utility data analysis tools file standard format · conversions of real data files using the...
TRANSCRIPT
De
sig
n a
nd
im
ple
menta
tio
ns o
f th
e n
ew
HU
PO
Pro
teo
mic
s S
tan
da
rds In
itia
tive
’s m
ass s
pe
ctr
om
ete
r o
utp
ut file
sta
nda
rd fo
rma
t: mzML 1.0
Eric W
Deuts
ch
1,
Pie
rre-A
lain
Bin
z2,
Darr
en K
essner3
, M
att C
ham
bers
4,
Luis
a M
onte
cchi-P
ala
zzi5
, Jim
Shofs
tahl6
, Josh T
asm
an
1,
Randall
K J
ulia
n7,
Fre
drik L
evander8
, P
uneet
Souda
9,
and L
ennart
Mart
ens
5
1In
stitu
te f
or
Syste
ms B
iolo
gy ,
Seatt
le, W
A;
2S
wis
s I
nstitu
te f
or
Bio
info
rmatics a
nd G
eneva B
ioin
form
atics,
Geneva,
Sw
itzerland;
3C
edars
-Sin
ai M
edic
al C
ente
r, L
os A
ngele
s,
CA
; 4
Vanderb
ilt U
niv
ers
ity,
Nashvill
ie,
TN
, 5
Euro
pean B
ioin
form
atics I
nstitu
te,
Hin
xto
n,
UK
,6
Therm
o F
isher,
San J
ose,
CA
, 7
Indig
o B
iosyste
ms,
Carm
el, I
N,
8Lund U
niv
ers
ity,
Lund,
Sw
eden,
9U
niv
ers
ity o
f C
alif
orn
ia L
os A
ngele
s,
Los A
ngele
s,
CA
Overv
iew
mzM
L is a
ne
w d
ata
form
at fo
r th
e s
tora
ge
and
exchan
ge
of
ma
ss s
pe
ctr
om
ete
r ou
tpu
t file
s.
It f
ollo
ws o
n t
he
su
cce
ssfu
l m
zX
ML
and
mzD
ata
fo
rma
ts.
mzM
L h
as b
een
de
sig
ned
by m
erg
ing t
he
be
st
aspe
cts
of
bo
th
pre
vio
us fo
rma
ts in
to a
sin
gle
un
ifie
d f
orm
at
tha
t is
in
tend
ed
to
rep
lace
all
ea
rlie
r fo
rma
ts.
Ve
rsio
n 1
.0.0
just
rele
ased
Accom
pa
nie
d b
y a
con
trolle
d v
ocab
ula
ry a
nd
sem
antic
va
lida
tio
n r
ule
s
Ma
ny im
ple
me
nta
tion
s o
f th
e fo
rma
t a
lre
ad
y e
xis
ts,
insu
ring
quic
k a
do
ptio
n o
f th
e fo
rma
t
De
ve
lop
ed
with
full
pa
rtic
ipa
tion
of a
cad
em
ic r
ese
arc
he
rs,
ha
rdw
are
and
so
ftw
are
ve
ndo
rs
Ve
nd
ors
ha
ve
co
mm
itte
d to
sup
po
rtin
g th
e n
ew
fo
rmat
on
ce
re
lease
d.
Fo
rmat
has b
ee
n t
este
d w
ith
se
ve
ral in
sta
nce
do
cu
men
ts
an
d m
an
y im
ple
me
nta
tion
s o
f th
e f
orm
at d
urin
g b
eta
testin
g
mzM
L is e
xp
ecte
d to
re
pla
ce
mzX
ML
an
d m
zD
ata
, b
ut n
ot
exp
ecte
d to
co
mple
tely
re
pla
ce
ve
nd
or
bin
ary
fo
rma
ts. H
isto
ry
mzM
L has been under
develo
pm
ent
for
two years
w
ith fu
ll part
icip
ation of
academ
ic re
searc
hers
, hard
ware
and soft
ware
vendors
. It w
as f
irst
conceiv
ed a
t th
e P
SI
meeting i
n 2
006,
two y
ears
aft
er
mzX
ML a
nd m
zD
ata
were
re
leased.
