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Publications

Refereed Academic Journals

  1. W. Shao, M. Zhang, H. Lam+, S. C. Lau+. “A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain level bacterial differentiation.” Scientific Reports 5, 14337 (2015). + Co-corresponding authors

  2. E. Caron, L. Espona, D. J. Kowalewski, H. Schuster, N. Ternette, A. Alpizar, R. B. Schittenhelm, S. H. Ramarathinam, C. S. Lindestam Arlehamn, C. C. Koh, L. C. Gillet, A. Rabsteyn, P. Navarro, S. Kim, H. Lam, T. Sturm, M. Marcilla, A. Sette, D. S. Campbell, E. W. Deutsch, R. L. Moritz, A. W. Purcell, H. Rammensee, S. Stevanovic, R. Aebersold. “An open-source computational and data resource to analyze digital maps of immunopeptidomes.” eLIFE 4, doi: 10.7554/eLife.07661 (2015).

  3. O. T. Schubert, L. C. Gillet, B. C. Collins, P. Navarro, G. Rosenberger, W. E. Wolski, H. Lam, D. Amodei, P. Mallick, B. MacLean, R. Aebersold. “Building high-quality assay libraries for targeted analysis of SWATH MS data.” Nature Protocols 10, 426-441 (2015).

  4. J. Chen, P. H. Chan, C. T. Lam, Z. Li, K. Y. Lam, P. Yao, T. T. Dong, H. Lin, H. Lam, K. W. K. Tsim. “Fruit of Ziziphus jujuba (jujube) at two stages of maturity: Distinction by metabolic profiling and biological assessment.” Journal of Agricultural and Food Chemistry 63, 739-744 (2015).

  5. G. Rosenberger, C. C. Koh, T. Guo, H. L. Roest, P. Kouvonen, B. C. Collins, M. Heusel, Y. Liu, E. Caron, A. Vichalkovski, M. Faini, O. T. Schubert, P. Faridi, H. A. Ebhardt, M. Matondo, H. Lam, S. L. Bader, D. S. Campbell, E. W. Deutsch, R. L. Moritz, S. Tate, R. Aebersold. “A repository of assays to quantify 10,000 human proteins by SWATH-MS.” Scientific Data 1, 140031 (2014).

  6. L. Lu, J. Wang, Y. Xu, K. Wang, Y. Hu, R. Tian, B. Yang, Q. Lai, Y. Li, W. Zhang, Z. Shao, H. Lam+, P.-Y. Qian+. “A high-resolution LC-MS-based secondary metabolite fingerprint database of marine bacteria.” Scientific Reports 4, 6537 (2014). + Co-corresponding authors

  7. S. Chaiyarit, N. Singhto, Y.-J. Chen, C.-Y. Cheng, W. Chiangjong, R. Kanlaya, H. Lam, P. Peerapen, T.-Y. Sung, P. Tipthara, A. Pandey, T. C. W. Poon, Y.-J. Chen, R. Sirdeshmukh, M. C. M. Chung, V. Thongboonkerd. “Chromosome-centric human proteome project (C-HPP): Chromosome 12.” Journal of Proteome Research 13, 3160-3165 (2014).

  8. C. W. M. Ma, H. Lam. “Hunting for unexpected post-translational modifications by spectral library searching with tier-wise scoring.” Journal of Proteome Research 13, 2262-2271 (2014).

  9. M. Kim, S. M. Pinto, D. Getnet, R. S. Nirujogi, S. S. Manda, R. Chaerkady, A. K. Madugundu, D. S. Kelkar, R. Isserlin, S. Jain, J. K. Thomas, B. Muthusamy, P. Leal-Rojas, P. Kumar, N. A. Sahasrabuddhe, L. Balakrishnan, J. Advani, B. George, S. Renuse, L. D. N. Selvan, A. H. Patil, V. Nanjappa, A. Radhakrishnan, S. Prasad, T. Subbannayya, R. Raju, M. Kumar, S. K. Sreenivasamurthy, A. Marimuthu, G. J. Sathe, S. Chavan, K. K. Datta, Y. Subbannayya, A. Sahu, S. D. Yelamanchi, S. Jayaram, P. Rajagopalan, J. Sharma, K. R. Murthy, N. Syed, R. Goel, A. A. Khan, S. Ahmad, G. Dey, K. Mudgal, A. Chatterjee, T. Huang, J. Zhong, X. Wu, P. G. Shaw, D. Freed, S. Zahari, K. K. Mukherjee, S. Shankar, A. Mahadevan, H. Lam, C. Mitchell, S. K. Shankar, P. Satishchandra, R. Sirdeshmukh, A. Maitra, S. D. Leach, C. G. Drake, M. K. Halushka, T. S. Keshava Prasad, R. H. Hruban, C. L. Kerr, G. D. Bader, C. A. Iacobuzio-Donahue, H. Gowda and A. Pandey. “A draft map of the human proteome.” Nature 509, 573-581 (2014).

