<s>
Mass	B-Application
spectrometry	I-Application
software	I-Application
is	O
software	O
used	O
for	O
data	O
acquisition	O
,	O
analysis	O
,	O
or	O
representation	O
in	O
mass	O
spectrometry	O
.	O
</s>
<s>
On	O
proteome	O
data	O
,	O
Andromeda	O
performs	O
as	O
well	O
as	O
Mascot	B-Application
,	O
a	O
widely	O
used	O
commercial	O
search	O
engine	O
,	O
as	O
judged	O
by	O
sensitivity	O
and	O
specificity	O
analysis	O
based	O
on	O
target	O
decoy	O
searches	O
.	O
</s>
<s>
Greylag	O
open	O
source	O
Database	O
search	O
algorithm	O
developed	O
at	O
the	O
Stowers	O
Institute	O
for	O
Medical	O
Research	O
designed	O
to	O
perform	O
large	O
searches	O
on	O
computational	B-Architecture
clusters	I-Architecture
having	O
hundreds	O
of	O
nodes	O
.	O
</s>
<s>
InsPecT	B-Application
open	O
source	O
A	O
MS-alignment	O
search	O
algorithm	O
available	O
at	O
the	O
Center	O
for	O
Computational	O
Mass	O
Spectrometry	O
at	O
the	O
University	O
of	O
California	O
,	O
San	O
Diego	O
Mascot	B-Application
proprietary	O
Performs	O
mass	O
spectrometry	O
data	O
analysis	O
through	O
a	O
statistical	O
evaluation	O
of	O
matches	O
between	O
observed	O
and	O
projected	O
peptide	O
fragments	O
.	O
</s>
<s>
MassMatrix	B-Application
freeware	O
MassMatrix	B-Application
is	O
a	O
database	O
search	O
algorithm	O
for	O
tandem	O
mass	O
spectrometric	O
data	O
.	O
</s>
<s>
PEAKS	B-Application
DBproprietary	O
Database	O
search	O
engine	O
,	O
run	O
in	O
parallel	O
with	O
de	O
novo	O
sequencing	O
to	O
automatically	O
validate	O
search	O
results	O
,	O
allowing	O
for	O
a	O
higher	O
number	O
of	O
found	O
sequences	O
for	O
a	O
given	O
false	O
discovery	O
rate	O
.	O
</s>
<s>
In	O
addition	O
to	O
providing	O
an	O
independent	O
database	O
search	O
,	O
results	O
can	O
be	O
incorporated	O
as	O
part	O
of	O
the	O
software	O
's	O
multi-engine	O
(	O
Sequest	B-Application
,	O
Mascot	B-Application
,	O
X	O
!	O
Tandem	O
,	O
OMSSA	O
,	O
PEAKS	B-Application
DB	I-Application
)	O
consensus	O
reporting	O
tool	O
,	O
inChorus	O
.	O
</s>
<s>
Instead	O
,	O
users	O
only	O
need	O
to	O
specify	O
the	O
range	O
of	O
modification	O
mass	O
for	O
each	O
individual	O
amino	O
acid.SimTandem	O
freeware	O
A	O
database	O
search	O
engine	O
for	O
identification	O
of	O
peptide	O
sequences	O
from	O
LC/MS/MS	O
data	O
;	O
the	O
engine	O
can	O
be	O
used	O
as	O
an	O
external	O
tool	O
in	O
OpenMS/TOPP	O
.	O
</s>
<s>
It	O
is	O
an	O
independent	O
reimplementation	O
of	O
the	O
SEQUEST	B-Application
algorithm	O
,	O
which	O
identifies	O
peptides	O
by	O
comparing	O
the	O
observed	O
spectra	O
to	O
a	O
catalog	O
of	O
theoretical	O
spectra	O
derived	O
in	O
silico	O
from	O
a	O
database	O
of	O
known	O
proteins	O
.	O
</s>
<s>
The	O
immediate	O
ancestor	O
of	O