The o
rigin
al
work
ing n
am
e o
f data
XM
Lw
as c
hanged t
o t
he f
inal
mzM
L nam
e in
L
yon.
The f
orm
at
was subm
itte
d to
th
e P
SI
docum
ent
pro
cess i
n N
ovem
ber
2007 w
here
in i
t passed t
hro
ugh f
orm
al
inte
rnal
and t
hen c
om
munity r
evie
w.
Vers
ion 1
.0.0
of
the f
orm
at
was c
om
ple
ted just prior
to this
confe
rence.
mzD
ata
1.0
5
mzX
ML
3.0
mzM
L
0.9
0
SF
O
2006-0
5
data
XM
L
0.6
DC
2006-0
9
ISB
2006-1
1
Lyon
2007-0
4
EB
I
2007-0
6
mzM
L
0.9
1
PS
I D
oc P
roc
2007-1
1
mzM
L
0.9
9 R
C
Tole
do
2008-0
4
mzM
L
1.0
.0
Done!
2008-0
6
Earl
y D
evelo
pm
ent
Fin
al D
evelo
pm
ent
Schem
a O
utlin
e
The m
zM
L s
chem
a is d
esig
ned t
o c
onta
in a
ll th
e info
rmation f
or
asin
gle
MS
run,
inclu
din
g m
eta
data
abo
ut
the s
pectr
a p
lus a
ll
the s
pectr
a t
hem
selv
es,
either
in c
entr
oid
ed
(peak l
ist)
or
pro
file
mode.
The h
eader
at
the t
op o
f th
e f
ile e
ncodes i
nfo
rmation
about th
e s
ourc
e o
f th
e d
ata
as w
ell
as info
rmation
about th
e s
am
ple
, in
str
um
ent and s
oft
ware
that pro
cessed the d
ata
.
Sem
antic V
alid
ato
r
One o
f th
e b
enefits
of
the p
revio
us m
zD
ata
form
at
was i
ts c
onsid
era
ble
fle
xib
ility
in a
llow
ing w
rite
rs o
f th
e f
orm
at
to e
ncode
additio
nal
info
rmation r
ele
vant
to t
he s
pecific
instr
um
ent
or
setu
p,
even i
f it c
annot
be h
andle
d b
y a
ll soft
ware
. H
ow
ever,
this
consid
era
ble
fle
xib
ility
led t
o d
iffe
rent
dia
lects
as t
he s
am
e info
rmation c
ould
be e
ncoded in d
iffe
rent
wa
ys.
We h
ave s
olv
ed t
his
pro
ble
m w
ith the s
em
antic v
alid
ato
r to
ol fo
r m
zM
L.
The s
em
antic v
alid
ato
r can:
Pro
teoW
izard
Softw
are
Im
ple
menta
tions
The b
est
wa
y t
o t
est
a n
ew
form
at
is b
y i
mple
menting i
t in
soft
ware
. In
evitably
as a
form
at
is i
mple
mente
d,
one f
inds m
inor
inconsis
tencie
s o
r m
issin
g f
eatu
res.
The initia
l re
lease o
f m
zM
Lis
str
ength
ened b
y t
he b
readth
of
imple
menta
tions t
hat
alread
y
exis
t and h
ave e
xerc
ised the v
arious u
se c
ases:
Ensure
that
an m
zM
L d
ocum
ent
is w
ell
form
ed a
nd c
onfo
rms t
o t
he x
sd
XM
L s
chem
a
Ensure
that
contr
olle
d v
ocab
ula
ry t
erm
s a
re u
sed in t
he c
orr
ect
pla
ces in t
he d
ocum
ent
Allo
w a
ltern
ate
rule
s b
ased o
n t
he
type o
f d
ata
bein
g w
ritt
en
Allo
w d
iffe
rent
levels
of
com
plia
nce (
e.g
., b
asic
mzM
L,
MIA
PE
-MS
com
plia
nt m
zM
L)
Sem
antic r
ule
s c
an b
e u
pdate
d a
long w
ith t
he c
ontr
olle
d v
ocab
ula
ry w
ith
out
cha
ngin
g
the s
chem
a
Availa
ble
as a
web p
age (
see b
elo
w)
or
as a
sta
nd
alo
ne t
ool
Conclu
sio
ns
The m
zM
L f
orm
at
is n
ow
com
ple
te a
nd m
zM
L 1
.0.0
is r
ele
ased.