  10. P. H. Chan, W. L. Zhang, C. H. Lau, C. Y. Cheung, H. C. Keun, K. W. K. Tsim, H. Lam. “Metabonomic analysis of water extracts from different Angelica roots by 1H nuclear magnetic resonance spectroscopy.” Molecules 19, 3460-3470 (2014).

  11. O. Onder +, W. Shao, B. D. Kemps, H. Lam +, D. Brisson. “Non-targeted blood meal source identification using unidentified tandem mass spectral libraries.” Nature Protocols 9, 842-850 (2014). + Co-corresponding authors

  12. P. H. Chan, W. L. Zhang, C. Y. Cheung, K. W. K. Tsim, H. Lam. “Quality control of Danggui Buxue Tang, a Traditional Chinese Medicine decoction, by 1H-NMR metabolic profiling.” Evidence-based Complementary and Alternative Medicine 2014, 567893 (2014).

  13. X. Liu, Y. Hu, P. Pai, H. Lam. “Label-free quantitative proteomics analysis of antibiotic response in Staphylococcus aureus to oxacillin.” Journal of Proteome Research 13, 1223-1233 (2014).

  14. R. Chalkley, N. Bandeira, M. Chambers, K. Clauser, J. Cottrell, E. Deustch, H. Lam, E. Kapp, W. Mcdonald, T. Neubert, R. Sun. “Proteome Informatics Research Group (iPRG) 2012: A study on the identification of biological modifications in a complex sample.” Molecular and Cellular Proteomics 13, 360-371 (2014).

  15. Y. Hu, H. Lam. “Expanding tandem mass spectral libraries of phosphorylated peptides: Advanced and applications.” Journal of Proteome Research 12, 5971-5977 (2013).

  16. W. Shao, K. Zhu, H. Lam. “Refining similarity scoring to enable decoy-free validation in spectral library searching.” Proteomics 13, 3273-3283 (2013). [Highlighted by a Commmentary]

  17. Z. Yang, G. Guo, M. Zhang, C. Y. Liu, Q. Hu, H. Lam, Y. Xue, J. Li, N. Li. “Stable isotope metabolic labeling-based quantitative phosphoproteomic analysis of Arabidopsis mutants reveals ethylene-regulated phosphoproteins and putative substrates for Constitutive Triple Response 1 kinase.” Molecular and Cellular Proteomics 12, 3559-3582 (2013).

  18. J. Wang, H. Lam. “Graph-based peak alignment algorithms for multiple liquid chromatography-mass spectrometry datasets.” Bioinformatics 29, 2469-2476 (2013).

  19. W. Shao, H. Lam. “Denoising peptide tandem mass spectra for spectral libraries: a Bayesian approach.” Journal of Proteome Research 12, 3223-3232 (2013).

  20. J. Y. Zhan, W. L. Zhang, K. Y. Zheng, K. Y. Zhu, J. P. Chen, P. H. Chan, T. T. Dong, R. C. Choi, H. Lam, K. W. Tsim, D. T. Lau “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 8, 12 (2013).

  21. O. Onder, W. Shao, B. D. Kemps, H. Lam+, D. Brisson+ “Blood meal source tracking through genome-free proteomics technology using unidentified tandem mass spectral libraries.” Nature Communications 4, 1746 (2013). + Co-corresponding authors

  22. P. Picotti*, M. Clement-Ziza*, H. Lam*, D. S. Campbell, A. Schmidt, E. W. Deutsch, H. Roest, Z. Sun, O. Rinner, L. Reiter, Q. Shen, J. J. Michaelson, A. Frei, S. Alberti, U. Kusebauch, B. Wollscheid, R. L. Moritz, A. Beyer, R. Aebersold. “A complete mass spectrometric reference map for the analysis of the yeast proteome and its application to quantitative trait analysis.” Nature 494, 266-270 (2013). * Authors contributing equally

  23. P. H. Chan, K. Y. Zheng, K. W. Tsim, H. Lam. “Metabonomic analysis of the extracts from Chinese and American ginsengs by 1H Nuclear magnetic resonance: an identification of chemical profile for quality control.” Chinese Medicine 7, 25 (2012). [Editor’s Pick in 2012]

  24. H. Lam. “Spectral library searching for peptide identification in proteomics.” Statistics and its Interface 5, 39-46 (2012).

