<s>
To	O
address	O
this	O
limitation	O
,	O
several	O
open	B-Application
,	O
XML-based	O
data	O
formats	O
have	O
recently	O
been	O
developed	O
by	O
the	O
Trans-Proteomic	B-Application
Pipeline	I-Application
at	O
the	O
Institute	O
for	O
Systems	O
Biology	O
to	O
facilitate	O
data	O
manipulation	O
and	O
innovation	O
in	O
the	O
public	O
sector	O
.	O
</s>
<s>
JCAMP-DX	O
is	O
an	O
ASCII	B-Protocol
based	O
format	O
and	O
therefore	O
not	O
very	O
compact	O
even	O
though	O
it	O
includes	O
standards	O
for	O
file	O
compression	O
.	O
</s>
<s>
Many	O
mass	B-Application
spectrometry	I-Application
software	I-Application
packages	O
can	O
read	O
or	O
write	O
ANDI	O
files	O
.	O
</s>
<s>
ANDI	O
is	O
based	O
on	O
netCDF	B-Application
which	O
is	O
a	O
software	O
tool	O
library	O
for	O
writing	O
and	O
reading	O
data	O
files	O
.	O
</s>
<s>
ANDI	O
was	O
initially	O
developed	O
for	O
chromatography-MS	O
data	O
and	O
therefore	O
was	O
not	O
used	O
in	O
the	O
proteomics	O
gold	O
rush	O
where	O
new	O
formats	O
based	O
on	O
XML	B-Protocol
were	O
developed	O
.	O
</s>
<s>
AnIML	O
is	O
a	O
joined	O
effort	O
of	O
IUPAC	O
and	O
ASTM	O
International	O
to	O
create	O
an	O
XML	B-Protocol
based	O
standard	O
that	O
covers	O
a	O
wide	O
variety	O
of	O
analytical	O
techniques	O
including	O
mass	O
spectrometry	O
.	O
</s>
<s>
mzData	B-Application
was	O
the	O
first	O
attempt	O
by	O
the	O
Proteomics	O
Standards	O
Initiative	O
(	O
PSI	O
)	O
from	O
the	O
Human	O
Proteome	O
Organization	O
(	O
HUPO	O
)	O
to	O
create	O
a	O
standardized	O
format	O
for	O
Mass	O
Spectrometry	O
data	O
.	O
</s>
<s>
mzXML	B-Application
is	O
a	O
XML	B-Protocol
(	O
eXtensible	B-Protocol
Markup	I-Protocol
Language	I-Protocol
)	O
based	O
common	O
file	O
format	O
for	O
proteomics	O
mass	O
spectrometric	O
data	O
.	O
</s>
<s>
This	O
format	O
was	O
developed	O
at	O
the	O
Seattle	O
Proteome	O
Center/Institute	O
for	O
Systems	O
Biology	O
while	O
the	O
HUPO-PSI	O
was	O
trying	O
to	O
specify	O
the	O
standardized	O
mzData	B-Application
format	O
,	O
and	O
is	O
still	O
in	O
use	O
in	O
the	O
proteomics	O
community	O
.	O
</s>
<s>
Yet	O
Another	O
Format	O
for	O
Mass	O
Spectrometry	O
(	O
YAFMS	O
)	O
is	O
a	O
suggestion	O
to	O
save	O
data	O
in	O
four	O
table	O
relational	O
server-less	O
database	B-Application
schema	I-Application
with	O
data	O
extraction	O
and	O
appending	O
being	O
exercised	O
using	O
SQL	B-Language
queries	O
.	O
</s>
<s>
As	O
two	O
formats	O
(	O
mzData	B-Application
and	O
mzXML	B-Application
)	O
for	O
representing	O
the	O
same	O
information	O
is	O
an	O
undesirable	O
state	O
,	O
a	O
joint	O
effort	O
was	O
set	O
by	O
HUPO-PSI	O
,	O
the	O
SPC/ISB	O
and	O
instrument	O
vendors	O
to	O
create	O
a	O
unified	O
standard	O
borrowing	O
the	O
best	O
aspects	O
of	O
both	O
mzData	B-Application
and	O
mzXML	B-Application
,	O
and	O
intended	O
to	O
replace	O
them	O
.	O
</s>
<s>
Instead	O
of	O
defining	O
new	O
file	O
formats	O
and	O
