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. Author manuscript; available in PMC: 2017 Mar 4.
Published in final edited form as: J Proteome Res. 2016 Feb 25;15(3):1023–1032. doi: 10.1021/acs.jproteome.5b01091

Table 1.

Software and options used in the Common Data Analysis Pipeline.

Program Versi
on		 Source Refere
nce		 Purpos
e		 Options Used iTR
AQ		 Phos
pho
ReAdW4Masc
ot2.exe 		ftp://chemdata.nist.gov/download/peptide_library/software/current_releases/ReAdw4Mascot2/ None MS and
MS/MS
data
extracti
ons,
precurs
or m/z
and
charge
state re-
evaluati
on		 -c -ChargeMgfOrbi -
FixPepmass -MaxPI -
metadata -
MonoisoMgfOrbi -
NoPeaks1 -PIvsRT -
sep1 -sepZC -msfr -
XmlOrbiMs1Profile -
iTRAQ -TolPPM 20		 -
iTRA
Q
MS-GF+ v973
3		 http://omics.pnl.gov/software/ms-gf Kim et
al.8 		Sequen
ce
databas
e search		 java –Xmx3500M –jar
MSGFPlus.jar -d
<file>.fasta -t 20ppm -e
1 -m (3 for QExactive, 1
for Orbitrap) -inst (1 for
QExactive, 1 for
Orbitrap) -ntt 1 -thread 2
-tda 1 -ti 0,0 -n 1 -
maxLength 50 -mod
<file>.txt		 -
proto
col 2
(3 for
phos
pho
and
iTRA
Q)		 -
protoc
ol 1
NIST-ProMS NIST (developer communication) MS1
data
analysis		 in a file called proms.ini
(<mzXML
file>.raw.mzXML

<search result
file>.raw.FT.hcd.ch.M
GF.mzid.tsv

<output file>.raw.txt

<search engine name:
MS-GF+,
MSPepSearch,
SpectraST, OMSSA)
<instrument:
ORBI_HCD, ORBI,
LTQ, QTOF>
PhosphoRS 1.0 http://ms.imp.ac.at/?goto=phosphors Taus et
al.11 		Phosph
osite
localiza
tion		 ActivationTypes="HCD
"

MassTolerance
Value="0.02"