Protein quantification by peptide quality control (PQPQ) of shotgun proteomics data

Methods in Molecular Biology

Volumn 1023, Issue , 2013, Pages 149-158

  Forshed, Jenny ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Data curation; Protein quantification; Quantitative accuracy; Quantitative precision; Quantitative shotgun proteomics

Indexed keywords

PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; DATA PROCESSING; MASS SPECTROMETRY; PEPTIDE QUALITY CONTROL; PRIORITY JOURNAL; PROTEOMICS; QUALITY CONTROL;

EID: 84883137067     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4614-7209-4_9     Document Type: Article

References (16)

1. Robinson TJ, Dinan MA, Dewhirst M, Garcia- Blanco MA, Pearson JL (2010) SplicerAV: A tool for mining microarray expression data for changes in RNA processing. BMC Bioinformatics 11(1):108
2. Duncan MW, Aebersold R, Caprioli RM (2010) The pros and cons of peptide-centric proteomics. Nat Biotechnol 28(7):659-664
3. Nesvizhskii A, Aebersold R (2005) Interpretation of shotgun proteomic data - The protein inference problem. Mol Cell Proteomics 4(10):1419-1440
4. Karp NA, Huber W, Sadowski PG, Charles PD, Hester SV, Lilley KS (2010) Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics 9(9):1885-1897
5. Boehm AM, Pütz S, Altenhöfer D, Sickmann A, Falk M (2007) Precise protein quantification based on peptide quantification using iTRAQ. BMC Bioinformatics 8(1):214
6. Lau KW, Jones AR, Swainston N, Siepen JA, Hubbard SJ (2007) Capture and analysis of quantitative proteomic data. Proteomics 7(16):2787-2799
7. Park SK, Venable JD, Xu T, Yates JR (2008) A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods 5:319-322
8. Mueller LN, Brusniak M-Y, Mani DR, Aebersold R (2008) An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res 7(1):51-61
9. Panchaud A, Affolter M, Moreillon P, Kussmann M (2008) Experimental and computational approaches to quantitative proteomics: Status quo and outlook. J Proteomics 71(1):19-33
10. D'Ascenzo M, Choe L, Lee KH (2008) iTRAQPak: An R based analysis and visualization package for 8-plex isobaric protein expression data. Brief Funct Genomic Proteomic 7(2):127-135
11. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b-range mass accuracies and proteome- wide protein quantification. Nat Biotechnol 26(12):1367-1372
12. Forshed J, Johansson HJ, Pernemalm M, Branca RMM, Sandberg A, Lehtio J (2011) Enhanced information output from shotgun proteomics data by protein quantification and peptide quality control (PQPQ). Mol Cell Proteomics 10(10):M111.010264
13. Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B (2007) Quantitative mass spectrometry in proteomics: A critical review. Anal Bioanal Chem 389:1017-1031
14. Song XM, Bandow J, Sherman J, Baker JD, Brown PW, McDowell MT, Molloy MP (2008) iTRAQ experimental design for plasma biomarker discovery. J Proteome Res 7:2952-2958
15. Reiter L, Claassen M, Schrimpf SP, Jovanovic M, Schmidt A, Buhmann JM et al (2009) Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics 8(11):2405-2417
16. Elias JE, Gygi SP (2007) Target-decoy search strategy for increased con fidence in large-scale protein identifications by mass spectrometry. Nat Methods 4(3):207-214