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Items: 1 to 20 of 104

1.

Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data.

Liu G, Zhang J, Choi H, Lambert JP, Srikumar T, Larsen B, Nesvizhskii AI, Raught B, Tyers M, Gingras AC.

Curr Protoc Bioinformatics. 2012 Sep;Chapter 8:Unit8.16. doi: 10.1002/0471250953.bi0816s39.

2.

Data Independent Acquisition analysis in ProHits 4.0.

Liu G, Knight JD, Zhang JP, Tsou CC, Wang J, Lambert JP, Larsen B, Tyers M, Raught B, Bandeira N, Nesvizhskii AI, Choi H, Gingras AC.

J Proteomics. 2016 Oct 21;149:64-68. doi: 10.1016/j.jprot.2016.04.042. Epub 2016 Apr 29.

PMID:
27132685
3.

Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT.

Choi H, Liu G, Mellacheruvu D, Tyers M, Gingras AC, Nesvizhskii AI.

Curr Protoc Bioinformatics. 2012 Sep;Chapter 8:Unit8.15. doi: 10.1002/0471250953.bi0815s39.

4.

SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments.

Choi H, Glatter T, Gstaiger M, Nesvizhskii AI.

J Proteome Res. 2012 Apr 6;11(4):2619-24. doi: 10.1021/pr201185r. Epub 2012 Mar 2.

5.

Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.

Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ.

Curr Protoc Bioinformatics. 2015 Mar 9;49:8.19.1-16. doi: 10.1002/0471250953.bi0819s49.

6.

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.

Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI.

Nat Methods. 2013 Aug;10(8):730-6. doi: 10.1038/nmeth.2557. Epub 2013 Jul 7.

7.

Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions.

Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR.

Nat Protoc. 2014 Nov;9(11):2539-54. doi: 10.1038/nprot.2014.164. Epub 2014 Oct 2.

8.

ProHits: integrated software for mass spectrometry-based interaction proteomics.

Liu G, Zhang J, Larsen B, Stark C, Breitkreutz A, Lin ZY, Breitkreutz BJ, Ding Y, Colwill K, Pasculescu A, Pawson T, Wrana JL, Nesvizhskii AI, Raught B, Tyers M, Gingras AC.

Nat Biotechnol. 2010 Oct;28(10):1015-7. doi: 10.1038/nbt1010-1015. No abstract available.

9.

Detection of protein complexes from affinity purification/mass spectrometry data.

Cai B, Wang H, Zheng H, Wang H.

BMC Syst Biol. 2012;6 Suppl 3:S4. doi: 10.1186/1752-0509-6-S3-S4. Epub 2012 Dec 17.

10.

Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions.

Gingras AC, Raught B.

FEBS Lett. 2012 Aug 14;586(17):2723-31. doi: 10.1016/j.febslet.2012.03.065. Epub 2012 Apr 10. Review.

11.

ROCS: a reproducibility index and confidence score for interaction proteomics studies.

Dazard JE, Saha S, Ewing RM.

BMC Bioinformatics. 2012 Jun 8;13:128. doi: 10.1186/1471-2105-13-128.

12.

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis.

Tucker G, Loh PR, Berger B.

BMC Bioinformatics. 2013 Oct 4;14:299. doi: 10.1186/1471-2105-14-299.

13.

Computational detection of protein complexes in AP-MS experiments.

Choi H.

Proteomics. 2012 May;12(10):1663-8. doi: 10.1002/pmic.201100508. Review.

PMID:
22711593
14.

Network inference from AP-MS data: computational challenges and solutions.

Teng B, Zhao C, Liu X, He Z.

Brief Bioinform. 2015 Jul;16(4):658-74. doi: 10.1093/bib/bbu038. Epub 2014 Nov 5. Review.

PMID:
25378435
15.

Identifying novel protein complexes in cancer cells using epitope-tagging of endogenous human genes and affinity-purification mass spectrometry.

Song J, Hao Y, Du Z, Wang Z, Ewing RM.

J Proteome Res. 2012 Dec 7;11(12):5630-41. doi: 10.1021/pr300598t. Epub 2012 Nov 7.

16.

Resolving protein interactions and complexes by affinity purification followed by label-based quantitative mass spectrometry.

Trinkle-Mulcahy L.

Proteomics. 2012 May;12(10):1623-38. doi: 10.1002/pmic.201100438. Review.

PMID:
22610586
17.

Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP-MS).

Keilhauer EC, Hein MY, Mann M.

Mol Cell Proteomics. 2015 Jan;14(1):120-35. doi: 10.1074/mcp.M114.041012. Epub 2014 Nov 2.

18.

CIG-P: Circular Interaction Graph for Proteomics.

Hobbs CK, Leung M, Tsang HH, Ebhardt HA.

BMC Bioinformatics. 2014 Oct 31;15:344. doi: 10.1186/1471-2105-15-344.

19.

Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks.

Saha S, Dazard JE, Xu H, Ewing RM.

J Proteome Res. 2012 Sep 7;11(9):4476-87. doi: 10.1021/pr300227y. Epub 2012 Aug 21.

20.

A novel scoring approach for protein co-purification data reveals high interaction specificity.

Yu X, Ivanic J, Wallqvist A, Reifman J.

PLoS Comput Biol. 2009 Sep;5(9):e1000515. doi: 10.1371/journal.pcbi.1000515. Epub 2009 Sep 25.

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