Tide	O
is	O
Crux	O
,	O
but	O
Tide	O
has	O
been	O
completely	O
re-engineered	O
to	O
achieve	O
a	O
thousandfold	O
improvement	O
in	O
speed	O
while	O
exactly	O
replicating	O
SEQUEST	B-Application
XCorr	O
scores	O
.	O
</s>
<s>
PEAKS	B-Application
proprietary	O
De	O
novo	O
sequencing	O
for	O
each	O
peptide	O
,	O
confidence	O
scores	O
on	O
individual	O
amino	O
acid	O
assignments	O
with	O
manually	O
assisted	O
mode	O
and	O
automated	O
de	O
novo	O
sequencing	O
on	O
an	O
entire	O
LC	O
run	O
processed	O
data	O
faster	O
than	O
1	O
spectrum	O
per	O
second	O
.	O
</s>
<s>
Name	O
Type	O
Description	O
MS-Homology	O
open	O
source	O
MS-Homology	O
is	O
a	O
database	O
search	O
program	O
within	O
the	O
Protein	O
Prospector	O
package	O
that	O
permits	O
searching	O
with	O
strings	O
that	O
combine	O
masses	O
and	O
amino	O
acid	O
stretches	O
,	O
where	O
one	O
can	O
specify	O
the	O
number	O
of	O
amino	O
acid	O
mismatches	O
allowed.SPIDER	O
proprietary	O
The	O
SPIDER	O
algorithm	O
matches	O
sequence	O
tags	O
with	O
errors	O
to	O
database	O
sequences	O
for	O
the	O
purpose	O
of	O
protein	O
and	O
peptide	O
identification	O
and	O
can	O
be	O
used	O
in	O
conjunction	O
with	O
PEAKS	B-Application
mass	O
spectrometry	O
data	O
analysis	O
software	O
.	O
</s>
<s>
Mascot	B-Application
Distiller	O
proprietary	O
Software	O
for	O
peak	O
picking	O
and	O
raw	O
data	O
preprocessing	O
.	O
</s>
<s>
Supports	O
raw	O
file	O
formats	O
from	O
all	O
major	O
instrument	O
vendors.Mascot	O
Server	O
proprietary	O
The	O
search	O
engine	O
supports	O
quantification	O
based	O
on	O
isobaric	O
labeling	O
as	O
long	O
as	O
all	O
the	O
required	O
information	O
is	O
part	O
of	O
the	O
MS/MS	O
spectrum.MassChroQ	O
open	O
source	O
Peptide	O
quantification	O
analysis	O
of	O
label	O
free	O
or	O
various	O
isotopic	O
labeling	O
methods	O
(	O
SILAC	O
,	O
ICAT	O
,	O
N-15	O
,	O
C-13	O
...	O
)	O
,	O
works	O
with	O
high	O
and	O
low	O
resolution	O
spectrometer	O
systems	O
,	O
supports	O
complex	O
data	O
treatments	O
as	O
peptide	O
or	O
protein	O
fractionation	O
prior	O
to	O
LC-MS	O
analysis	O
(	O
SCX	O
,	O
SDS-PAGE	O
,	O
etc	O
.	O
)	O
.	O
</s>
<s>
MaxQuant	O
freeware	O
Quantitative	O
proteomics	O
software	O
developed	O
by	O
Jürgen	O
Cox	O
and	O
others	O
at	O
the	O
Max	O
Planck	O
Institute	O
of	O
Biochemistry	O
in	O
Martinsried	O
,	O
Germany	O
written	O
in	O
C#	B-Application
that	O
allows	O
the	O
analysis	O
of	O
label	O
free	O
and	O
SILAC	O
based	O
proteomics	O
experiments.MultiQuant	O
Software	O
proprietary	O
Can	O
process	O
quantitative	O
data	O
sets	O
from	O
TripleTOF	O
or	O
QTRAP	O
systems	O
,	O
including	O
MRM	O
and	O
SWATH	O
Acquisition	O
.	O
</s>
<s>
OpenMS	B-Application
/	O
TOPP	O
open	O
source	O
Software	O
C++	O
