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Tutorial References and Additional Suggested Reading

Protein Identification Strategies

  1. Olsen JV, Ong SE, Mann M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics. 2004 Jun;3(6):608-14. Epub 2004 Mar 19.
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  2. Search Optimization Presentation (.pdf presentation)
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Peptide-Mass Fingerprinting

  1. Henzel, W. J.; Stults, J. T.; Watanabe, C. Proceedings of the Third Symposium of the Protein Society; Seattle, WA, 1989.
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  2. Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C.  Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases.  Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5011-5.
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  3. Mann M, Hojrup P, Roepstorff P. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom. 1993 Jun;22(6):338-45.
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  4. Pappin DJ, Hojrup P, Bleasby AJ. Rapid identification of proteins by peptide-mass fingerprinting.
    Curr Biol. 1993 Jun 1;3(6):327-32.  (first to coin the term "peptide-mass fingerprinting")
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  5. James P, Quadroni M, Carafoli E, Gonnet G. Protein identification by mass profile fingerprinting.
    Biochem Biophys Res Commun. 1993 Aug 31;195(1):58-64.
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  6. Yates JR 3rd, Speicher S, Griffin PR, Hunkapiller T. Peptide mass maps: a highly informative approach to protein identification. Anal Biochem. 1993 Nov 1;214(2):397-408.
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  7. Jensen ON, Podtelejnikov AV, Mann M.  Identification of the components of simple protein mixtures by high-accuracy peptide mass mapping and database searching. Anal Chem. 1997 Dec 1;69(23):4741-50.
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  8. Clauser KR, Baker P, Burlingame AL.Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching.
    Anal Chem. 1999 Jul 15;71(14):2871-82. PMID: 10424174
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  9. Henzel WJ, Watanabe C, Stults JT. Protein identification: the origins of peptide mass fingerprinting.  J Am Soc Mass Spectrom. 2003 Sep;14(9):931-42.
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Peptide Sequence Tag

  1. Mann M, Wilm M., Error-tolerant identification of peptides in sequence databases by peptide sequence tags.  Anal Chem. 1994 Dec 15;66(24):4390-9.
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  2. Mortz E, O'Connor PB, Roepstorff P, Kelleher NL, Wood TD, McLafferty FW, Mann M. Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases. Proc Natl Acad Sci U S A. 1996 Aug 6;93(16):8264-7.PMID: 8710858
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  3. Shevchenko A, Jensen ON, Podtelejnikov AV, Sagliocco F, Wilm M, Vorm O, Mortensen P, Shevchenko A, Boucherie H, Mann M.  Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels.
    Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14440-5. PMID: 8962070
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MS/MS Protein ID

  1. Jimmy K. Eng, Ashley L. McCormack and John R. Yates, III An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database JASMS, Volume 5, Issue 11, November 1994, Pages 976-989

  2. Yates JR 3rd, Eng JK, McCormack AL, Schieltz D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database.
    Anal Chem. 1995 Apr 15;67(8):1426-36. PMID: 7741214 

  3. Yates JR 3rd, Eng JK, McCormack AL. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases.
    Anal Chem. 1995 Sep 15;67(18):3202-10. PMID: 8686885

  4. Lim H, Eng J, Yates JR 3rd, Tollaksen SL, Giometti CS, Holden JF, Adams MW, Reich CI, Olsen GJ, Hays LG. Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry.  J Am Soc Mass Spectrom. 2003 Sep;14(9):957-70. PMID: 12954164

 

Searching With Complex Proteomics Data 

  1. Olsen JV, Mann M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A. 2004 Sep 14;101(37):13417-22. Epub 2004 Sep 03. PMID: 15347803

  2. Colinge J, Masselot A, Cusin I, Mah� E, Niknejad A, Argoud-Puy G, Reffas S, Bederr N, Gleizes A, Rey P-A, Bougueleret L. "High performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics," Proteomics. 2004 Jul;4(7):1977-84.

  3. Colinge J, Masselot A. "Mass spectrometry has married statistics: uncle is functionality, children are selectivity and sensitivity," DDT: TARGETS, Vol. 3, No. 2 (Suppl.), 2004, pp. 50-55.