  25. Y. Hu, Y. Li, H. Lam. “A semi-empirical approach to predict unobserved peptide MS/MS spectra from spectral ibraries.” Proteomics 11, 4702-4711 (2011).

  26. H. Lam. “Building and searching tandem mass spectral libraries for peptide identification.” Molecular and Cellular Proteomics 10, R111.008565 (2011).

  27. D. Shteynberg, E. W. Deustch, H. Lam, J. K. Eng, Z. Sun, N. Tasman, L. Mendoza, R. L. Moritz, R. Aebersold, A. I. Nesvizhskii. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” Molecular and Cellular Proteomics 10, M111.007690 (2011).

  28. H. Lam. “Spectral archives: a vision for future proteomics data repositories.” Nature Methods 8, 546-548 (2011).

  29. A. Schmidt, M. Beck, J. Malmstroem, H. Lam, M. Claassen, D. Campbell, R. Aebersold. “Absolute quantification of microbial proteomes at different cellular states by directed mass spectrometry: Application to the human pathogen Leptospira interrogans.” Molecular Systems Biology 7, 510 (2011).

  30. L. Baumgardner, A. Shanmugam, H. Lam, J. Eng, D. Martin. “Fast parallel tandem mass spectral library searching using GPU hardware acceleration.” Journal of Proteome Research 10, 2882-2888 (2011).

  31. H. Lam, R. Aebersold. “Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics.” Methods 54, 424-431 (2011).

  32. X. Zhang, Y. Li, W. Shao, H. Lam. “Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis.” Proteomics 11, 1075-1085 (2011).

  33. B. Bodenmiller, S. Wanka, C. Kraft, J. Urban, D. Campbell, P. Pedrioli, B. Gerrits, P. Picotti, H. Lam, O. Vitek, M. Brusniak, B. Roschitzki, C. Zhang, R. Schlapbach, K. Shokat, A. Colman-Lerner, A. Nesvizhskii, M. Peter, R. Loewith, C. von Mering, and R. Aebersold. “Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.” Science Signaling 3, rs4 (2010).

  34. E. W. Deutsch, L. Mendoza, D. Shteynberg, T. Farrah, H. Lam, N. Tasman, Z. Sun, E. Nilsson, B. Pratt, B. Prazen, J. K. Eng, D. B. Martin, A. Nesvizhskii, R. Aebersold. “A guided tour of the Trans Proteomic Pipeline.” Proteomics 10, 1150-1159 (2010).

  35. E. W. Deutsch, D. Shteynberg, H. Lam, Z. Sun, J. K. Eng, C. Carapito, P. D. von Haller, N. Tasman, L. Mendoza, T. Farrah, R. Aebersold. “Trans Proteomic Pipeline supports and improves analysis of electron transfer dissociation datasets.” Proteomics 10, 1190-1195 (2010).

  36. H. Lam, E. W. Deustch, R. Aebersold. “Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics.” Journal of Proteome Research 9, 605-610 (2010).

  37. T. Srikumar, S. M. Jeram, H. Lam, B. Raught. “A ubiquitin and ubiquitin-like protein spectral library.” Proteomics 10, 337-342 (2010).

  38. C. A. Sherwood, A. Eastham, L. W. Lee, A. Peterson, J. K. Eng, D. Shteynberg, L. Mendoza, E. W. Deustch, J. Risler, N. Tasman, R. Aebersold, H. Lam, D. B. Martin. “MaRiMba: A software application for spectral library-based MRM transition list assembly.” Journal of Proteome Research 8, 4396-4405 (2009).

  39. H. Lam, E. W. Deutsch, J. S. Eddes, J. K. Eng, S. E. Stein, and R. Aebersold. “Building consensus spectral libraries for peptide identification in proteomics.” Nature Methods 5, 873-875 (2008).

  40. P. Picotti*, H. Lam*, D. Campbell, E. Deutsch, H. Mirzaei, J. Ranish, B. Domon, and R. Aebersold. “A database of validated assays for the targeted mass spectrometric analysis of the S. cerevisiae proteome.” Nature Methods 5, 913-914 (2008). * Authors contributing equally

  41. B. Bodenmiller, D. Campbell, B. Gerrits, H. Lam, M. Jovanovic, P. Picotti, R. Schlapbach, and R. Aebersold. “PhosphoPep – a database of protein phosphorylation sites for systems level research in model organisms.” Nature Biotechnology 26, 1339-1340 (2008).

  42. E. W. Deutsch, H. Lam, and R. Aebersold. “PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows.” EMBO Reports 9, 429-434 (2008).