library	O
for	O
LC-MS/MS	O
data	O
management	O
and	O
analysis	O
that	O
offers	O
an	O
infrastructure	O
for	O
the	O
development	O
of	O
mass	O
spectrometry-related	O
software	O
.	O
</s>
<s>
Allows	O
peptide	O
and	O
metabolite	O
quantification	O
,	O
supporting	O
label-free	O
and	O
isotopic-label-based	O
quantification	O
(	O
such	O
as	O
iTRAQ	O
and	O
TMT	O
and	O
SILAC	O
)	O
as	O
well	O
as	O
targeted	O
SWATH-MS	O
quantification.OpenPIPwebsite	O
,	O
open	O
accessOpenPIP	O
is	O
an	O
open	O
access	O
,	O
web	O
based	O
tool	O
,	O
developed	O
by	O
InterVenn	O
Biosciences	O
to	O
integrate	O
peaks	B-Application
acquired	O
in	O
multiple	O
reaction	O
monitoring	O
(	O
MRM	O
)	O
experiments	O
.	O
</s>
<s>
The	O
software	O
is	O
powered	O
by	O
recurrent	O
neural	O
networks	O
and	O
was	O
trained	O
on	O
a	O
massive	O
collection	O
of	O
manually-annotated	O
chromatographic	O
peaks.ProtMax	O
freeware	O
ProtMAX	O
is	O
a	O
software	O
tool	O
for	O
analyzing	O
shotgun	O
proteomics	O
mass	O
spectrometry	O
data	O
sets	O
,	O
developed	O
by	O
Volker	O
Egelhofer	O
at	O
the	O
University	O
of	O
Vienna	O
.	O
</s>
<s>
Skyline	B-Application
open	O
source	O
Open	O
source	O
(	O
Apache	O
2.0	O
)	O
Windows	O
client	O
software	O
developed	O
in	O
the	O
MacCoss	O
lab	O
at	O
University	O
of	O
Washington	O
that	O
supports	O
building	O
Selected	O
Reaction	O
Monitoring	O
(	O
SRM	O
)	O
/	O
Multiple	O
Reaction	O
Monitoring	O
(	O
MRM	O
)	O
,	O
Parallel	O
Reaction	O
Monitoring	O
(	O
PRM	O
-	O
Targeted	O
MS/MS	O
)	O
,	O
Data	O
Independent	O
Acquisition	O
(	O
DIA/SWATH	O
)	O
and	O
targeted	O
DDA	O
with	O
MS1	O
quantitative	O
methods	O
and	O
analyzing	O
the	O
resulting	O
mass	O
spectrometer	O
data.Spectronaut	O
proprietary	O
Commercial	O
software	O
for	O
quantitative	O
proteomics	O
developed	O
by	O
Biognosys	O
AG	O
(	O
Schlieren	O
,	O
Switzerland	O
)	O
based	O
on	O
the	O
mProphet	O
algorithm	O
that	O
allows	O
the	O
targeted	O
analysis	O
of	O
data	O
independent	O
acquisition	O
(	O
DIA	O
)	O
data	O
sets	O
for	O
label-free	O
peptide	O
quantitation	O
,	O
also	O
called	O
SWATH	O
acquisition	O
.	O
</s>
<s>
Name	O
Type	O
Description	O
Advanced	B-Application
Chemistry	I-Application
Development	I-Application
proprietary	O
Commercial	O
solutions	O
for	O
the	O
interpretation	O
of	O
MS	O
and	O
xC/MS	O
data	O
with	O
spectrum/structure	O
matching	O
,	O
identification	O
of	O
known	O
and	O
unknown	O
metabolites	O
,	O
as	O
well	O
as	O
for	O
the	O
identification	O
of	O
compounds	O
through	O
spectral	O
comparison	O
.	O
</s>
<s>
Analyst	B-Application
proprietary	O
Software	O
by	O
AB	O
Sciex	O
,	O
a	O
division	O
of	O
The	O
Danaher	O
Corporation.AnalyzerPro	O
proprietary	O
A	O
vendor	O
independent	O
software	O
application	O
