<s>
The	O
Trans-Proteomic	B-Application
Pipeline	I-Application
(	O
TPP	O
)	O
is	O
an	O
open-source	B-Application
data	O
analysis	O
software	O
for	O
proteomics	O
developed	O
at	O
the	O
Institute	O
for	O
Systems	O
Biology	O
(	O
ISB	O
)	O
by	O
the	O
Ruedi	O
Aebersold	O
group	O
under	O
the	O
Seattle	O
Proteome	O
Center	O
.	O
</s>
<s>
The	O
TPP	O
includes	O
PeptideProphet	B-Application
,	O
ProteinProphet	B-Application
,	O
ASAPRatio	B-Application
,	O
XPRESS	O
and	O
Libra	O
.	O
</s>
<s>
PeptideProphet	B-Application
performs	O
statistical	O
validation	O
of	O
peptide-spectra-matches	O
(	O
PSM	O
)	O
using	O
the	O
results	O
of	O
search	O
engines	O
by	O
estimating	O
a	O
false	B-General_Concept
discovery	I-General_Concept
rate	I-General_Concept
(	O
FDR	O
)	O
on	O
PSM	O
level	O
.	O
</s>
<s>
The	O
initial	O
PeptideProphet	B-Application
used	O
a	O
fit	O
of	O
a	O
Gaussian	O
distribution	O
for	O
the	O
correct	O
identifications	O
and	O
a	O
fit	O
of	O
a	O
gamma	O
distribution	O
for	O
the	O
incorrect	O
identification	O
.	O
</s>
<s>
In	O
the	O
PeptideProphet	B-Application
,	O
specifying	O
a	O
decoy	O
tag	O
will	O
use	O
the	O
variable	O
component	O
mixture	O
model	O
while	O
selecting	O
a	O
non-parametric	O
model	O
will	O
use	O
the	O
semi-parametric	O
mixture	O
model	O
.	O
</s>
<s>
ProteinProphet	B-Application
identifies	O
proteins	O
based	O
on	O
the	O
results	O
of	O
PeptideProphet	B-Application
.	O
</s>
<s>
Mayu	O
performs	O
statistical	O
validation	O
of	O
protein	O
identification	O
by	O
estimating	O
a	O
False	B-General_Concept
Discovery	I-General_Concept
Rate	I-General_Concept
(	O
FDR	O
)	O
on	O
protein	O
level	O
.	O
</s>