We e
ncoura
ge a
ll auth
ors
and v
endors
to b
egin
support
ing t
his
new
fo
rmat
in new
and update
d soft
ware
. T
he fo
rmat
inclu
des th
e best
featu
res fr
om
pre
-exis
ting open fo
rmats
and has
additio
nal support
for
chro
mato
gra
ms a
nd s
om
e o
ther
featu
res d
eem
ed h
ighly
de
sirable
.
It i
s e
xpecte
d t
hat
the s
chem
a w
ill r
em
ain
sta
ble
for
at
least
ayear,
hopefu
lly m
ore
. H
ow
ever,
the c
ontr
olle
d v
ocabula
ry a
nd
sem
antic v
alid
ation r
ule
s w
ill c
ontinue to b
e u
pdate
d a
nd r
efined a
s a
ll auth
ors
and v
endors
fin
ish im
ple
menting t
heir s
oft
ware
for
mzM
L.
To
le
arn
more
, se
e th
e m
zM
L D
eve
lopm
en
t P
ag
e:
The m
zM
L e
ffort
has involv
ed m
an
y p
eople
in the P
SI
and in the c
om
munity. W
e g
rate
fully
acknow
ledge th
e c
ontr
ibutions o
f:
Ja
ri H
äkkin
en
(Lu
nd
)
Bri
an
Pra
tt (
Insili
co
s)
Eri
k N
ilsso
n (
Insili
cos)
Mik
e C
ole
ma
n (
Sto
we
rs)
Lu
is M
en
do
za
(IS
B)
Da
vid
Sh
teynb
erg
(IS
B)
La
rs N
ilse
(M
an
ch
este
r)
Be
nito
Ca
ña
s (
Ma
dri
d)
Lo
la G
utie
rre
z (
Ma
dri
d)
Alb
ert
o M
ed
ina
(M
ad
rid
)
Tri
sh
Whe
zte
l (U
Pen
n)
Eva
Du
ch
osla
v (
MD
S S
cie
x)
He
nn
ing
He
rmja
kob
(E
BI)
An
ge
l P
iza
rro
(U
Pe
nn
)
Ph
il Jo
ne
s (
EB
I)
Jim
my E
ng
(U
Wash
ing
ton
)
Ke
nt
La
urs
en
(In
dig
o)
Sa
nd
ra O
rch
ard
(E
BI)
Ch
ris T
aylo
r (E
BI)
Pa
tric
k P
ed
rioli
(ET
HZ
)
Se
an
Se
ym
ou
r (A
BI)
Da
vid
Cre
asy (
Ma
trix
Scie
nce
)
Ho
wa
rd R
ea
d (
Wate
rs)
Jim
Lan
grid
ge
(W
ate
rs)
Ja
yson
Falk
ne
r (U
Mic
hig
an
)
Da
vid
Ho
rn (
Ag
ilen
t)
Ru
th M
cN
ally
(C
ard
iff)
Ro
n B
ea
vis
(U
BC
)
No
rma
n P
ato
n (
Ma
nch
este
r)
Ru
ed
i A
eb
ers
old
(E
TH
Z)
Ma
rc S
turm
(U
Tu
eb
ing
en
)
Pa
rag
Ma
llick (
CS
HS
)
Ru
ne
Philo
so
f
Da
vid
Sp
ark
ma
n (
U P
acific
)
Wilf
red
Ta
ng
(A
BI)
Ma
riu
s K
allh
ard
t (B
ruke
r)
PS
I S
tee
rin
g G
rou
p
PS
I P
art
icip
an
ts
htt
p://p
sid
ev.info
/index.p
hp?q=node/2
57
proprietary
format
mass
spectrometer B
mass
spectrometer A
converter
mzXML
mzData
mzML
search
engine A
search
engine B
Native format
pepXML
analysisXML
Public repository
mzM
L is a
com
mon o
pen form
at to
record
the o
utp
ut of m
ass s
pectr
om
ete
rs p
rior
to d
ata
base s
earc
hin
g o
r oth
er
dow
nstr
eam
pro
cessin
g o
f th
e s
pectr
a. It is
expecte
d that by 2
009:
Instr
um
en
t ve
nd
