<s>
The	B-Application
OpenMS	I-Application
Proteomics	I-Application
Pipeline	I-Application
(	O
TOPP	O
)	O
is	O
a	O
set	O
of	O
computational	O
tools	O
that	O
can	O
be	O
chained	O
together	O
to	O
tailor	O
problem-specific	O
analysis	O
pipelines	O
for	O
HPLC-MS	O
data	O
.	O
</s>
<s>
It	O
transforms	O
most	O
of	O
the	O
OpenMS	B-Application
functionality	O
into	O
small	O
command	O
line	O
tools	O
that	O
are	O
the	O
building	O
blocks	O
for	O
more	O
complex	O
analysis	O
pipelines	O
.	O
</s>
<s>
The	O
functionality	O
of	O
the	O
tools	O
ranges	O
from	O
data	B-General_Concept
preprocessing	I-General_Concept
(	O
file	B-General_Concept
format	I-General_Concept
conversion	I-General_Concept
,	O
baseline	O
reduction	O
,	O
noise	O
reduction	O
,	O
peak	O
picking	O
,	O
map	O
alignment	O
,...	O
)	O
over	O
quantitation	O
(	O
isotope-labeled	O
and	O
label-free	O
)	O
to	O
identification	O
(	O
wrapper	O
tools	O
for	O
Mascot	B-Application
,	O
Sequest	B-Application
,	O
InsPecT	B-Application
and	O
OMSSA	O
)	O
.	O
</s>
<s>
The	B-Application
OpenMS	I-Application
Proteomics	I-Application
Pipeline	I-Application
is	O
free	B-Application
software	I-Application
released	O
under	O
the	O
3-clause	O
BSD	B-Operating_System
license	I-Operating_System
.	O
</s>
