Citing the TPP

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Revision as of 02:35, 13 December 2023; view current revision
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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.

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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