ors
will
wri
te o
ut
or
co
nve
rt t
o m
zM
L
Se
arc
h e
ng
ine
s o
r o
the
r sp
ectr
um
pro
ce
ssin
g
so
ftw
are
will
rea
d a
nd
pro
ce
ss m
zM
L
Da
ta r
ep
osito
rie
s w
ill a
ccep
t, p
rocess, a
nd
sto
re
mzM
L d
ocu
men
ts
Natively
mass s
pectr
om
ete
rs s
tore
outp
ut
in a
variety
of
pro
prieta
ry f
orm
ats
•H
inders
data
sharin
g
•M
akes w
riting v
en
dor-
ne
utr
al softw
are
difficult
Solu
tion:
de
velo
p a
ve
nd
or-
neutr
al ope
n f
orm
at
•th
at
all
vend
or
soft
ware
can w
rite
•ven
dor-
ne
utr
al soft
ware
can r
ead a
nd w
rite
Contr
olle
d V
ocabula
ry
Much o
f th
e m
eta
data
encoded in t
he m
zM
L is in t
he f
orm
of
cvP
ara
ms,
an X
ML e
lem
ent
that
pro
vid
es a
refe
rence t
o a
specific
concept
within
the P
SI
MS
contr
olle
d v
ocabula
ry.
Ea
ch t
erm
has a
n e
xplic
it a
nd d
eta
iled d
efinitio
n,
an
d m
ay h
ave i
nfo
rmation
about
its d
ata
type a
nd w
ha
t kin
d o
f units it
requires,
if a
ny.
The c
ontr
olle
d v
ocabula
ry is e
dited in
OB
O f
orm
at
with t
he O
BO
-Edit
soft
ware
and i
s r
ead i
n b
y m
ost
readers
and w
rite
rs o
f m
zM
L.
The
contr
olle
d v
ocabula
ry c
an b
e e
asily
ad
juste
d a
nd e
xte
nded
without m
odifyin
g the s
chem
a.
Exam
ple
Insta
nce D
ocum
ents
In o
rder
to e
xerc
ise the s
chem
a a
nd d
em
onstr
ate
that th
e v
arious
use c
ases h
ave b
een a
dequate
ly m
odele
d, w
e h
ave d
evelo
ped
severa
l exam
ple
insta
nce d
ocum
ents
. S
om
e o
f th
e d
ocum
ents
are
hand-c
rafted w
ith a
n o
rdin
ary
editor,
wh
ile o
thers
are
written
out
as a soft
ware
te
st
as part
of
the P
rote
oW
izard
refe
rence im
ple
menta
tion.
In additio
n,
severa
l in
sta
nce docum
ents
are
convers
ions o
f re
al data
file
s u
sin
g the r
efe
rence o
r oth
er
imple
menta
tions o
f convert
ers
.
Docum
enta
tion
The f
ull
specific
ation o
f th
e f
orm
at
is p
resente
d i
n a
specific
ation d
ocum
ent
that
described v
arious
aspects
of
the f
orm
at
as w
ell
as a
ll deta
ils o
f th
e f
orm
at
ele
ments
. H
TM
L a
nd P
DF
docum
enta
tion
are
genera
ted
by
pro
gra
mm
atically
com
bin
ing
4
diffe
rent
com
ponents
: xsd
schem
a,
contr
olle
d
vocabula
ry, sem
antic v
alid
ation m
appin
g file
, exam
ple
docum
ents
.
Pro
teoW
izard
C+
+ lib
rary
refe
rence im
ple
menta
tion:
reads m
zM
L a
nd w
rite
s m
zM
L.
Can c
onvert
mzX
ML a
nd R
AW
to m
zM
L.
