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PMID: 20101611 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Review

A guided tour of the Trans-Proteomic Pipeline.

Proteomics ·Vol. 10 ·No. 6 ·2010-03-00 ·Pages 1150-9

Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R

Abstract

The Trans-Proteomic Pipeline (TPP) is a suite of software tools for the analysis of MS/MS data sets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein-level statistical validation, including quantification by stable isotope ratios. We describe here the full workflow of the TPP and the tools therein, along with an example on a sample data set, demonstrating that the setup and use of the tools are straightforward and well supported and do not require specialized informatic resources or knowledge.

MeSH Terms
Computational Biology Databases, Protein Information Storage and Retrieval Isotope Labeling Proteomics/methods Sequence Analysis, Protein Software Tandem Mass Spectrometry
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Deutsch Eric W
Institute for Systems Biology, Seattle, WA, USA. edeutsch@systemsbiology.org
Mendoza Luis
Shteynberg David
Farrah Terry
Lam Henry
Tasman Natalie
Sun Zhi
Nilsson Erik
Pratt Brian
Prazen Bryan
Eng Jimmy K
Martin Daniel B
Nesvizhskii Alexey I
Aebersold Ruedi
References (49)
49 references, click to expand
  1. False discovery rates and related statistical concepts in mass spectrometry-based proteomics.
    J Proteome Res. 2008 Jan;7(1):47-50 PMID: 18067251
  2. YPED: a web-accessible database system for protein expression analysis.
    J Proteome Res. 2007 Oct;6(10):4019-24 PMID: 17867667
  3. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.
    Bioinformatics. 2006 Nov 15;22(22):2830-2 PMID: 16877754
  4. Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments.
    J Proteome Res. 2006 Jan;5(1):112-21 PMID: 16396501
  5. Stable isotope labeling by amino acids in cell culture for quantitative proteomics.
    Methods Mol Biol. 2007;359:37-52 PMID: 17484109
  6. The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.
    Bioinformatics. 2008 Sep 15;24(18):2110-1 PMID: 18635572
  7. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.
    Nat Biotechnol. 2008 Dec;26(12):1367-72 PMID: 19029910
  8. PRIDE: the proteomics identifications database.
    Proteomics. 2005 Aug;5(13):3537-45 PMID: 16041671
  9. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.
    J Proteome Res. 2007 Feb;6(2):654-61 PMID: 17269722
  10. MaRiMba: a software application for spectral library-based MRM transition list assembly.
    J Proteome Res. 2009 Oct;8(10):4396-405 PMID: 19603829
  11. Open mass spectrometry search algorithm.
    J Proteome Res. 2004 Sep-Oct;3(5):958-64 PMID: 15473683
  12. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry.
    Anal Chem. 2003 Dec 1;75(23):6648-57 PMID: 14640741
  13. SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology.
    BMC Bioinformatics. 2006 Jun 06;7:286 PMID: 16756676
  14. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling.
    J Proteome Res. 2008 Jan;7(1):286-92 PMID: 18078310
  15. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.
    Nat Methods. 2007 Mar;4(3):207-14 PMID: 17327847
  16. A uniform proteomics MS/MS analysis platform utilizing open XML file formats.
    Mol Syst Biol. 2005;1:2005.0017 PMID: 16729052
  17. High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics.
    Proteomics. 2004 Jul;4(7):1977-84 PMID: 15221758
  18. Getting started in computational mass spectrometry-based proteomics.
    PLoS Comput Biol. 2009 May;5(5):e1000366 PMID: 19492072
  19. The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation.
    Mol Cell Proteomics. 2003 Jul;2(7):428-42 PMID: 12832459
  20. Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software.
    Nat Methods. 2006 Jul;3(7):533-9 PMID: 16791211
  21. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
    Anal Chem. 2002 Oct 15;74(20):5383-92 PMID: 12403597
  22. MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.
    Mol Cell Proteomics. 2008 Nov;7(11):2270-8 PMID: 18641041
  23. Probability-based protein identification by searching sequence databases using mass spectrometry data.
