Skip to main content
. Author manuscript; available in PMC: 2019 Nov 11.
Published in final edited form as: Methods Mol Biol. 2017;1558:395–413. doi: 10.1007/978-1-4939-6783-4_19

Table 1.

Common Software Applications for the Analysis of DIA-MS Spectra Data.

Software Input spectra format Type of quantitation Reference Website
Skyline mzML, mzXML, mz5, other vendor specific formats MS2 MacLean et al. 2010 https://brendanx-uwl.gs.washington.edu/labkey/project/home/software/Skyline/begin.view
Open Swath msML, mzXML MS2 Röst et al. 2014 http://www.openswath.org
Spectronaut (Biognosys) HTRMS, WIFF, RAW MS1. MS2 Reiter et al. 2011 https://shop.biognosys.ch/spectronaut
PeakView WIFF MS2 Sciex http://sciex.com/products/software/peakview.-software
SWATHProphet mzML, mzXML MS2 Keller et al. 2016 http://tools.proteomecenter.org/wiki/index.php?title=Software:SWATHProphet
DIA-Umpire mzXML MS2 Tsou et al. 2015 http://diaumpire.sourceforge.net/
Pinnacle RAW M52 http://www.optystech.com/home http://www.optystech.com/