GS5002 Academic Professional Skills and Techniques:
International Journal Club on MS-based Proteomics
Instructor: Professor Wong Limsoon / 2017/2018 Semester 2

• Class will be held in Meeting Room 1 (COM1, level 3)
• Time will be Thursdays 2-5pm on 18 and 25 Jan, 1, 8, 15, and 22 Feb 2018

Reading List

1. General MS-based proteomics
   • Steen and Mann, "The ABC’s (and XYZ’s) of peptide sequencing", Nature Reviews, 5:699--711, 2008
   • Cottrell, "Protein identification using MS/MS data", Journal of Proteomics, 74:1842-1851, 2011

2. SWATH proteomics
   • Guo et al., "Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps", Nature Medicine, 21:407-413, 2015

3. Peptide-identification basics
   • Sung, "Peptide sequencing", Algorithms in Bioinformatics: A Practical Introduction, chapter 12, 2010

4. Graph-based de novo peptide-identification approaches
   • Dancik et al., "De novo peptide sequencing via tandem mass spectrometry", Journal of Computational Biology, 6:327-342, 1999
   • Frank and Pevzner, "PepNovo: De novo peptide sequencing via probabilistic network modeling", Analytical Chemistry, 77:964-973, 2005
   • Frank et al., "De novo peptide sequencing and identification with precision mass spectrometry", Eletrophoresis, 6:114-123, 2007

5. Non-graph-based peptide-identification approaches
   • Ma et al., "PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry", Rapid Communications in Mass Spectrometry, 17:2337-2342, 2003

6. DB-searching peptide-identification approaches
   • Eng et al., "An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database", J Am Soc Mass Spectrom, 5:976-989, 1994
   • Perkins et al., "Probability-based protein identification by searching sequence databases using mass spectrometry data", Electrophoresis, 20:3551-3567, 1999

7. Protein quantitation approaches
   • Yergey et al., "Quantifying proteins by mass spectrometry", LCGC North America, 32:726-735, 2014
   • Zhang et al., "Protein quantitation using mass spectrometry", Methods in Molecular Biology, 673:211-222, 2010
   • Liebler and Zimmerman, "Targeted quantitation of proteins by mass spectrometry", Biochemistry, 52:3797-3806, 2013

8. Coverage and consistency issues
   • Webb-Robertson et al., "Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics", Journal of Proteome Research, 14:1993-2001, 2015
   • Langley and Mayr, "Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics", Journal of Proteomics, 129:83-92, 2015

9. Coverage-improvement approaches
   • Goh et al., "Comparative network-based recovery analysis and proteomic profiling of neurological changes in valporic acid-treated mice", Journal of Proteome Research, 12:2116-2127, 2013
   • Goh and Wong, "Recovering missing proteins based on biological complexes", manuscript draft, September 2016

10. Consistency-improvement approaches
    • Goh et al., "Quantitative proteomics signature profiling based on network contextualization", Biology Direct, 10:71, 2015
    • Goh and Wong, "Advancing clinical proteomics via analysis based on biological complexes: A tale of five paradigms", Journal of Proteome Research, 15:3167-3179, 2016

11. Impact of batch effects
    • Leek et al., "Tackling the widespread and critical impact of batch effects in high-throughput data", Nature Reviews Genetics, 11:733-739, 2010
    • Luo et al., "A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data", The Pharmacogenomics Journal, 10:278-291, 2010

12. Batch-effect resistant approaches
    • Belorkar and Wong, "GFS: Fuzzy preprocessing for effective gene expression analysis", BMC Bioinformatics, 17:1327, 2016
    • Goh and Wong, "Protein complex-based analysis is resistant to the obfuscating consequences of batch effects---a case study in clinical proteomics", BMC Genomics, in press

Contact: Wong Limsoon / Last updated 12/7/2018.