<s>
OpenMS	B-Application
is	O
an	O
open-source	O
project	O
for	O
data	O
analysis	O
and	O
processing	O
in	O
mass	O
spectrometry	O
and	O
is	O
released	O
under	O
the	O
3-clause	B-Operating_System
BSD	I-Operating_System
licence	I-Operating_System
.	O
</s>
<s>
It	O
supports	O
most	O
common	O
operating	O
systems	O
including	O
Microsoft	B-Application
Windows	I-Application
,	O
MacOS	B-Application
and	O
Linux	B-Application
.	O
</s>
<s>
OpenMS	B-Application
has	O
tools	O
for	O
analysis	O
of	O
proteomics	O
data	O
,	O
providing	O
algorithms	O
for	O
signal	O
processing	O
,	O
feature	O
finding	O
(	O
including	O
de-isotoping	O
)	O
,	O
visualization	O
in	O
1D	O
(	O
spectra	O
or	O
chromatogram	O
level	O
)	O
,	O
2D	O
and	O
3D	O
,	O
map	O
mapping	O
and	O
peptide	O
identification	O
.	O
</s>
<s>
OpenMS	B-Application
also	O
supports	O
metabolomics	O
workflows	O
and	O
targeted	O
analysis	O
of	O
DIA/SWATH	O
data	O
.	O
</s>
<s>
Furthermore	O
,	O
OpenMS	B-Application
provides	O
tools	O
for	O
the	O
analysis	O
of	O
cross	O
linking	O
data	O
,	O
including	O
protein-protein	O
,	O
protein-RNA	O
and	O
protein-DNA	O
cross	O
linking	O
.	O
</s>
<s>
Lastly	O
,	O
OpenMS	B-Application
provides	O
tools	O
for	O
analysis	O
of	O
RNA	O
mass	O
spectrometry	O
data	O
.	O
</s>
<s>
OpenMS	B-Application
was	O
originally	O
released	O
in	O
2007	O
in	O
version	O
1.0	O
and	O
was	O
described	O
in	O
two	O
articles	O
published	O
in	O
Bioinformatics	O
in	O
2007	O
and	O
2008	O
and	O
has	O
since	O
seen	O
continuous	O
releases	O
.	O
</s>
<s>
In	O
2013	O
,	O
a	O
complete	O
high-throughput	O
label-free	O
analysis	O
pipeline	O
using	O
OpenMS	B-Application
1.8	O
was	O
described	O
and	O
compared	O
with	O
similar	O
,	O
proprietary	B-Application
software	I-Application
(	O
such	O
as	O
MaxQuant	O
and	O
Progenesis	O
QI	O
)	O
.	O
</s>
<s>
However	O
,	O
the	O
performance	O
of	O
OpenMS	B-Application
is	O
on	O
par	O
with	O
that	O
of	O
its	O
two	O
tested	O
competitors	O
 [ ... ] 	O
 "	O
.	O
</s>
<s>
The	O
OpenMS	B-Application
1.10	O
release	O
contained	O
several	O
new	O
analysis	O
tools	O
,	O
including	O
OpenSWATH	O
(	O
a	O
tool	O
for	O
targeted	O
DIA	O
data	O
analysis	O
)	O
,	O
a	O
metabolomics	O
feature	O
finder	O
and	O
a	O
TMT	O
analysis	O
tool	O
.	O
</s>
<s>
The	O
OpenMS	B-Application
1.11	O
release	O
was	O
the	O
first	O
release	O
to	O
contain	O
fully	O
integrated	O
bindings	O
to	O
the	O
Python	B-Language
programming	I-Language
language	I-Language
(	O
termed	O
pyOpenMS	B-Application
)	O
.	O
</s>
<s>
With	O
OpenMS	B-Application
2.0	O
,	O
released	O
in	O
April	O
2015	O
,	O
the	O
project	O
provides	O
a	O
new	O
version	O
that	O
has	O
been	O
completely	O
cleared	O
of	O
GPL	B-License
code	O
and	O
uses	O
git	B-Application
(	O
in	O
combination	O
with	O
GitHub	B-Application
)	O
for	O
its	O
version	O
control	O
and	O
ticketing	O
system	O
.	O
</s>
<s>
In	O
2016	O
,	O
the	O
new	O
features	O
of	O
OpenMS	B-Application
2.0	O
were	O
described	O
in	O
an	O
article	O
in	O
Nature	O
Methods	O
.	O
</s>
<s>
OpenMS	B-Application
is	O
currently	O
developed	O
with	O
contributions	O
from	O
the	O
group	O
of	O
Knut	O
Reinert	O
at	O
the	O
Free	O
University	O
of	O
Berlin	O
,	O
the	O
group	O
of	O
Oliver	O
Kohlbacher	O
at	O
the	O
University	O
of	O
Tübingen	O
and	O
the	O
group	O
of	O
Ruedi	O
Aebersold	O
at	O
ETH	O
Zurich	O
.	O
</s>
<s>
OpenMS	B-Application
provides	O
a	O
set	O
of	O
over	O
100	O
different	O
executable	O
tools	O
than	O
can	O
be	O
chained	O
together	O
into	O
pipelines	O
for	O
mass	O
spectrometry	O
data	O
analysis	O
(	O
the	O
TOPP	O
Tools	O
)	O
.	O
</s>
<s>
Finally	O
,	O
OpenMS	B-Application
also	O
provides	O
a	O
C++	B-Language
library	O
(	O
with	O
bindings	O
to	O
Python	B-Language
available	O
since	O
1.11	O
)	O
for	O
LC/MS	O
data	O
management	O
and	O
analyses	O
accessible	O
to	O
developers	O
to	O
create	O
new	O
tools	O
and	O
implement	O
their	O
own	O
algorithms	O
using	O
the	O
OpenMS	B-Application
library	O
.	O
</s>
<s>
OpenMS	B-Application
is	O
free	O
software	O
available	O
under	O
the	O
3-clause	B-Operating_System
BSD	I-Operating_System
licence	I-Operating_System
(	O
previously	O
under	O
the	O
LGPL	O
)	O
.	O
</s>
<s>
OpenMS	B-Application
is	O
compatible	O
with	O
current	O
and	O
upcoming	O
Proteomics	O
Standard	O
Initiative	O
(	O
PSI	O
)	O
formats	O
for	O
mass	O
spectrometric	O
data	O
.	O
</s>
