mzResults: an interactive viewer for interrogation and distribution of proteomics results.
The growing use of mass spectrometry in the context of biomedical research has been accompanied by an increased demand for distribution of results in a format that facilitates rapid and efficient validation of claims by reviewers and other interested parties. However, the continued evolution of mass spectrometry hardware, sample preparation methods, and peptide identification algorithms complicates standardization and creates hurdles related to compliance with journal submission requirements. Moreover, the recently announced Philadelphia Guidelines (1, 2) suggest that authors provide native mass spectrometry data files in support of their peer-reviewed research articles. These trends highlight the need for data viewers and other tools that work independently of manufacturers' proprietary data systems and seamlessly connect proteomics results with original data files to support user-driven data validation and review. Based upon our recently described API(1)-based framework for mass spectrometry data analysis (3, 4), we created an interactive viewer (mzResults) that is built on established database standards and enables efficient distribution and interrogation of results associated with proteomics experiments, while also providing a convenient mechanism for authors to comply with data submission standards as described in the Philadelphia Guidelines. In addition, the architecture of mzResults supports in-depth queries of the native mass spectrometry files through our multiplierz software environment. We use phosphoproteomics data to illustrate the features and capabilities of mzResults.
Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute Boston, MA 02115-6084, USA
James T
JT
Webber
Manor
M
Askenazi
Jarrod A
JA
Marto
D019295:Computational Biology; D003627:Data Interpretation, Statistical; D017408:Guidelines as Topic; D006801:Humans; D017712:Peer Review, Research / Q000379:methods; D010506:Periodicals as Topic / Q000592:standards; D010750:Phosphoproteins / Q000737:chemistry; D020543:Proteome / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods* / Q000592:standards; D014584:User-Computer Interface
D010750:Phosphoproteins; D020543:Proteome
Proteomics. 2007 Oct;7(20):3651-60
17880003
Proteomics. 2004 Aug;4(8):2363-5
15274131
J Proteome Res. 2008 Aug;7(8):3373-81
18563926
Anal Chem. 2009 May 1;81(9):3440-7
19331382
BMC Bioinformatics. 2009 Oct 29;10:364
19874609
Bioinformatics. 2006 Mar 1;22(5):632-3
16434446
Mol Cell Proteomics. 2004 Dec;3(12):1154-69
15385600
Nat Biotechnol. 2006 Oct;24(10):1285-92
16964243
Proteomics. 2009 Dec;9(23):5350-8
19834895
Nat Biotechnol. 2008 Aug;26(8):860-1
18688232
Anal Chem. 2003 Apr 15;75(8):1895-904
12713048
Methods Mol Biol. 2007;367:261-70
17185781
Proteomics. 2010 Jun;10(11):2113-22
20336676
Mol Syst Biol. 2005;1:2005.0017
16729052
J Proteome Res. 2009 Nov;8(11):4887-8
19891508
Mol Cell Proteomics. 2006 May;5(5):787-8
16670253
Expert Rev Proteomics. 2005 Dec;2(6):839-45
16307524
Proteomics. 2009 Feb;9(4):861-81
19212957
Anal Chem. 2008 Dec 15;80(24):9735-47
19012417
Nat Methods. 2009 Apr;6(4):240-1
19333238
Mol Cell Proteomics. 2005 Sep;4(9):1223-5
16160100
Bioinformatics. 2007 Jan 15;23(2):e191-7
17237091
Bioinformatics. 2004 Jun 12;20(9):1466-7
14976030
J Proteome Res. 2009 Nov;8(11):5347-55
19754192
Proteomics. 2007 Aug;7(16):2769-86
17654461