Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 109

1.

Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker.

Holman JD, Ma ZQ, Tabb DL.

Curr Protoc Bioinformatics. 2012 Mar;Chapter 13:Unit13.17. doi: 10.1002/0471250953.bi1317s37.

2.

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.

Ma ZQ, Dasari S, Chambers MC, Litton MD, Sobecki SM, Zimmerman LJ, Halvey PJ, Schilling B, Drake PM, Gibson BW, Tabb DL.

J Proteome Res. 2009 Aug;8(8):3872-81. doi: 10.1021/pr900360j.

3.

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

Griss J, Reisinger F, Hermjakob H, Vizcaíno JA.

Proteomics. 2012 Mar;12(6):795-8. doi: 10.1002/pmic.201100578.

4.

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency.

Zhang B, Chambers MC, Tabb DL.

J Proteome Res. 2007 Sep;6(9):3549-57. Epub 2007 Aug 4.

5.

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.

BMC Bioinformatics. 2008 Dec 16;9:542. doi: 10.1186/1471-2105-9-542.

6.

LC-MSsim--a simulation software for liquid chromatography mass spectrometry data.

Schulz-Trieglaff O, Pfeifer N, Gröpl C, Kohlbacher O, Reinert K.

BMC Bioinformatics. 2008 Oct 8;9:423. doi: 10.1186/1471-2105-9-423.

7.

MassUntangler: a novel alignment tool for label-free liquid chromatography-mass spectrometry proteomic data.

Ballardini R, Benevento M, Arrigoni G, Pattini L, Roda A.

J Chromatogr A. 2011 Dec 9;1218(49):8859-68. doi: 10.1016/j.chroma.2011.06.062. Epub 2011 Jun 22.

PMID:
21783198
8.

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
9.

An automated proteomic data analysis workflow for mass spectrometry.

Pendarvis K, Kumar R, Burgess SC, Nanduri B.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S17. doi: 10.1186/1471-2105-10-S11-S17.

10.

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.

Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.

Bioinformatics. 2015 Sep 1;31(17):2903-5. doi: 10.1093/bioinformatics/btv250. Epub 2015 Apr 24.

11.

Data reduction of isotope-resolved LC-MS spectra.

Du P, Sudha R, Prystowsky MB, Angeletti RH.

Bioinformatics. 2007 Jun 1;23(11):1394-400. Epub 2007 May 11.

PMID:
17496000
12.

MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data.

Hartler J, Thallinger GG, Stocker G, Sturn A, Burkard TR, Körner E, Rader R, Schmidt A, Mechtler K, Trajanoski Z.

BMC Bioinformatics. 2007 Jun 13;8:197.

13.

MSSimulator: Simulation of mass spectrometry data.

Bielow C, Aiche S, Andreotti S, Reinert K.

J Proteome Res. 2011 Jul 1;10(7):2922-9. doi: 10.1021/pr200155f. Epub 2011 Apr 28.

PMID:
21526843
14.

Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides.

Heller M, Ye M, Michel PE, Morier P, Stalder D, Jünger MA, Aebersold R, Reymond F, Rossier JS.

J Proteome Res. 2005 Nov-Dec;4(6):2273-82.

PMID:
16335976
15.
16.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6.

17.

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.

Jaitly N, Mayampurath A, Littlefield K, Adkins JN, Anderson GA, Smith RD.

BMC Bioinformatics. 2009 Mar 17;10:87. doi: 10.1186/1471-2105-10-87.

18.

The EIPeptiDi tool: enhancing peptide discovery in ICAT-based LC MS/MS experiments.

Cannataro M, Cuda G, Gaspari M, Greco S, Tradigo G, Veltri P.

BMC Bioinformatics. 2007 Jul 15;8:255.

19.

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
20.

The mzIdentML data standard for mass spectrometry-based proteomics results.

Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D.

Mol Cell Proteomics. 2012 Jul;11(7):M111.014381. doi: 10.1074/mcp.M111.014381. Epub 2012 Feb 27.

Supplemental Content

Support Center