from	O
SpectralWorks	O
for	O
processing	O
mass	O
spectrometry	O
data	O
.	O
</s>
<s>
Python	B-Language
script	I-Language
or	O
standalone	O
executables	O
for	O
Linux	O
and	O
Windows	O
.	O
</s>
<s>
El-MAVENopen-sourceDesktop	O
software	O
by	O
Elucidata	O
for	O
processing	O
labeled	O
LC-MS	O
,	O
GC-MS	O
and	O
LC-MS/MS	O
data	O
in	O
open-formats	O
(	O
mzXML	B-Application
,	O
mzML	O
,	O
CDF	O
)	O
.	O
</s>
<s>
)	O
,	O
processing	O
,	O
database	O
building	O
(	O
MS	O
or	O
multiple	O
techniques	O
including	O
IR	O
,	O
Raman	O
,	O
NMR	O
,	O
UV	O
,	O
Chromatograms	O
)	O
,	O
spectral	O
subtraction	O
,	O
plus	O
tools	O
for	O
reporting	O
and	O
ChemWindow	B-Application
structure	O
drawing	O
,	O
and	O
MASSTransit	O
file	O
conversion	O
software	O
(	O
updated	O
with	O
more	O
formats	O
)	O
.LabSolutions	O
LCMS	O
proprietary	O
Software	O
by	O
Shimadzu	O
Corporation	O
used	O
with	O
mass	O
spectrometry	O
and	O
HPLC	O
instruments	O
.	O
</s>
<s>
LipidXplorer	O
open	O
source	O
high-throughput	O
lipid	O
identification	O
from	O
shotgun	O
mass	O
spectra	O
(	O
Python	B-Language
)	O
Mass++	O
open	O
source	O
Analysis	O
software	O
for	O
mass	O
spectrometry	O
that	O
can	O
import	O
and	O
export	O
files	O
with	O
open-formats	O
(	O
mzXML	B-Application
,	O
mzML	O
)	O
and	O
load	O
some	O
instrument	O
vendor	O
formats	O
;	O
users	O
can	O
develop	O
and	O
add	O
original	O
functions	O
as	O
Mass++	O
plug-ins.MassBankopen	O
sourceMassBank	O
and	O
RMassBank	O
development	O
website	O
provided	O
by	O
the	O
MassBank	O
consortium	O
.	O
</s>
<s>
MassCenter	B-Application
proprietary	O
Software	O
by	O
JEOL	O
used	O
with	O
mass	O
spectrometry	O
instruments	O
.	O
</s>
<s>
MassLynx	B-Application
proprietary	O
Software	O
by	O
Waters	O
Corporation	O
.	O
</s>
<s>
Mass-Up	O
open-source	O
Utility	O
for	O
proteomics	O
designed	O
to	O
support	O
the	O
preprocessing	O
and	O
analysis	O
of	O
MALDI-TOF	O
mass	O
spectrometry	O
data	O
that	O
loads	O
data	O
from	O
mzML	O
,	O
mzXML	B-Application
and	O
CSV	O
files	O
and	O
allows	O
users	O
to	O
apply	O
baseline	O
correction	O
,	O
normalization	O
,	O
smoothing	O
,	O
peak	O
detection	O
and	O
peak	O
matching	O
.	O
</s>
<s>
matchms	O
open	O
source	O
Python	B-Language
library	O
to	O
import	O
,	O
clean	O
,	O
process	O
and	O
quantitatively	O
compare	O
MS/MS	O
spectra	O
.	O
</s>
<s>
A	O
program	O
of	O
the	O
msxpertsuite.org	O
software	O
suite.mMass	O
open	O
source	O
Multi-platform	O
package	O
of	O
tools	O
for	O
mass	O
spectrometric	O
data	O
analysis	O
and	O
interpretation	O
written	O
in	O
Python	B-Language
(	O
no	O
more	O
developed	O
)	O
.	O
</s>
<s>
MSGraph	B-Application
open	O
source	O
MSight	O
freeware	O
Software	O
for	O
mass	O
spectrometry	O
imaging	O
developed	O
by	O
the	O