  43. E. W. Deutsch, H. Lam, and R. Aebersold. “Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics.” Physiological Genomics 33, 18-25 (2008).

  44. B. Bodenmiller, J. Malmstrom, B. Gerrits, D. Campbell, H. Lam, A. Schmidt, O. Rinner, L. N. Mueller, P. T. Shannon, C. Panse, H. Lee, and R. Aebersold. “PhosphoPep – A phosphoproteome resource for systems biology research in D. melanogaster Kc167 cells.” Molecular Systems Biology 3, 139 (2007).

  45. H. Lam, E. W. Deutsch, J. S. Eddes, J. K. Eng, N. King, S. E. Stein, and R. Aebersold. “Development and validation of a spectral library searching method for peptide identification from tandem mass spectrometry.” Proteomics 7, 655-667 (2007).

  46. P. G. Mazzola, H. Lam, M. Kavoosi, C. A. Haynes, A. Pessoa Jr., T. C. V. Penna, D. I. C. Wang, and D. Blankschtein. “Affinity-tagged green fluorescent protein (GFP) extraction from E. coli cell lysate using a two-phase aqueous micellar system.” Biotechnology and Bioengineering 93, 998-1004 (2006).

  47. H. Lam, M. Kavoosi, C. A. Haynes, D. I. C. Wang, and D. Blankschtein. “Affinity-enhanced protein partitioning in decyl beta-D-glucopyranoside two-phase aqueous micellar systems.” Biotechnology and Bioengineering 89, 381-392 (2005).

  48. C. O. Rangel-Yagui, H. Lam, D. T. Kamei, D. I. C. Wang, A. Pessoa Jr., and D. Blankschtein. “Glucose 6-phosphate dehydrogenase partitioning in two-phase aqueous mixed (nonionic/cationic) micellar systems.” Biotechnology and Bioengineering 82, 445-456 (2003).

Book Chapters

  1. H. Lam, R. Aebersold. “Using spectral libraries for peptide identification from tandem mass spectrometry (MS/MS) data.” Proteome Bioinformatics, Current Protocols in Protein Science 25, 25.5.1-25.5.9, Wiley (2010).

  2. H. Lam, R. Aebersold. “Spectral library searching for peptide identification via tandem MS.” Proteome Bioinformatics, ed. S. J. Hubbard. and A. R. Jones , Methods in Molecular Biology Series 604, 95-103, Humana Press (2010).

Invited Lectures

  1. H. Lam. “Discovery of new targets in antibiotic response and resistance in bacteria by proteomics.” National Conference on the Appropriate Use of Antibiotics, Shanghai, China (2014).

  2. H. Lam. “Computational methods for high-throughput PTM identifications by shotgun proteomics,” Gordon Research Conference on Post-translational Modification Networks, Hong Kong (2013).

  3. H. Lam. “Identifying sources of tick blood meals using unidentified tandem mass spectral libraries.” Hong Kong Society of Mass Spectrometry Annual Meeting, Hong Kong (2013).

  4. H. Lam. “The current status of proteomics technologies and the Human Proteome Project.” Medical Engineering Programme, Faculty of Engineering, University of Hong Kong, Hong Kong (2013).

  5. H. Lam. “Collective intelligence: the role of spectral libraries in targeted proteomics.” Leiden University Medical Center, Leiden, Netherlands (2013).

  6. H. Lam. “The transition from discovery to hypothesis-driven Science: The role of spectral libraries in proteomics.” 2nd China Workshop on Computational Proteomics, Institute of Computing Technology, Chinese Academy of Science, Beijing, China (2012).

  7. H. Lam. “The transition from discovery to hypothesis-driven Science: The role of spectral libraries in proteomics.” Department of Pharmacy, University of Groningen, Groningen, Netherlands (2011).

  8. H. Lam. “Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis.” Research in Computational Molecular Biology (RECOMB) Satellite Conference on Computational Proteomics, San Diego, CA, USA (2011).

  9. H. Lam. “Collective intelligence: the role of spectral libraries in targeted proteomics.” Center for Algorithmic and Systems Biology (CASB) Computational Proteomics Meeting, San Diego, CA, USA (2011).

  10. H. Lam. “Building and using MS/MS spectral libraries for peptide identifications in proteomics.” Association of Biomolecular Resource Facilities (ABRF) Annual Meeting, San Antonio, TX, USA (2011).

  11. H. Lam. “The transition from discovery to hypothesis-driven science: The role of spectral libraries in proteomics.” Croucher Advanced Study Institute on Functional Phosphoproteomics and Molecular Systems Biology, Hong Kong, China (2011).

