A Cross-platform Toolkit for Mass Spectrometry and Proteomics

Bouwmeester T, Bauch A, Ruffner H, Angrand P, Bergamini G, Croughton K . A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol. 2004; 6(2):97-105. DOI: 10.1038/ncb1086. View

Luethy R, Kessner D, Katz J, MacLean B, Grothe R, Kani K . Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J Proteome Res. 2008; 7(9):4031-9. PMC: 4673049. DOI: 10.1021/pr800307m. View

Benton H, Wong D, Trauger S, Siuzdak G . XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem. 2008; 80(16):6382-9. PMC: 2728033. DOI: 10.1021/ac800795f. View

Raj L, Ide T, Gurkar A, Foley M, Schenone M, Li X . Selective killing of cancer cells by a small molecule targeting the stress response to ROS. Nature. 2011; 475(7355):231-4. PMC: 3316487. DOI: 10.1038/nature10167. View

Pedrioli P, Eng J, Hubley R, Vogelzang M, Deutsch E, Raught B . A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol. 2004; 22(11):1459-66. DOI: 10.1038/nbt1031. View

Askenazi M, Parikh J, Marto J . mzAPI: a new strategy for efficiently sharing mass spectrometry data. Nat Methods. 2009; 6(4):240-1. PMC: 2691659. DOI: 10.1038/nmeth0409-240. View

Eisenacher M . mzIdentML: an open community-built standard format for the results of proteomics spectrum identification algorithms. Methods Mol Biol. 2010; 696:161-77. DOI: 10.1007/978-1-60761-987-1_10. View

MacLean B, Tomazela D, Shulman N, Chambers M, Finney G, Frewen B . Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 2010; 26(7):966-8. PMC: 2844992. DOI: 10.1093/bioinformatics/btq054. View

Orchard S, Albar J, Deutsch E, Eisenacher M, Binz P, Hermjakob H . implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada. Proteomics. 2010; 10(10):1895-8. DOI: 10.1002/pmic.201090034. View

10.

Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J . Global quantification of mammalian gene expression control. Nature. 2011; 473(7347):337-42. DOI: 10.1038/nature10098. View

11.

Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J . mzML--a community standard for mass spectrometry data. Mol Cell Proteomics. 2010; 10(1):R110.000133. PMC: 3013463. DOI: 10.1074/mcp.R110.000133. View

12.

Kessner D, Chambers M, Burke R, Agus D, Mallick P . ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics. 2008; 24(21):2534-6. PMC: 2732273. DOI: 10.1093/bioinformatics/btn323. View

13.

Sturm M, Bertsch A, Gropl C, Hildebrandt A, Hussong R, Lange E . OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics. 2008; 9:163. PMC: 2311306. DOI: 10.1186/1471-2105-9-163. View

14.

Patterson S . Data analysis--the Achilles heel of proteomics. Nat Biotechnol. 2003; 21(3):221-2. DOI: 10.1038/nbt0303-221. View