Swiss	O
Institute	O
of	O
Bioinformatics	O
.	O
</s>
<s>
;	O
submodules	O
such	O
as	O
mspire-lipidomics	O
,	O
mspire-sequest	O
,	O
and	O
mspire-simulator	O
extend	O
the	O
functionality.MSqRob	O
open-source	O
R	B-Language
package	O
with	O
graphical	O
user	O
interface	O
for	O
robust	O
differential	O
abundance	O
analysis	O
of	O
label-free	O
quantitative	O
proteomics	O
data.ms2mz	O
freeware	O
Utility	O
for	O
converting	O
between	O
mass	O
spectrometer	O
file	O
formats	O
,	O
e.g.	O
</s>
<s>
OpenChrom	B-Language
open	O
source	O
Chromatography	O
and	O
mass	B-Application
spectrometry	I-Application
software	I-Application
that	O
can	O
be	O
extended	O
using	O
plug-ins	O
and	O
is	O
available	O
for	O
several	O
operating	O
systems	O
(	O
Microsoft	O
Windows	O
,	O
Linux	O
,	O
Unix	O
,	O
Mac	O
OS	O
X	O
)	O
and	O
processor	O
architectures	O
(	O
x86	O
,	O
x86_64	O
,	O
ppc	O
)	O
.	O
</s>
<s>
converters	O
for	O
mzXML	B-Application
,	O
netCDF	O
,	O
Agilent	O
,	O
Finnigan	O
and	O
Varian	O
file	O
formats	O
.	O
</s>
<s>
PatternLab	O
freeware	O
Software	O
for	O
post-analysis	O
of	O
SEQUEST	B-Application
,	O
ProLuCID	O
or	O
Comet	O
database	O
search	O
results	O
filtered	O
by	O
DTASelect	O
or	O
Census	O
.	O
</s>
<s>
pyOpenMS	B-Application
open	O
source	O
pyOpenMS	B-Application
is	O
an	O
open-source	O
Python	B-Language
library	O
for	O
mass	O
spectrometry	O
,	O
specifically	O
for	O
the	O
analysis	O
of	O
proteomics	O
and	O
metabolomics	O
data	O
in	O
Python	B-Language
.	O
</s>
<s>
PeakStrainer	O
open	O
source	O
Intensity-Independent	O
Noise	O
Filtering	O
in	O
FT	O
MS	O
and	O
FT	O
MS/MS	O
Spectra	O
for	O
Shotgun	O
Lipidomics	O
(	O
Python	B-Language
)	O
Peacock	O
open	O
source	O
Mac	O
OS	O
X	O
application	O
developed	O
by	O
Johan	O
Kool	O
that	O
can	O
be	O
used	O
to	O
interpret	O
gas-chromatography/mass	O
-spectrometry	O
(	O
GC/MS	O
)	O
data	O
files	O
.	O
</s>
<s>
Veritomyx	O
advanced	O
signal	O
processing	O
software	O
for	O
peak	O
detection	O
,	O
deconvolution	O
,	O
and	O
centroiding	O
of	O
raw	O
profile	O
mass	O
spec	O
data	O
reveals	O
multiple	O
peaks	B-Application
hidden	O
in	O
overlapped	O
data	O
.	O
</s>
<s>
Notable	O
features	O
:	O
order-of-magnitude	O
improvements	O
in	O
mass	O
and	O
abundance	O
precision	O
for	O
deconvolved	O
peaks	B-Application
;	O
local	O
dynamic	O
baselining	O
;	O
advanced	O
thresholding	O
algorithm	O
increases	O
sensitivity	O
across	O
wide	O
dynamic	O
range	O
;	O
statistically	O
driven	O
and	O
completely	O
automated	O
(	O
no	O
user-to-user	O
variation	O
)	O
.	O
</s>
<s>
It	O
is	O
also	O
available	O
in	O
a	O
"	O
lite	O
"	O
browser-based	O
format	O
called	O
ProMass	O
for	O
the	O
Web	O
that	O
does	O
not	O
require	O
any	O
installation	O
or	O
software	O