  12. H. Lam. “Building and using MS/MS spectral libraries of peptides for targeted discovery in proteomics.” Institute of Molecular and Cell Biology (IMCB) Workshop: An introduction to computational proteomics, Singapore (2009).

  13. H. Lam. “Spectrum library building and searching.” National Cancer Institute/National Institute of Standards and Technology - Strategies for Improving Reliability Protein/Peptide Identification Workshop, Gaithersburg, MD (2007).

  14. H. Lam. “PeptideAtlas and data management in proteomics.” International Cancer Biomarker Consortium Bioinformatics Workshop, Seoul, Korea (2007).

  15. H. Lam. “Data analysis in proteomics: current status and remaining challenges.” National Heart, Lung and Blood Institute Proteomics Initiative Investigators Meeting, Chevy Chase, MD (2007).

Conference Proceedings/Presentations

  1. P. Pai, Y. Hu, H. Lam. “Site-specific N-linked glycoproteomics analysis by nano-LC tandem mass spectrometry and spectral library searching.” 62nd Annual Conference of the American Society for Mass Spectrometry (ASMS), Baltimore, MD, USA (2014).

  2. Y. Hu, P. Pai, H. Lam. “A new N-linked glycopeptides identification tool for large-scale glycoproteomics analysis by spectral library searching.” 62nd Annual Conference of the American Society for Mass Spectrometry (ASMS), Baltimore, MD, USA (2014).

  3. X. Liu, P. Pai, Y. Hu, D. Chen, H. Lam. “Label-free quantitative proteomics study of the synergistic effect of oxacillin and a novel erythromycin derivative against methicillin-resistant Staphylococcus aureus.” 62nd Annual Conference of the American Society for Mass Spectrometry (ASMS), Baltimore, MD, USA (2014).

  4. W. Shao, M. Zhang, S. C. K. Lau, H. Lam. “A shotgun proteomics-bsaed method to differentiate E. coli strains for microbial source tracking.” 62nd Annual Conference of the American Society for Mass Spectrometry (ASMS), Baltimore, MD, USA (2014).

  5. P. H. Chan, Y. Zhu, K. W. K. Tsim, H. Lam. “Quality control of cooking oils by GC-MS profiling and spectral fingerprinting.” 62nd Annual Conference of the American Society for Mass Spectrometry (ASMS), Baltimore, MD, USA (2014).

  6. W. Shao, M. Zhang, S. C. K. Lau, H. Lam. “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) General Meeting, Boston, MA, USA (2014).

  7. P. Pai, Y. Hu, H. Lam. “Site-specific N-linked glycosylation analysis by nano-LC tandem mass spectrometry coupled with a spectral library searching approach.” Human Proteome Organization (HUPO) 12th Annual World Congress, Yokohama, Japan (2013).

  8. W. Shao, H. Lam. “Utilizing unidentified tandem mass spectral libraries for biological sample fingerprinting.” 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Berlin, Germany (2013).

  9. R. Chalkley, N. Bandeira, M. Chambers, J. Cottrell, E. Deutsch, E. Kapp, H. Lam, T. Neubert, R. Sun, O. Vitek, S. Weintraub. “iPRG-2013: Proteome Informatics Research Group Study: Using RNA-Seq data to refine proteomic data analysis.” 61st Annual Conference of the American Society for Mass Spectrometry (ASMS), Minneapolis, MN, USA (2013).

  10. J. Wang, H. Lam. “Graph-based time alignment algorithms for LC-MS datasets with large retention-time drifts.” 61st Annual Conference of the American Society for Mass Spectrometry (ASMS), Minneapolis, MN, USA (2013).

  11. L. Lu, J. Wang p, Y. Xu, H. Lam, P. Y. Qian. “A chemical fingerprint database of marine bacteria based on high-resolution LC-MS.” 61st Annual Conference of the American Society for Mass Spectrometry (ASMS), Minneapolis, MN, USA (2013).

  12. X. Liu, Y. Hu, P. Pai, D. Chen, H. Lam. “Oxacillin resistance study on methicillin resistant and susceptible Staphylococcus aureus by label-free quantitative proteomics.” 61st Annual Conference of the American Society for Mass Spectrometry (ASMS), Minneapolis, MN, USA (2013).

  13. K. Zhu, W. Shao, Y. Hu, H. Lam. “Optimization of MSMS spectral library searching for high mass accuracy spectra of peptides.” 61st Annual Conference of the American Society for Mass Spectrometry (ASMS)/, Minneapolis, MN, USA (2013).

