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Items: 1 to 20 of 97

1.

RockerBox: analysis and filtering of massive proteomics search results.

van den Toorn HW, Muñoz J, Mohammed S, Raijmakers R, Heck AJ, van Breukelen B.

J Proteome Res. 2011 Mar 4;10(3):1420-4. doi: 10.1021/pr1010185. Epub 2011 Feb 7.

PMID:
21184612
2.

Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells.

Bouyssié D, Gonzalez de Peredo A, Mouton E, Albigot R, Roussel L, Ortega N, Cayrol C, Burlet-Schiltz O, Girard JP, Monsarrat B.

Mol Cell Proteomics. 2007 Sep;6(9):1621-37. Epub 2007 May 28.

3.

Andromeda: a peptide search engine integrated into the MaxQuant environment.

Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M.

J Proteome Res. 2011 Apr 1;10(4):1794-805. doi: 10.1021/pr101065j. Epub 2011 Feb 22.

PMID:
21254760
4.

ProteinQuant Suite: a bundle of automated software tools for label-free quantitative proteomics.

Mann B, Madera M, Sheng Q, Tang H, Mechref Y, Novotny MV.

Rapid Commun Mass Spectrom. 2008 Dec;22(23):3823-34. doi: 10.1002/rcm.3781.

PMID:
18985620
5.

VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins.

Matthiesen R, Trelle MB, Højrup P, Bunkenborg J, Jensen ON.

J Proteome Res. 2005 Nov-Dec;4(6):2338-47.

PMID:
16335983
6.

Recent developments in proteome informatics for mass spectrometry analysis.

Wright JC, Hubbard SJ.

Comb Chem High Throughput Screen. 2009 Feb;12(2):194-202. Review.

PMID:
19199887
7.
8.

Using ontologies in PROTEUS for modeling proteomics data mining applications.

Cannataro M, Guzzi PH, Mazza T, Tradigo G, Veltri P.

Stud Health Technol Inform. 2005;112:17-26.

PMID:
15923712
9.

Analysis of mass spectrometry data in proteomics.

Matthiesen R, Jensen ON.

Methods Mol Biol. 2008;453:105-22. doi: 10.1007/978-1-60327-429-6_4.

PMID:
18712299
10.

Open mass spectrometry search algorithm.

Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH.

J Proteome Res. 2004 Sep-Oct;3(5):958-64.

PMID:
15473683
11.

A case study on the comparison of different software tools for automated quantification of peptides.

Colaert N, Vandekerckhove J, Martens L, Gevaert K.

Methods Mol Biol. 2011;753:373-98. doi: 10.1007/978-1-61779-148-2_25.

PMID:
21604136
12.

TOPPView: an open-source viewer for mass spectrometry data.

Sturm M, Kohlbacher O.

J Proteome Res. 2009 Jul;8(7):3760-3. doi: 10.1021/pr900171m.

PMID:
19425593
13.

Protein identification using 2D-LC-MS/MS.

Delahunty C, Yates JR 3rd.

Methods. 2005 Mar;35(3):248-55. Epub 2005 Jan 12.

PMID:
15722221
14.

imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.

Römpp A, Schramm T, Hester A, Klinkert I, Both JP, Heeren RM, Stöckli M, Spengler B.

Methods Mol Biol. 2011;696:205-24. doi: 10.1007/978-1-60761-987-1_12.

PMID:
21063949
15.

Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data.

Chamrad DC, Körting G, Stühler K, Meyer HE, Klose J, Blüggel M.

Proteomics. 2004 Mar;4(3):619-28.

PMID:
14997485
16.

Compid: a new software tool to integrate and compare MS/MS based protein identification results from Mascot and Paragon.

Lietzén N, Natri L, Nevalainen OS, Salmi J, Nyman TA.

J Proteome Res. 2010 Dec 3;9(12):6795-800. doi: 10.1021/pr100824w. Epub 2010 Nov 11.

PMID:
20973569
17.

Algorithms and tools for analysis and management of mass spectrometry data.

Veltri P.

Brief Bioinform. 2008 Mar;9(2):144-55. doi: 10.1093/bib/bbn007. Epub 2008 Mar 20.

PMID:
18356204
18.

A proteomic tool for protein identification from tandem mass spectral data.

Zhao Y, Lin YH.

Proteomics. 2005 Mar;5(4):853-5.

PMID:
15668998
19.

CHOMPER: a bioinformatic tool for rapid validation of tandem mass spectrometry search results associated with high-throughput proteomic strategies.

Eddes JS, Kapp EA, Frecklington DF, Connolly LM, Layton MJ, Moritz RL, Simpson RJ.

Proteomics. 2002 Sep;2(9):1097-103.

PMID:
12362328
20.

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis.

Kapp EA, Schütz F, Connolly LM, Chakel JA, Meza JE, Miller CA, Fenyo D, Eng JK, Adkins JN, Omenn GS, Simpson RJ.

Proteomics. 2005 Aug;5(13):3475-90.

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