download.ProteoIQ	O
proprietary	O
Software	O
for	O
the	O
post-analysis	O
of	O
Mascot	B-Application
,	O
SEQUEST	B-Application
,	O
or	O
X	O
!	O
Tandem	O
database	O
search	O
results	O
.	O
</s>
<s>
ProteomicsTools	O
open	O
source	O
Software	O
for	O
the	O
post-analysis	O
of	O
MASCOT	B-Application
,	O
SEQUEST	B-Application
,	O
Comet	O
,	O
XTandem	O
,	O
PFind	O
,	O
PeptidePhophet	O
,	O
MyriMatch	O
,	O
MSGF	O
,	O
OMSSA	O
,	O
MSAmanda	O
or	O
Percolator	O
database	O
search	O
result	O
.	O
</s>
<s>
ProteoWizard	B-Application
open	O
source	O
Link	O
library	O
and	O
tools	O
that	O
are	O
a	O
set	O
of	O
modular	O
and	O
extensible	O
open-source	O
,	O
cross-platform	O
tools	O
and	O
software	O
libraries	O
that	O
facilitate	O
proteomics	O
data	O
analysis	O
.	O
</s>
<s>
ProteoWorkerproprietary	O
Cloud-based	O
software	O
for	O
proteomics	O
data	O
analysis	O
including	O
COMET	O
,	O
Peptide	O
Prophet	O
,	O
ProteinProphet	B-Application
and	O
extensive	O
data	O
sorting	O
,	O
filtering	O
and	O
annotation	O
tools.Provisionopen	O
source	O
Cloud-based	O
software	O
written	O
in	O
R	B-Language
for	O
analysing	O
proteomics	O
data	O
generated	O
by	O
MaxQuant	O
.	O
</s>
<s>
It	O
is	O
possible	O
to	O
process	O
label-free	O
and	O
tandem	O
mass	O
tagged	O
data.pymzML	O
open	O
source	O
Python	B-Language
module	O
to	O
interface	O
mzML	B-Application
data	I-Application
in	O
Python	B-Language
based	O
on	O
cElementTree	O
with	O
additional	O
tools	O
for	O
MS-informatics	O
.	O
</s>
<s>
Pyteomics	O
open	O
source	O
A	O
Python	B-Language
framework	O
for	O
proteomics	O
data	O
analysis	O
.	O
</s>
<s>
SCIEX	O
OSproprietaryNext	O
generation	O
software	O
by	O
SCIEX	O
controlling	O
the	O
X-series	O
mass	O
spectrometers	O
and	O
support	O
for	O
data	O
analysis	O
acquired	O
using	O
the	O
Analyst	B-Application
software	O
suite.SCiLS	O
Labproprietary	O
Multi-vendor	O
software	O
for	O
statistical	O
analysis	O
of	O
mass	O
spectrometry	O
imaging	O
data	O
.	O
</s>
<s>
It	O
is	O
accessible	O
via	O
its	O
web-interface	O
and	O
as	O
an	O
R	B-Language
package.SIM-XL	O
freeware	O
Spectrum	O
Identification	O
Machine	O
for	O
Cross-linked	O
Peptides	O
(	O
SIM-XL	O
)	O
is	O
a	O
fast	O
and	O
sensitive	O
XL	O
search	O
engine	O
which	O
is	O
part	O
of	O
the	O
PatternLab	O
for	O
proteomics	O
environment	O
,	O
to	O
analyze	O
tandem	O
mass	O
spectrometry	O
data	O
derived	O
from	O
cross-linked	O
peptides.SimGlycan	O
proprietary	O
Predicts	O
the	O
structure	O
of	O
glycans	O
and	O
glycopeptides	O
using	O
mass	O
spectrometry	O
MS/MS	O
data	O
.	O
</s>
<s>
SIMION	B-Application
proprietary	O
Ion	O
optics	O
simulation	O
program	O
Spectrolyzer	O
proprietary	O
Spectrolyzer	O
is	O
a	O
Microsoft	O
Windows-based	O
software	O
package	O