RA
MP
(R
andom
Access M
inim
al P
ars
er)
C lib
rary
can r
ea
d m
zM
L, m
zX
ML,
mzD
ata
file
s v
ia s
am
e A
PI.
mzM
L r
eadin
g p
erf
orm
ed w
ith P
rote
oW
izard
Tra
ns P
rote
om
ic P
ipelin
e (
TP
P)
can r
ead a
nd p
rocess d
ata
in m
zM
Lfo
rmat
via
RA
MP
ISB
form
at convert
ers
: R
eA
dW
(Therm
o),
Wolf (
Wate
rs),
mzW
iff(A
BI/
MD
S),
Tra
pper
(Agile
nt)
Therm
o F
isher
beta
RA
W →
mzM
L c
onvert
er
Sem
antic V
alid
ato
r an
d J
ava lib
rary
reads a
nd v
alid
ate
s t
hat
a d
ocum
ent is
sem
antically
corr
ect
Phen
yx
searc
h e
ngin
e c
an r
ea
d a
nd s
earc
h s
pectr
a in m
zM
L f
orm
at
NC
BI
C+
+ m
zM
L r
ead
er
cla
sses
Insili
cos V
iew
er
–file
bro
wser
and
spectr
um
vie
wer
can r
ead a
nd d
ispla
y s
pectr
a f
rom
mzM
L, m
zX
ML,
mzD
ata
, R
AW
form
ats
SeeM
Sfile
bro
wser,
spectr
um
vie
wer,
chro
mato
gra
m v
iew
er,
ann
ota
ter
for
mzM
L, m
zX
ML
Pro
teio
sS
oft
ware
En
vironm
ent
inclu
des c
onvert
ers
for
peak lis
ts o
f various f
orm
ats
to m
zM
L a
nd p
erf
orm
s r
eadin
g o
f m
zM
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iles
InS
ilicoS
pectr
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n s
ourc
e lib
rary
(P
erl)
has a
spectr
um
file
form
at convers
ion t
ool th
at
reads m
zM
L
Herm
es m
zM
L ↔
mzD
ata
↔m
zX
ML c
onvert
er
(Java)
Onlin
e valid
ato
r at
the P
roD
aC
site allo
ws
an
yone
to
uplo
ad
any
file
and
perf
orm
sem
antic v
alid
ation o
n a
ny m
zM
L f
ile
A
dow
nlo
adable
vers
ion
of
the
sem
antic
valid
ato
r ca
n
be
run
locally
on
an
y
pla
tform
support
ing J
ava to v
alid
ate
file
s w
ithout needin
g t
o tra
nsm
it them
to a
rem
ote
web s
ite.
On-lin
e v
alidato
r
Local validato
r
New
term
requests
may b
e e
maile
d t
o:
psid
ev-m
s-v
ocab@
lists
.sourc
efo
rge.n
et
Sem
antic v
alidato
r: c
oncept
Onto
log
y A
ccess
com
pone
nt
Valid
ato
r la
yer
Actu
al valid
ato
r im
ple
menta
tion
CV
rule
read
er
com
pone
nt
OLS
–htt
p:/
/ww
w.e
bi.ac.u
k/o
ls
OB
O f
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ath
based
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de
xer
com
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XM
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ile t
o v
alid
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Onto
log
y c
onfig
file
Obje
ctr
ule
sfile
Seman
tically
correc
tfile
Sem
antic
ally
inco
rrec
t file
OB
O-E
dit is
used to
m
ain
tain
th
e contr
olle
d vocabula
ry:
org
aniz
e the s
tructu
re, add n
ew
term
s, update
defin
itio
ns.
The c
ontr
olle
d v
ocabula
ry i
s e
asily
pars
ed b
y s
oft
ware
, such
as r
eader
and w
rite
r soft
ware
, as w
ell
as c
entr
al
vocabula
ry
serv
ices, lik
e the O
nto
log
y L
ookup S
erv
ice w
eb s
ite
.
Main
tenance o
n m
zM
L w
ill c
ontinue
with the P
SI M
ass S
pectr
om
etr
y
Sta
ndard
s W
ork
ing G
roup. It is
expecte
d that th
e s
chem
a w
ill r
em
ain
sta
ble
, but m
inor
update
s to the
contr
olle
d v
ocabula
ry a
nd s
em
antic
valid
ation r
ule
s m
ay b
e n
ecessary
.
mzM
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run
spectr
um
spectr
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Description
bin
ary
Data
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bin
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m
chro
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m
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Data
Arr
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bin
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Data
Arr
ay
Each s
pectr
um
conta
ins a
header
with s
can info
rmation
and o
ptionally
pre
curs
or
info
rmation, fo
llow
ed b
y t
wo o
r
more
base64-e
ncoded b
inary
data
arr
ays.
