<s>
PEAKS	B-Application
is	O
a	O
proteomics	O
software	O
program	O
for	O
tandem	O
mass	O
spectrometry	O
designed	O
for	O
peptide	O
sequencing	O
,	O
protein	O
identification	O
and	O
quantification	O
.	O
</s>
<s>
PEAKS	B-Application
is	O
commonly	O
used	O
for	O
peptide	O
identification	O
(	O
Protein	O
ID	O
)	O
through	O
de	O
novo	O
peptide	O
sequencing	O
assisted	O
search	B-Application
engine	I-Application
database	O
searching	O
.	O
</s>
<s>
PEAKS	B-Application
has	O
also	O
integrated	O
PTM	O
and	O
mutation	O
characterization	O
through	O
automatic	O
peptide	O
sequence	O
tag	O
based	O
searching	O
(	O
SPIDER	O
)	O
and	O
PTM	O
Identification	O
.	O
</s>
<s>
PEAKS	B-Application
provides	O
a	O
complete	O
sequence	O
for	O
each	O
peptide	O
,	O
confidence	O
scores	O
on	O
individual	O
amino	O
acid	O
assignments	O
,	O
simple	O
reporting	O
for	O
high-throughput	O
analysis	O
,	O
amongst	O
other	O
information	O
.	O
</s>
<s>
The	O
software	O
has	O
the	O
ability	O
to	O
compare	O
results	O
of	O
multiple	O
search	B-Application
engines	I-Application
.	O
</s>
<s>
PEAKS	B-Application
inChorus	O
will	O
cross	O
check	O
test	O
results	O
automatically	O
with	O
other	O
protein	O
ID	O
search	B-Application
engines	I-Application
,	O
like	O
Sequest	O
,	O
OMSSA	O
,	O
X	O
!	O
Tandem	O
and	O
Mascot	O
.	O
</s>
<s>
PEAKS	B-Application
Q	O
is	O
an	O
add-on	O
tool	O
for	O
protein	O
quantification	O
,	O
supporting	O
label	O
(	O
ICAT	O
,	O
iTRAQ	O
,	O
SILAC	O
,	O
TMT	O
,	O
018	O
,	O
etc	O
.	O
)	O
</s>
<s>
SPIDER	O
is	O
a	O
sequence	O
tag	O
based	O
search	O
tool	O
within	O
PEAKS	B-Application
,	O
which	O
deals	O
with	O
the	O
possible	O
overlaps	O
between	O
the	O
de	O
novo	O
sequencing	O
errors	O
and	O
the	O
homology	O
mutations	O
.	O
</s>
<s>
A	O
collection	O
of	O
algorithms	O
used	O
within	O
the	O
PEAKS	B-Application
software	O
have	O
been	O
adapted	O
and	O
configured	O
into	O
a	O
specialized	O
project	O
,	O
PEAKS	B-Application
AB	O
,	O
which	O
has	O
proven	O
to	O
be	O
the	O
first	O
method	O
for	O
automatic	O
monoclonal	O
antibody	O
sequencing	O
.	O
</s>
