Table 1.

General Overview of Open source Tools for SRM Post Acquisition.

License	Open Source (Apache 2.0)	Open Source (Apache 2.0)	Free	Open Source (Apache 2.0)	Open Source (Apache 2.0)	Open Source (Apache 2.0)	Open Source (Apache 2.0)
Input files and format (such as transition list in txt and .raw for SRM data measurement)	mzXML	.raw, .d, .wiff and mzXML	.cvs file containing sample classification, replicate, peptide, transition and standard and indigenous quantification	mzXML	mzXML and mzML	tsv file containing peptide group, transitions and parameters for semi- supervised learning algorithm	tsv containg protein, peptide, transition intensity, sample classification
Multi Input file Processing Capability	No (Single mzXML)	Yes	Single .csv	Yes	Yes	one file containing data from many SRM runs	one file containing quantification data from many SRM runs
Operating System	Windows, Linux and Mac	Windows	Windows, Linux and Mac by web browser	Windows VM	Linux	Windows & Linux	Windows, Linux and Mac
Web based or stand- alone	stand-alone	stand-alone	Web service by GenePattern website	stand-alone	stand-alone	stand-alone	stand-alone
Reference	http://proteomics.fhcrc.org/CPL/MRMer.html	https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view	http://www.broadinstitute.org/cancer/software/genepattern/modules/AuDIT.html		http://tools.proteomecenter.org/ATAQS/ATAQS.html	http://www.mprophet.org/	http://www.stat.purdue.edu/~ovitek/Software.html
Applications	Yeast	Plasma	Plasma	Spiked in heavy/light peptides in C. elegans, H. sapiens cell, interrogans.	Yeast and Human Cancer Cell Line	Human Cell Line	Yeast and Human Plasma
Internal Standard Peptide Measurement Required	No	No	Yes	No	Yes	No	No
Software Language	Java	C/C#	R	perl	Java	R	R
Automation	Manual	semi-automated	fully automated	fully automated	fully automated	fully automated	fully automated