  14. R. Chalkley, N. Bandeira, M. Chambers, J. Cottrell, E. Deutsch, E. Kapp, H. Lam, T. Neubert, R. Sun, O. Vitek, S. Weintraub. “iPRG-2013 Proteome Informatics Research Group study: Using RNA-seq data to refine proteomic data analysis.” 61st Annual Conference of the American Society for Mass Spectrometry (ASMS), Minneapolis, MN, USA (2013).

  15. Y. Hu, H. Lam. “Expanding spectral libraries of phosphorylated peptides: Progress in coverage and accuracy.” Human Proteome Organization (HUPO) 11th Annual World Congress, Boston, MA, USA (2012).

  16. D. Shteynberg, L. Mendoza, J. Slagel, H. Lam, A. Nesvizhskii, R. Moritz. “PTMProphet: TPP software for validation of modified site locations on post-translationally modified peptides.” 60th Annual Conference of the American Society for Mass Spectrometry (ASMS), Vancouver, BC, Canada (2012).

  17. K. H. Wu, A. C. S. Chung, H. Lam. “Multi-resolution LC-MS images alignment using dynamic time warping and Kullback-Leibler distance.” IEEE International Conference on Image Processing, Orlando, FL, USA (2012).

  18. W. Shao, H. Lam. “Development and validation of an unidentified spectral library searching method for biological sample fingerprinting.” Research in Computational Molecular Biology (RECOMB) Satellite Conference on Computational Proteomics, San Diego, CA, USA (2012).

  19. W. Shao, H. Lam. “Building unidentified tandem mass spectral libraries for biological sample fingerprinting.” Human Proteome Organization (HUPO) 10th Annual World Congress, Geneva, Switzerland (2011).

  20. D. Shteynberg, E. Deustch, C. Chu, U. Kusebauch, J. Stevens, K. Swearingen, Z. Sun, X. Zhang, H. Lam, R. Mortiz. “RTCatalog: TPP-integrated open-source software tool for cataloging of sequence-specific retentions of peptides on liquid chromatography systems.” Human Proteome Organization (HUPO) 10th Annual World Congress, Geneva, Switzerland (2011).

  21. P. H. Chan, K. Tsim, H. Lam. “1H-NMR metabonomics analysis of Danggui Buxue Tang effects in HEK293T kidney cell lines.” 7th International Conference of the Metabolomics Society, Cairns, Australia (2011).

  22. P. H. Chan, K. Tsim, H. Lam. “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).

  23. Y. Hu, H. Lam. “Identification of peptides with single amino acid polymorphisms by using semi-empirical MSMS spectral library.” China Human Proteome Organization (CNHUPO) 7th Annual Congress/, Hangzhou, China (2011).

  24. W. Shao, H. Lam. “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).

  25. L. Martens, M. Askenazi, N. Bandeira, R. Chalkley, K. Clauser, E. Deutsch, H. Lam, W. Mcdonald, T. Neubert, P. Rudnick. “iPRG 2011: A study on the identification of electron transfer dissociation (ETD) mass spectra.” Annual Conference of the American Society of Mass Spectrometry, Denver, CO, USA (2011).

  26. A. Schmidt, M. Beck, J. Malmstroem, M. Claassen, H. Lam, D. Campbell, R. Aebersold. “Absolute quantification of microbial proteomes at different cellular states by directed mass spectrometry: Application to the human pathogen Leptospira interrogans.” Annual Conference of the American Society of Mass Spectrometry, Denver, CO, USA (2011).

  27. D. Shteynberg, E. Deutsch, H. Lam, D. Fermin, J. Eng, Z. Sun, N. Tasman, L. Mendoza, R. Moritz, R. Aebersold, A. Nesvizhskii. “iProphet: Improved statistical validation of peptide and protein identifications in shotgun proteomics.” Annual Conference of the American Society of Mass Spectrometry, Denver, CO, USA (2011).

  28. L. Mendoza, D. Shteynberg, J. Slagel, N. Tasman, B. Pratt, H. Lam, M. Hoopmann, J. Eng, V. Sharma, A. Nesvizhskii, A. Keller, E. Deutsch, R. Aebersold, R. Moritz. “New functionality for the Trans-Proteomic Pipeline: tools for analysis of proteomics data.” Annual Conference of the American Society of Mass Spectrometry, Denver, CO, USA (2011).

  29. D. Shteynberg, E. Deutsch, C. Chu, U. Kusebauch, J. Stevens, Z. Sun, K. Swearingen, H. Lam, R. Moritz. “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, Denver, CO, USA (2011).