developed	O
by	O
Binary	O
Detect	O
(	O
previously	O
named	O
Medicwave	O
)	O
that	O
provides	O
bioinformatics	O
data	O
analysis	O
tools	O
for	O
different	O
mass	O
spectrometers	O
that	O
focuses	O
on	O
finding	O
protein	O
biomarkers	O
and	O
detecting	O
protein	O
deviations	O
.	O
</s>
<s>
StavroX	O
freeware	O
Software	O
to	O
identify	O
cross-linked	O
peptides	O
from	O
mass	O
spectrometric	O
data	O
written	O
in	O
Java	B-Language
that	O
can	O
be	O
used	O
for	O
a	O
wide	O
variety	O
of	O
cross	O
linkers	O
and	O
proteases	O
used	O
in	O
the	O
cross	O
linking	O
MS	O
experiment	O
;	O
it	O
compares	O
theoretical	O
peptide-peptide	O
cross	O
link	O
combinations	O
for	O
the	O
analyzed	O
proteins	O
to	O
MS/MS	O
data	O
.	O
</s>
<s>
It	O
groups	O
top-down	O
spectral	O
peaks	B-Application
into	O
isotopomer	O
envelopes	O
and	O
converts	O
isotopomer	O
envelopes	O
to	O
monoisotopic	O
neutral	O
masses	O
.	O
</s>
<s>
Trans-Proteomic	B-Application
Pipeline	I-Application
(	O
TPP	O
)	O
open	O
source	O
The	O
Trans-Proteomic	B-Application
Pipeline	I-Application
(	O
TPP	O
)	O
is	O
a	O
collection	O
of	O
integrated	O
tools	O
for	O
MS/MS	O
proteomics	O
that	O
includes	O
PeptideProphet	B-Application
for	O
the	O
Statistical	O
validation	O
of	O
PSMs	O
using	O
search	O
engine	O
results	O
,	O
iProphet	O
for	O
distinct	O
peptide	O
sequence	O
validation	O
,	O
using	O
PeptideProphet	B-Application
results	O
(	O
can	O
also	O
combine	O
the	O
results	O
of	O
multiple	O
search	O
engines	O
)	O
and	O
ProteinProphet	B-Application
for	O
Protein	O
identification	O
and	O
validation	O
,	O
using	O
PeptideProphet	B-Application
OR	O
iProphet	O
results	O
.	O
</s>
<s>
TPP	O
does	O
also	O
Protein	O
Quantification	O
with	O
XPRESS	O
(	O
Calculation	O
of	O
relative	O
abundances	O
of	O
peptides	O
and	O
proteins	O
from	O
isotopically	O
labeled	O
MS/MS	O
samples	O
)	O
,	O
ASAPRatio	B-Application
(	O
Automated	O
Statistical	O
Analysis	O
on	O
Protein	O
Ratio	O
;	O
an	O
alternative	O
to	O
XPRESS	O
)	O
and	O
Libra	O
(	O
Quantification	O
of	O
isobarically	O
labeled	O
samples	O
(	O
e.g.	O
</s>
<s>
The	O
TPP	O
currently	O
supports	O
Sequest	B-Application
,	O
Mascot	B-Application
,	O
ProbID	O
,	O
X	O
!	O
Tandem	O
,	O
Comet	O
,	O
SpectraST	O
,	O
MSGF+	O
,	O
Inspect	B-Application
,	O
MyriMatch	O
,	O
and	O
Phenyx	O
.	O
</s>
<s>
Xcalibur	B-Application
proprietary	O
Software	O
by	O
Thermo	O
Fisher	O
Scientific	O
used	O
with	O
mass	O
spectrometry	O
instruments	O
.	O
</s>
<s>
XCMS	B-Application
Online	I-Application
(	O
Cloud-Based	O
)	O
proprietary	O
Freely	O
available	O
and	O
the	O
most	O
widely	O
used	O
metabolomic	O
and	O
lipidomic	O
data	O
processing	O
platform	O
with	O
over	O
21,000	O
users	O
as	O
of	O
2017	O
.	O
</s>