writing	O
converters	O
for	O
proprietary	O
vendor	O
formats	O
a	O
group	O
of	O
scientists	O
proposed	O
to	O
define	O
a	O
common	O
application	B-Application
program	I-Application
interface	I-Application
to	O
shift	O
the	O
burden	O
of	O
standards	O
compliance	O
to	O
the	O
instrument	O
manufacturers	O
 '	O
existing	O
data	O
access	O
libraries	O
.	O
</s>
<s>
The	O
mz5	O
format	O
addresses	O
the	O
performance	O
problems	O
of	O
the	O
previous	O
XML	B-Protocol
based	O
formats	O
.	O
</s>
<s>
It	O
uses	O
the	O
mzML	O
ontology	O
,	O
but	O
saves	O
the	O
data	O
using	O
the	O
HDF5	B-Application
backend	O
for	O
reduced	O
storage	O
space	O
requirements	O
and	O
improved	O
read/write	O
speed	O
.	O
</s>
<s>
The	O
imzML	O
standard	O
was	O
proposed	O
to	O
exchange	O
data	O
from	O
mass	O
spectrometry	O
imaging	O
in	O
a	O
standardized	O
XML	B-Protocol
file	O
based	O
on	O
the	O
mzML	O
ontology	O
.	O
</s>
<s>
It	O
splits	O
experimental	O
data	O
into	O
XML	B-Protocol
and	O
spectral	O
data	O
in	O
a	O
binary	O
file	O
.	O
</s>
<s>
mzDB	O
saves	O
data	O
in	O
an	O
SQLite	B-Language
database	O
to	O
save	O
on	O
storage	O
space	O
and	O
improve	O
access	O
times	O
as	O
the	O
data	O
points	O
can	O
be	O
queried	O
from	O
a	O
relational	B-Application
database	I-Application
.	O
</s>
<s>
Toffee	O
is	O
an	O
open	B-Application
lossless	O
file	O
format	O
for	O
data-independent	O
acquisition	O
mass	O
spectrometry	O
.	O
</s>
<s>
It	O
leverages	O
HDF5	B-Application
and	O
aims	O
to	O
achieve	O
file	O
sizes	O
similar	O
to	O
those	O
from	O
the	O
proprietary	O
and	O
closed	O
vendor	O
formats	O
.	O
</s>
<s>
mzMLb	O
is	O
another	O
take	O
on	O
using	O
a	O
HDF5	B-Application
backend	O
for	O
performant	O
raw	O
data	O
saving	O
.	O
</s>
<s>
It	O
,	O
however	O
,	O
preserves	O
the	O
mzML	O
XML	B-Protocol
data	O
structure	O
and	O
stays	O
compliant	O
to	O
the	O
existing	O
standard	O
.	O
</s>
<s>
Known	O
converters	O
for	O
mzData	B-Application
to	O
mzXML	B-Application
:	O
</s>
<s>
Known	O
converters	O
for	O
mzXML	B-Application
:	O
</s>
<s>
msConvert	B-Application
:	O
A	O
command	O
line	O
tool	O
converting	O
to/from	O
various	O
mass	O
spectrometry	O
formats	O
.	O
</s>
<s>
ReAdW	B-Application
:	O
The	O
Institute	O
for	O
Systems	O
Biology	O
command	O
line	O
converter	O
for	O
Thermo	O
RAW	O
files	O
,	O
part	O
of	O
the	O
TransProteomicPipeline	O
.	O
</s>
<s>
Users	O
are	O
now	O
redirected	O
by	O
the	O
TPP	O
development	O
team	O
to	O
use	O
the	O
msConvert	B-Application
software	O
(	O
see	O
above	O
)	O
.	O
</s>
<s>
msConvert	B-Application
:	O
A	O
command	O
line	O
tool	O
converting	O
to/from	O
various	O
mass	O
spectrometry	O
formats	O
including	O
multiple	O
proprietary	O
formats	O
.	O
</s>
<s>
CompassXport	B-Application
,	O
Bruker	O
's	O
free	O
tool	O
generating	O
mzXML	B-Application
(	O
and	O
now	O
mzData	B-Application
)	O
files	O
for	O
many	O
of	O
their	O
native	O
file	O
formats	O
(	O
.baf	O
)	O
.	O
</s>
