Citing the TPP

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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. 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 ==+== TPP Overall Latest Paper ==
-Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.+Please reference the following publication when using TPP in your work:
-Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL.+''Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite''
-Proteomics Clin Appl. 2015 Aug;9(7-8):745-54. doi: 10.1002/prca.201400164. Epub 2015 Apr 2. Review.+Eric W. Deutsch, Luis Mendoza, David D. Shteynberg, Michael R. Hoopmann, Zhi Sun, Jimmy K. Eng, and Robert L. Moritz
-PMID:+Journal of Proteome Research 2023 22 (2), 615-624
- 25631240 +
 +DOI: 10.1021/acs.jproteome.2c00624
-== reSPECT ==+PMID: [https://pubmed.ncbi.nlm.nih.gov/36648445/ 36648445]
-reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.+ 
 + 
 +== 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: [https://www.ncbi.nlm.nih.gov/pubmed/16729052 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: [https://www.ncbi.nlm.nih.gov/pubmed/21876204 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: [https://www.ncbi.nlm.nih.gov/pubmed/23720762 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: [https://www.ncbi.nlm.nih.gov/pubmed/12403597 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: [https://www.ncbi.nlm.nih.gov/pubmed/14632076 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: [https://www.ncbi.nlm.nih.gov/pubmed/25812159 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: [https://www.ncbi.nlm.nih.gov/pubmed/29400476 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: [https://www.ncbi.nlm.nih.gov/pubmed/14640741 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: [https://www.ncbi.nlm.nih.gov/pubmed/16791211 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. Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL.
Line 22: Line 123:
J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47. doi: 10.1007/s13361-015-1252-5. Epub 2015 Sep 29. J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47. doi: 10.1007/s13361-015-1252-5. Epub 2015 Sep 29.
-PMID:+PMID: [https://www.ncbi.nlm.nih.gov/pubmed/26419769 26419769]
- 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: [https://www.ncbi.nlm.nih.gov/pubmed/27577934 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: [https://www.ncbi.nlm.nih.gov/pubmed/18212004 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: [https://www.ncbi.nlm.nih.gov/pubmed/17295354 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: [https://www.ncbi.nlm.nih.gov/pubmed/18806791 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: [https://www.ncbi.nlm.nih.gov/pubmed/19916561 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: [https://www.ncbi.nlm.nih.gov/pubmed/22956731 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: [https://www.ncbi.nlm.nih.gov/pubmed/16729052 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: [https://www.ncbi.nlm.nih.gov/pubmed/27469004 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: [https://www.ncbi.nlm.nih.gov/pubmed/15529173 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: [https://www.ncbi.nlm.nih.gov/pubmed/25418363 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: [https://www.ncbi.nlm.nih.gov/pubmed/23216909 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: [https://www.ncbi.nlm.nih.gov/pubmed/20082347 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: [https://www.ncbi.nlm.nih.gov/pubmed/20101611 20101611]

Current revision

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.

Contents

[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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


[edit]

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

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