, E.; Lam, Henry H N; Aebersold, R.
Conference paper

The PeptideAtlas as a tool for targeted proteomics

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

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

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

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

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

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

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

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.
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CENG2310	Modeling for Chemical and Biological Engineering
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