Citing the TPP
From SPCTools
If you use the TPP or any of its components in your research, please cite us in your publications. Below is a list of citations categorized by topic.
TPP Overall Latest Paper
Please reference the following publication when using TPP in your work:
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite
Eric W. Deutsch, Luis Mendoza, David D. Shteynberg, Michael R. Hoopmann, Zhi Sun, Jimmy K. Eng, and Robert L. Moritz
Journal of Proteome Research 2023 22 (2), 615-624
DOI: 10.1021/acs.jproteome.2c00624
PMID: 36648445
TPP Overall First Paper
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
Keller A, Eng J, Zhang N, Li XJ, Aebersold R.
Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2.
PMID: 16729052
iProphet and Combining Search Results Review
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.
Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29.
PMID: 21876204
Combining results of multiple search engines in proteomics
Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW.
Mol Cell Proteomics. 2013 Sep;12(9):2383-93. doi: 10.1074/mcp.R113.027797. Epub 2013 May 29. Review.
PMID: 23720762
PeptideProphet
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
Keller A, Nesvizhskii AI, Kolker E, Aebersold R.
Anal Chem. 2002 Oct 15;74(20):5383-92.
PMID: 12403597
ProteinProphet
A statistical model for identifying proteins by tandem mass spectrometry
Nesvizhskii AI, Keller A, Kolker E, Aebersold R.
Anal Chem. 2003 Sep 1;75(17):4646-58.
PMID: 14632076
Kojak for Cross-linking analysis
Kojak: efficient analysis of chemically cross-linked protein complexes
Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL.
J Proteome Res. 2015 May 1;14(5):2190-8. doi: 10.1021/pr501321h. Epub 2015 Apr 15.
PMID: 25812159
StPeter Label-free Quantitation
StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline
Hoopmann MR, Winget JM, Mendoza L, Moritz RL.
J Proteome Res. 2018 Mar 2;17(3):1314-1320. doi: 10.1021/acs.jproteome.7b00786. Epub 2018 Feb 14.
PMID: 29400476
ASAPRatio Isotopic Labeling Quantitation (e.g. SILAC, ICAT)
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry
Li XJ, Zhang H, Ranish JA, Aebersold R.
Anal Chem. 2003 Dec 1;75(23):6648-57.
PMID: 14640741
Libra Isobaric Labeling Quantitation (e.g TMT, iTRAQ)
Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software
Pedrioli PG, Raught B, Zhang XD, Rogers R, Aitchison J, Matunis M, Aebersold R.
Nat Methods. 2006 Jul;3(7):533-9.
PMID: 16791211
reSpect
reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra
Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL.
J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47. doi: 10.1007/s13361-015-1252-5. Epub 2015 Sep 29.
PMID: 26419769
THISP Human Sequence Databases
Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics
Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL.
J Proteome Res. 2016 Nov 4;15(11):4091-4100. Epub 2016 Sep 12.
PMID: 27577934
Proteomics Informatics Review
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
Deutsch EW, Lam H, Aebersold R.
Physiol Genomics. 2008 Mar 14;33(1):18-25. doi: 10.1152/physiolgenomics.00298.2007. Epub 2008 Jan 22. Review.
PMID: 18212004
SpectraST - Library Searching
Development and validation of a spectral library searching method for peptide identification from MS/MS
Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R.
Proteomics. 2007 Mar;7(5):655-67.
PMID: 17295354
SpectraST - Library Building
Building consensus spectral libraries for peptide identification in proteomics
Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R.
Nat Methods. 2008 Oct;5(10):873-5. doi: 10.1038/nmeth.1254. Epub 2008 Sep 21.
PMID: 18806791
SpectraST - Artificial Decoys
Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics
Lam H, Deutsch EW, Aebersold R.
J Proteome Res. 2010 Jan;9(1):605-10. doi: 10.1021/pr900947u.
PMID: 19916561
Mass Spectrometry File Formats in General
File formats commonly used in mass spectrometry proteomics
Deutsch EW.
Mol Cell Proteomics. 2012 Dec;11(12):1612-21. doi: 10.1074/mcp.R112.019695. Epub 2012 Sep 6.
PMID: 22956731
pepXML and protXML Initial Paper
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
Keller A, Eng J, Zhang N, Li XJ, Aebersold R.
Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2.
PMID: 16729052
pepXML for Cross-linking Data
An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results
Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL.
J Am Soc Mass Spectrom. 2016 Nov;27(11):1728-1734. Epub 2016 Jul 28.
PMID: 27469004
mzXML
A common open representation of mass spectrometry data and its application to proteomics research
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.
Nat Biotechnol. 2004 Nov;22(11):1459-66.
PMID: 15529173
TPP on Amazon Web Services
Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline
Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL.
Mol Cell Proteomics. 2015 Feb;14(2):399-404. doi: 10.1074/mcp.O114.043380. Epub 2014 Nov 23.
PMID: 25418363
Hydra
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.
BMC Bioinformatics. 2012 Dec 5;13:324. doi: 10.1186/1471-2105-13-324.
PMID: 23216909
ETD analysis
Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets
Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R.
Proteomics. 2010 Mar;10(6):1190-5. doi: 10.1002/pmic.200900567.
PMID: 20082347
Other articles
A guided tour of the Trans-Proteomic Pipeline
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.
Proteomics. 2010 Mar;10(6):1150-9. doi: 10.1002/pmic.200900375. Review.
PMID: 20101611
