Table 1.

Current Software Tools for Development of Large Scale Targeted Proteomic Assays

Software	Vendor/Lab	Publication Date	Platform
1. Assay Development
Databases and Spectral Libraries
PeptideAtlas	Institute for Systems Biology (ISB)	2006	Web
SRMAtlas	ISB	2009	Web
PRIDE	Martens, EMBL/EBI	2006	Web
GPMdb	Gpmdb	2004	Windows
NIST Peptide Mass Spectral Libraries	NIST	2009	Web
PABST	Seattle Proteome center	2006	Web
Peptide and Transition Selection and Method Export
Skyline	MacCoss Lab, U Washington	2010	Windows
MRMPilot	ABSciex	Commercial	Windows
Pinpoint	Thermo Scientific	Commercial	Windows
MRMaid	Bessant, Cranfield U.	2009	Web
ATAQS	Aebersold, ISB	2011	Web
2. MRM Data Collection
iRT calculator	Biognosys	2012	Web
scheduled MRM (sMRM)	AB Sciex, Waters, Thermo Scientific, and Agilent	Commercial	Windows
iSRM (intelligent MRM)	Thermo Scientific	Commercial	Windows
xMRM (triggered MRM)	AB Sciex	Commercial	Windows
tMRM (triggered MRM)	Agilent	N/A	Windows
3. Data Analysis
Peak Detection and Integration
Multiquant	AB Sciex	Commercial	Windows
Skyline	MacCoss Lab, U Washington	2010	Windows
MRMer	McIntosh Lab, ISB	2008	Java
Pinpoint	Thermo Scientific	Commercial	Windows
OpenMS	Kohlbacher & Reinert, FU Berlin & U of Tübingen	2008	Windows, Linux, Mac (C++ library)
ATAQS	Seattle Proteome Center, ISB	2011	Web
TIQAM	Seattle Proteome Center, ISB	2008	Java (Mac, Win, Linux)
mQUEST	Biognosys	2011	Linux on a VM; Windows
Quaility Assessment and Data Filtering
mProphet	Biognosys	2011	Linux on a VM; Windows
Audit	Carr, Broad	2010	Web
Multiquant	AB Sciex	Commercial	Windows
Fold change or statistical analysis
SRMstats	Vitek Lab, Purdue	2012	Windows, Linux, Mac (R libraries)
QuaSAR	Carr, Broad	N/A	Web