  4. Colinge J, Magnin J, Masselot A. A systematic statistical analysis of ion trap tandem mass spectra in view of peptide scoring. In: Proceeding of the Workshop on Algorithms in Bioinformatics (WABI), R. Page and G. Benson (Eds), Budapest, September 2003, LNBI 2812, Springer, 25-38, 2003.

  5. Colinge J, Masselot A, Giron M, Dessingy T, Magnin J. "OLAV: towards high-throughput tandem mass spectrometry data identification," Proteomics, Vol. 3, No. 8, August 2003, pp. 1454-1463.

  6. McDonald WH, Yates JR 3rd. Shotgun proteomics: integrating technologies to answer biological questions. Curr Opin Mol Ther. 2003 Jun;5(3):302-9. Review. PMID: 12870441
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  7. Colinge J, Magnin J, Dessingy T, Giron M and Masselot A. Improved peptide charge state assignment. Proteomics, 3:1434-1440, 2003.

  8. Lin D, Tabb DL, Yates JR 3rd. Large-scale protein identification using mass spectrometry.
    Biochim Biophys Acta. 2003 Mar 21;1646(1-2):1-10. Review.PMID: 12637006

  9. Hunter TC, Andon NL, Koller A, Yates JR, Haynes PA. The functional proteomics toolbox: methods and applications. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Dec 25;782(1-2):165-81. Review. No abstract available.PMID: 12458005

  10. McDonald WH, Yates JR 3rd. Shotgun proteomics and biomarker discovery.
    Dis Markers. 2002;18(2):99-105. Review. PMID: 12364816
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Proteomics

  1. Lin D, Tabb DL, Yates JR 3rd. Large-scale protein identification using mass spectrometry.
    Biochim Biophys Acta. 2003 Mar 21;1646(1-2):1-10. Review.PMID: 12637006
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  2. Hunter TC, Andon NL, Koller A, Yates JR, Haynes PA. The functional proteomics toolbox: methods and applications. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Dec 25;782(1-2):165-81. Review. No abstract available.PMID: 12458005
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  3. McDonald WH, Yates JR 3rd. Shotgun proteomics and biomarker discovery.
    Dis Markers. 2002;18(2):99-105. Review. PMID: 12364816
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  4. McDonald WH, Yates JR 3rd. Shotgun proteomics: integrating technologies to answer biological questions. Curr Opin Mol Ther. 2003 Jun;5(3):302-9. Review. PMID: 12870441
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  5. Olsen JV, Mann M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A. 2004 Sep 14;101(37):13417-22. Epub 2004 Sep 03. PMID: 15347803
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  6. Lim H, Eng J, Yates JR 3rd, Tollaksen SL, Giometti CS, Holden JF, Adams MW, Reich CI, Olsen GJ, Hays LG.  Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry.J Am Soc Mass Spectrom. 2003 Sep;14(9):957-70.
    PMID: 12954164
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  7. Yates JR 3rd. Database searching using mass spectrometry data.
    Electrophoresis. 1998 May;19(6):893-900. Review.PMID: 9638935
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  8. Jonscher KR, Yates JR 3rd. Mixture analysis using a quadrupole mass filter/quadrupole ion trap mass spectrometer. Anal Chem. 1996 Feb 15;68(4):659-67. PMID: 8999740

 

De-Novo

  1. Dancik V, Addona TA, Clauser KR, Vath JE, Pevzner PA.  De novo peptide sequencing via tandem mass spectrometry. J Comput Biol. 1999 Fall-Winter;6(3-4):327-42.
    PMID: 10582570
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  2. Shevchenko A, Chernushevic I, Shevchenko A, Wilm M, Mann M."De novo" sequencing of peptides recovered from in-gel digested proteins by nanoelectrospray tandem mass spectrometry. Mol Biotechnol. 2002 Jan;20(1):107-18. PMID: 11876295

  3. High-Throughput de novo Sequencing (PDF at Thermo)

 

 

 

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