Protein identification and peptide expression resolver: Harmonizing protein identification with protein expression data

Journal of Proteome Research

Volumn 7, Issue 1, 2008, Pages 234-244

  Kearney, Paul ^a   Butler, Heather ^a   Eng, Kevin ^a   Hugo, Patrice ^a  

^a Caprion Pharmaceuticals   (Canada)

Author keywords

Biomarkers; Expression; Fingerprinting; Protein identification; Proteomics

Indexed keywords

BIOLOGICAL MARKER; PEPTIDE; PROTEIN;

ARTICLE; CLINICAL ARTICLE; CONFIDENCE INTERVAL; CONTROLLED STUDY; DIFFERENTIAL DISPLAY; FEMALE; GENE EXPRESSION PROFILING; HUMAN; HYPOTHESIS; MALE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN IDENTIFICATION AND PEPTIDE EXPRESSION RESOLVER; PROTEOMICS; SAMPLE;

BIOLOGICAL MARKERS; GENE EXPRESSION PROFILING; MASS SPECTROMETRY; PEPTIDE FRAGMENTS; PROTEINS; PROTEOMICS; SOFTWARE;

EID: 38649135071     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr0705439     Document Type: Article

References (27)

1. Roy, S. M.; Anderle, M.; Lim, H.; Becker, C. H. Differential expression profiling of serum proteins and metabolites for biomarker discovery. Int. J. Mass Spectrom. 2004, 238, 163-171.
2. Wiener, M. C.; Sachs, J. R.; Deyanova, E. G.; Yates, N. A. Differential mass spectrometry: A label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal. Chem. 2004, 76, 6085-6096.
3. Silva, J. C.; Denny, R.; Dorschel, C. A.; Gorenstein, M. Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem. 2005, 77 (7), 2187-2200.
4. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
5. Lamontagne, J.; Butler, H.; Chaves-Olarte, E.; Hunter, J. Extensive cell envelope modulation is associated with virulence in Brucella abortus. J. Proteome Res. 2007, 6 (4), 1519-1529.
6. Bellew, M.; Coram, M.; Fitzgibbon, M.; Igra, M. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 2006, 22 (15), 1902-9, 2006.
7. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J. Proteome Res. 2003, 2, 43-50.
8. Benjamini, Y.; Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Royal Stat. Soc., Ser. B 1995, 57, 289-300.
9. Weatherly, D. B.; Astwood, J. A., III; Minning, T.A.; Cavola, C. A heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results. Mol. Cell. Proteomics 2005, 4 (6), 762-772.
10. Anderson, N. L.; Polanski, M.; Pieper, R.; Gatlin, T., et al. The human plasma proteome: A non-redundant list developed by combination of four separate sources. Mol. Cell. Proteomics 2004, 3, 311-326.
11. Eng, J. K.; McCormack, A. L.; Yates, J. R., III. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. JASMS 1994, 5 (11), 976-989.
12. Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Probability- based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20 (18), 3551-3567.
13. Ma, B.; Zhang, K.; Hendrie, C.; Liang, C. PEAKS: Powerful software for peptide de novo sequencing by MS/MS. Rapid Commun. Mass Spectrom. 2003, 17 (20), 2337-2342.
14. Lekpor, K.; Benoit, M.-J.; Butler, H.; Schirm, M. An evaluation of multidimensional fingerprinting in the context of clinical proteomics. Proteomics - Clin. Appl. 2007, 1 (5), 457-466.
15. Pappin, D. J.; Hojrup, P.; Bleasby, A. J. Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 1993, 3 (6), 327-32.
16. Conrads, T. P.; Anderson, G. A.; Veenstra, T. D.; Pasa-Tolic, L.; Smith, R. D. Utility of accurate mass tags for proteome-wide protein identification. Anal. Chem. 2000, 72, 3349-3354.
17. Palmblad, M.; Ramstrom, M.; Markides, K. E.; Hakansson, P.; Bergquist, J. Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry. Anal. Chem. 2002, 74 (21), 5826-5830.
18. Adkins, J. N.; Monroe, M. E.; Auberry, K. J.; Yufeng, S. A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy. Proteomics 2005, 5, 3454-3466.
19. Smith, R. D.; Anderson, G. A.; Lipton, M. S.; Pasa-Tolic, L.; Shen, Y. An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2002, 2, 513-523.
20. Gay, S.; Binz, P. A.; Hochstrasser, D. F.; Appel, R. D. Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra. Proteomics 2002, 2 (10), 1374-1391.
21. Carr, S.; Aebersold, R.; Baldwin, M.; Burlingame, A. The need for guidelines in publication of peptide and protein identification data. Mol. Cell. Proteomics 2004, 3 (6), 531-533.
22. Lamerz, J.; Selle, H.; Scapozza, L.; Crameri, R. Correlation-associated peptide networks of human cerebrospinal fluid. Proteomics 2005, 511, 2789-2798.
23. Xie, Y.; Pan, W.; Khodursky, A. B. A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data. Bioinformatics 2005, 21 (23), 4280-4288.
24. Kersey, P. J.; Duarte, J.; Williams, A.; Karavidopoulou, Y. The International Protein Index: An integrated database for proteomics experiments. Proteomics 2004, 4 (7), 1985-1988.
25. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J. Proteome Res. 2003, 2, 43-50.
26. Troyanskaya, O.; Cantor, M.; Sherlock, G.; Brown, P. Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17 (6), 520-525.
27. Cox, M. F.; Cox, M. A. A. Multidimensional Scaling, Chapman and Hall: New York, 2001.