  30. Y. Hu, Y. Li, H. Lam. “A semi-empirical approach to predict unobserved peptide MS/MS spectra from spectral libraries.” Human Proteome Organization (HUPO) 9th Annual World Congress, Sydney, Australia (2010). [“Proteomics Idol” Finalist (Best Ten Posters)]

  31. T. Srikumar, S. Jeram, X. Zhang, H. Eisenhauer, R. Rogers, P. Pedrioli, M. Matunis, H. Lam, B. Raught. “Improved methodologies for the identification of ubiquitin and ubiquitin-like protein (Ubl) conjugation sites identify novel Ubl chain linkages.” Annual Conference of the American Society of Mass Spectrometry, Salt Lake City, UT, USA (2010).

  32. L. Mendoza, D. Shteynberg, J. Slagel, C. Holstein, N. Tasman, B. Pratt, H. Lam, J. Eng, A. Nesvizhskii, D. Martin, E. Deutsch, R. Moritz, R. Aebersold. “New functionality for the Trans-Proteomic Pipeline: tools for analysis of proteomics data.” US Human Proteome Organization (USHUPO) 6th Annual Conference, Denver, CO, USA (2010).

  33. P. H. Chan, R. C. Y. Choi, G. K. L. Chan, K. W. K. Tsim, H. Lam. “Quality control of ginseng by 1H NMR metabolic profiling.” International Conference on Resource Development of Chinese Medicines from Northwestern China, Hong Kong, China (2009).

  34. W. Shao, X. Zhang, H. Lam. “A Bayesian approach to distinguish signal and noise peaks in peptide tandem mass spectra.” Human Proteome Organization 6th Annual Conference, Toronto, Canada (2009).

  35. L. Mendoza, D. Shteynberg, N. Tasman, B. Pratt, H. Lam, J. Eng, A. Nesvizhskii, E. Deutsch, R. Aebersold. “New functionality for the Trans-Proteomic Pipeline: tools for the analysis of proteomics data.” Human Proteome Organization 6th Annual Conference, Toronto, Canada (2009).

  36. T. Ferrah, E. Deutsch, N. Zhang, D. Shteynberg, H. Lam, D. Campbell, N. Tasman, Z. Sun, L. Mendoza, G. S. Omenn, R. Aebersold. “A human plasma proteome in the PeptideAtlas with estimated protein concentrations.” Human Proteome Organization 6th Annual Conference, Toronto, Canada (2009).

  37. T. Srikumar, S. Jeram, P. Pedrioli, H. Lam, B. Raught. “Identification of UbUbl chains in an integrated mass spectrometrySpectraSTSUMmOn-based work-flow.” Human Proteome Organization (HUPO) 8th Annual Conference/, Toronto, Canada (2009).

  38. T. Srikumar, S. Jeram, P. Pedrioli, H. Lam, B. Raught. “Identification of UbUbl chains using an integrated mass spectrometrySpectraSTSUMmOn-based work-flow.” International Mass Spectrometry Conference/, Bremen, Germany (2009).

  39. X. Zhang, W. Shao, H. Lam. “A systematic investigation on the improvement in sensitivity of spectral library searching over sequence database searching in proteomics.” American Society of Mass Spectrometry Annual Conference, Philadelphia, PA, USA (2009).

  40. T. Ferrah, E. Deustch, D. Shteynberg, D. Campbell, H. Lam, Z. Sun, G. Omenn, R. Aebersold. “A high quality human plasma proteome available in the PeptideAtlas.” Annual Conference of the American Society of Mass Spectrometry, Philadelphia, PA, USA (2009).

  41. L. Mendoza, D. Shteynberg, N. Tasman, B. Pratt, J. Eng, H. Lam, A. Nesvizhskii, E. Deutsch, R. Aebersold. “New functionality for the Trans-Proteomic Pipeline: tools for the analysis of proteomics data.” US Human Proteome Organization 5th Annual Conference, San Diego, CA, USA (2009).

  42. D. Campbell, E. Deutsch, H. Lam, P. Picotti, R. Aebersold. “Improved support for targeted proteomics workflows in PeptideAtlas.” US Human Proteome Organization 5th Annual Conference, San Diego, CA, USA (2009).

  43. L. Mendoza, J. Tasman, D. Shteynberg, J. Eddes, N. Zhang, C. Wong, B. S. Pratt, H. Lam, J. Eng, E. Deutsch, and R. Aebersold. “New developments for open-source shotgun proteomics analysis with the Trans-Proteomic Pipeline.” Human Proteome Organization 7th World Congress, Amsterdam, the Netherlands (2008).

  44. D. Shteynberg, R. Aebersold, E. Deustch, H. Lam, L. Mendoza, J. Tasman, and A. Nesvizhskii. “iProphet: Improved validation of peptide and protein IDs in the Trans-Proteomic Pipeline.” Human Proteome Organization 7th World Congress, Amsterdam, the Netherlands (2008).

