<s>
Mascot	B-Application
is	O
a	O
software	O
search	O
engine	O
that	O
uses	O
mass	O
spectrometry	O
data	O
to	O
identify	O
proteins	O
from	O
peptide	O
sequence	O
databases	O
.	O
</s>
<s>
Mascot	B-Application
is	O
widely	O
used	O
by	O
research	O
facilities	O
around	O
the	O
world	O
.	O
</s>
<s>
Mascot	B-Application
uses	O
a	O
probabilistic	O
scoring	O
algorithm	O
for	O
protein	O
identification	O
that	O
was	O
adapted	O
from	O
the	O
MOWSE	O
algorithm	O
.	O
</s>
<s>
Mascot	B-Application
is	O
freely	O
available	O
to	O
use	O
on	O
the	O
website	O
of	O
Matrix	O
Science	O
.	O
</s>
<s>
Eventually	O
this	O
software	O
was	O
named	O
Mascot	B-Application
and	O
to	O
reach	O
a	O
wider	O
audience	O
,	O
an	O
external	O
bioinformatics	O
company	O
named	O
Matrix	O
Science	O
was	O
created	O
by	O
David	O
Creasy	O
and	O
John	O
Cottrell	O
to	O
develop	O
and	O
distribute	O
Mascot	B-Application
.	O
</s>
<s>
Mascot	B-Application
has	O
been	O
available	O
as	O
a	O
free	O
service	O
on	O
the	O
Matrix	O
Science	O
website	O
since	O
1999	O
and	O
has	O
been	O
cited	O
in	O
scientific	O
literature	O
over	O
5,000	O
times	O
.	O
</s>
<s>
Matrix	O
Science	O
still	O
continues	O
to	O
work	O
on	O
improving	O
Mascot	B-Application
’s	O
functionality	O
.	O
</s>
<s>
Mascot	B-Application
identifies	O
proteins	O
by	O
interpreting	O
mass	O
spectrometry	O
data	O
.	O
</s>
<s>
Mascot	B-Application
then	O
compares	O
these	O
molecular	O
weights	O
against	O
a	O
database	O
of	O
known	O
peptides	O
.	O
</s>
<s>
Mascot	B-Application
then	O
computes	O
a	O
score	O
based	O
on	O
the	O
probability	O
that	O
the	O
peptides	O
from	O
a	O
sample	O
match	O
those	O
in	O
the	O
selected	O
protein	O
database	O
.	O
</s>
<s>
The	O
more	O
peptides	O
Mascot	B-Application
identifies	O
from	O
a	O
particular	O
protein	O
,	O
the	O
higher	O
the	O
Mascot	B-Application
score	O
for	O
that	O
protein	O
.	O
</s>
<s>
Fixed	O
modifications	O
are	O
applied	O
universally	O
to	O
every	O
amino	O
acid	O
residue	O
of	O
the	O
specified	O
type	O
or	O
to	O
the	O
N-terminus	O
or	O
C-terminus	O
of	O
the	O
peptide	O
.	O
</s>
<s>
Mascot	B-Application
’s	O
fundamental	O
approach	O
to	O
identifying	O
peptides	O
is	O
to	O
calculate	O
the	O
probability	O
whether	O
an	O
observed	O
match	O
between	O
experimental	O
data	O
and	O
peptide	O
sequences	O
found	O
in	O
a	O
reference	O
database	O
has	O
occurred	O
by	O
chance	O
.	O
</s>
<s>
Mascot	B-Application
employs	O
the	O
widely	O
used	O
significance	B-General_Concept
level	I-General_Concept
of	O
0.05	O
,	O
meaning	O
that	O
in	O
a	O
single	O
test	O
the	O
probability	O
of	O
observing	O
an	O
event	O
at	O
random	O
is	O
less	O
than	O
or	O
equal	O
to	O
1	O
in	O
20	O
.	O
</s>
<s>
For	O
a	O
database	O
of	O
that	O
size	O
,	O
by	O
applying	O
a	O
Bonferroni	B-General_Concept
correction	I-General_Concept
to	O
account	O
for	O
multiple	B-General_Concept
comparisons	I-General_Concept
,	O
the	O
significance	O
threshold	O
drops	O
to	O
5*10−8	O
.	O
</s>
<s>
In	O
addition	O
to	O
the	O
calculated	O
peptide	O
scores	O
,	O
Mascot	B-Application
also	O
estimates	O
the	O
False	B-General_Concept
Discovery	I-General_Concept
Rate	I-General_Concept
(	O
FDR	O
)	O
by	O
searching	O
against	O
a	O
decoy	O
database	O
.	O
</s>
<s>
When	O
performing	O
a	O
decoy	O
search	O
,	O
Mascot	B-Application
generates	O
a	O
randomized	O
sequence	O
of	O
the	O
same	O
length	O
for	O
every	O
sequence	O
in	O
the	O
target	O
database	O
.	O
</s>
<s>
Mascot	B-Application
's	O
FDR	O
calculation	O
incorporates	O
ideas	O
from	O
different	O
publications	O
.	O
</s>
<s>
The	O
most	O
common	O
alternative	O
database	O
search	O
programs	O
are	O
listed	O
in	O
the	O
Mass	B-Application
spectrometry	I-Application
software	I-Application
article	O
.	O
</s>
<s>
The	O
performance	O
of	O
a	O
variety	O
of	O
mass	B-Application
spectrometry	I-Application
software	I-Application
,	O
including	O
Mascot	B-Application
,	O
can	O
be	O
observed	O
in	O
the	O
.	O
</s>