    Electrophoresis. 1999 Dec;20(18):3551-67 PMID: 10612281
  24. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
    J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89 PMID: 24226387
  25. Mass spectrometry-based proteomics.
    Nature. 2003 Mar 13;422(6928):198-207 PMID: 12634793
  26. Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets.
    Proteomics. 2010 Mar;10(6):1190-5 PMID: 20082347
  27. DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra.
    Bioinformatics. 2008 Apr 1;24(7):1021-3 PMID: 18304935
  28. ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data.
    Proteomics. 2002 Oct;2(10):1406-12 PMID: 12422357
  29. A common open representation of mass spectrometry data and its application to proteomics research.
    Nat Biotechnol. 2004 Nov;22(11):1459-66 PMID: 15529173
  30. Reporting protein identification data: the next generation of guidelines.
    Mol Cell Proteomics. 2006 May;5(5):787-8 PMID: 16670253
  31. Development and validation of a spectral library searching method for peptide identification from MS/MS.
    Proteomics. 2007 Mar;7(5):655-67 PMID: 17295354
  32. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry.
    Nat Biotechnol. 2001 Oct;19(10):946-51 PMID: 11581660
  33. Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics.
    Physiol Genomics. 2008 Mar 14;33(1):18-25 PMID: 18212004
  34. Revised draft guidelines for proteomic data publication.
    Mol Cell Proteomics. 2005 Sep;4(9):1223-5 PMID: 16160100
  35. Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring.
    Mol Cell Proteomics. 2008 Aug;7(8):1489-500 PMID: 18408245
  36. mzML: a single, unifying data format for mass spectrometer output.
    Proteomics. 2008 Jul;8(14):2776-7 PMID: 18655045
  37. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools.
    J Proteome Res. 2008 Jan;7(1):96-103 PMID: 17711323
  38. TOPP--the OpenMS proteomics pipeline.
    Bioinformatics. 2007 Jan 15;23(2):e191-7 PMID: 17237091
  39. TANDEM: matching proteins with tandem mass spectra.
    Bioinformatics. 2004 Jun 12;20(9):1466-7 PMID: 14976030
  40. A statistical model for identifying proteins by tandem mass spectrometry.
    Anal Chem. 2003 Sep 1;75(17):4646-58 PMID: 14632076
  41. A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry.
    Anal Chem. 2004 Jul 1;76(13):3856-60 PMID: 15228367
  42. Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.
    J Proteome Res. 2008 Jan;7(1):254-65 PMID: 18159924
  43. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS.
    Anal Chem. 2003 Apr 15;75(8):1895-904 PMID: 12713048
  44. Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS.
    Drug Discov Today. 2004 Feb 15;9(4):173-81 PMID: 14960397
  45. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra.
    Anal Chem. 2005 Jul 15;77(14):4626-39 PMID: 16013882
  46. ProteoWizard: open source software for rapid proteomics tools development.
    Bioinformatics. 2008 Nov 1;24(21):2534-6 PMID: 18606607
  47. A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies.
    J Exp Bot. 2006;57(7):1501-8 PMID: 16574745
  48. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows.
    EMBO Rep. 2008 May;9(5):429-34 PMID: 18451766
  49. Quantitative mass spectrometry in proteomics: a critical review.
    Anal Bioanal Chem. 2007 Oct;389(4):1017-31 PMID: 17668192
Article Info
Journal
Proteomics
Abbr.
Proteomics
ISSN
1615-9861
DOI
10.1002/pmic.200900375
Email
edeutsch@systemsbiology.org
Published
2010-03-00
Pages
1150-9
Language
English
Region
Germany
NLM ID
101092707
PMCID
PMC3017125
Subset
IM
Grants
NHGRI NIH HHS · R44 HG004537 · United States
NHLBI NIH HHS · N01 HV028179 · United States
NHGRI NIH HHS · R44HG004537 · United States
NHLBI NIH HHS · N01-HV-28179 · United States
NCI NIH HHS · R01 CA126239 · United States
PHS HHS · PM50 GMO76547 · United States
NHLBI NIH HHS · N01HV28179 · United States
NHGRI NIH HHS · R44 HG004537-03 · United States
NIGMS NIH HHS · P50 GM076547-01 · United States
NIGMS NIH HHS · P50 GM076547 · United States
External Links
PubMed source DOI: 10.1002/pmic.200900375 PMC Full Text View journal details
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