  45. L. Mendoza, N. Tasman, D. Shteynberg, J. Eddes, N. Zhang, N. King, C. Wong, B. Pratt, P. Pedrioli, H. Lam, E. Deutsch, J. Eng, X. Li, A. Nesvizhskii, A. Keller, and R. Aebersold. “New developments for open-source shotgun proteomics analysis with the Trans-Proteomic Pipeline.” Human Proteome Organization 7th World Congress, Amsterdam, the Netherlands (2008).

  46. N. Zhang, E. Deutsch, H. Lam, H. Mirzaei, P. Picotti, A. Pratap, D. Shteynberg, L. Mendoza, D. Campbell, J. Watts, and R. Aebersold. “Absolute protein quantification estimated by spectral counting using large datasets in PeptideAtlas.” Annual Conference of the American Society of Mass Spectrometry, Denver, CO, USA (2008).

  47. D. Campbell, E. Deutsch, H. Lam, H. Mirzaei, P. Picotti, J. Ranish, N. Zhang, and R. Aebersold. “The PeptideAtlas as a tool for targeted proteomics.” Annual Conference of the American Society of Mass Spectrometry, Denver, CO, USA (2008).

  48. J. Tasman, L. Mendoza, D. Shteynberg, J. Eddes, N. Zhang, C. Wong, B. S. Pratt, H. Lam, J. Eng, E. Deutsch, and R. Aebersold. “New development for open-source shotgun proteomics analysis with the Trans-Proteomic Pipeline.” Annual Conference of the American Society of Mass Spectrometry, Denver, CO, USA (2008).

  49. D. Shteynberg, A. Nesvizhskii, E. Deutsch, H. Lam, and R. Aebersold. “iProphet: A new tool for combining PeptideProphet results from multiple search engines improves spectrum validation.” Annual Conference of the American Society of Mass Spectrometry, Denver, CO, USA (2008).

  50. H. Lam, E. Deutsch, D. Shteynberg, N. Zhang, S. Stein, and R. Aebersold. “Encoding the observed human plasma proteome in spectral libraries.” Human Proteome Organization 6th World Congress, Seoul, Korea (2007).

  51. H. Lam, E. Deutsch, J. Eddes, and R. Aebersold. “Estimating false discovery rates in spectral searching using decoy spectral libraries.” Human Proteome Organization 6th World Congress, Seoul, Korea (2007).

  52. H. Lam, E. Deutsch, J. Eddes, J. Eng, N. King, S. Stein and R. Aebersold. “Development of a spectral library building tool and re-analysis of Human Plasma PeptideAtlas datasets using spectral searching.” US Human Proteome Organization 3rd Annual Conference, Seattle, WA (2007).

  53. H. Lam, E. Deutsch, J. Eddes, J. Eng, N. King, S. Stein and R. Aebersold. “Development and validation of a spectral library searching method for human peptide identification from tandem mass spectrometry.” Human Proteome Organization 5th Annual World Congress, Long Beach, CA (2006).

  54. H. Lam, E. Deutsch, J. Eddes, J. Eng, N. King, S. Yang, J. Roth, L. Kilpatrick, P. Neta, S. Stein and R. Aebersold. “SpectraST: An open-source MSMS spectra-matching search tool for targeted proteomics.” Annual Conference of the American Society of Mass Spectrometry/, Seattle, WA (2006).

  55. N. King, E. Deutsch, J. Eng, J. Ranish, B. Raught, J. Eddes, A. Nesvizhskii, P. Mallick, D. Martin, M. Flory, H. Lee, H. Lam and R. Aebersold. “Annotation of the yeast Proteome with PeptideAtlas.” Annual Conference of the American Society of Mass Spectrometry, Seattle, WA (2006).

  56. E. Deutsch, J. Eddes, J. Eng, N. King , H. Lam, D. Campbell, S. Loevenich, P. Mallick, D. Martin, L. Mendoza, A. Nesvizhiskii, J. Ranish, B. Raught, D. Shteynberg, J. Tasman, N. Zhang, O. Vitek and R. Aebersold. “The PeptideAtlas Project.” International Symposium of the Institute for Systems Biology, Seattle, WA (2006).

  57. H. Lam, M. Kavoosi, C. A. Haynes, D. I. C. Wang and D. Blankschtein. “Affinity-enhanced protein partitioning in decyl beta-D-glucopyranoside two-phase aqueous micellar systems.” International Biopartitioning and Purification Conference, Amsterdam, the Netherlands (2005).

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