Chro
mato
gra
ms m
ay b
e e
ncoded in m
zM
L in a
specia
l
ele
ment th
at conta
ins o
ne o
r m
ore
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to d
escri
be
the t
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f chro
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m, fo
llow
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wo b
ase64-
encoded b
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data
arr
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mzM
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ay b
e e
nclo
sed in a
specia
l in
dexin
g w
rapper
schem
a to a
llow
random
access into
the file
, allo
win
g
soft
ware
to p
ull
out one o
r m
ore
arb
itra
ry s
pectr
a.
C+
+ lib
rary
, w
ith m
odula
r desig
n f
or
testa
bili
ty a
nd e
xte
nsib
ility
build
s w
ith n
ative c
om
pile
rs o
n a
ll m
ajo
r pla
tform
s (
MS
VC
on W
indow
s,
gcc
on L
inu
x,
XC
od
eon O
SX
)
ope
n s
ourc
e lic
ense s
uitable
for
both
acad
em
ic a
nd c
om
merc
ial pro
jects
(A
pache v
2)
inte
rnal d
ata
model is
a o
ne-t
o-o
ne t
ransla
tion o
f m
zM
L d
ata
ele
ments
to C
++
data
str
uctu
res
plu
g-in R
ead
er
inte
rface f
or
rea
din
g o
f both
op
en a
nd v
end
or
pro
prie
tary
data
form
ats
: m
zX
ML,
Therm
o R
AW
, M
GF
, w
ith m
ore
Read
ers
in d
evelo
pm
ent
msconvert
tool pro
vid
es g
enera
l file
form
at convers
ion,
inclu
din
g n
ative c
entr
oid
ing
an
d z
libcom
pre
ssio
n
SeeMS
and mspicture
vis
ualiz
ation t
ools
allo
ws v
isualiz
ation o
f m
ass s
pec d
ata
used b
y R
AM
P a
nd T
PP
for
mzM
L s
upp
ort
CLI
bin
din
g a
llow
s u
se f
rom
.N
ET
lang
ua
ges (
C+
+/C
LI, C
#,
VB
.NE
T);
SW
IG b
indin
gs f
or
scripting (
from
Java,
Pyth
on,
Perl,
R)
in d
evelo
pm
ent.
an "
Applic
ation N
ote
" d
escribin
g P
rote
oW
izard
has b
een a
ccepte
d f
or
public
ation b
y t
he journ
al B
ioin
form
atics
http://p
rote
ow
izard
.sourc
efo
rge.n
et
--develo
per
contr
ibutions a
re w
elc
om
e!
The P
rote
oW
izard
soft
ware
pro
ject, in
itia
ted b
y th
e S
pie
lberg
F
am
ily C
ente
r fo
r A
pplie
d P
rote
om
ics at
the C
edars
-Sin
ai
Medic
al
Cente
r, p
rovid
es a
modula
r and e
xte
nsib
le s
et
of
op
en-s
ourc
e,
cro
ss-p
latform
tools
and l
ibra
ries.
The
tools
perf
orm
pro
teom
ics d
ata
analy
ses;
the l
ibra
ries e
nable
rapid
too
l cre
ation b
y p
rovid
ing a
robust, p
luggable
develo
pm
ent
fram
ew
ork
that
sim
plif
ies a
nd u
nifie
s
data
file
access,
and p
erf
orm
s s
tandard
chem
istr
y a
nd
LC
MS
data
set
com
puta
tions.
During t
he f
inal
sta
ges o
f m
zM
L d
evelo
pm
ent,
refinem
ent, a
nd testing, th
e P
rote
oW
izard
libra
ry h
as p
rovid
ed the testing a
nd r
efe
rence im
ple
menta
tion
of m
zM
L.
analy
sis
pe
ak
de
tectio
n 1
pre
pro
ce
ssin
g
tools
Se
eM
Sm
sco
nve
rt
data
da
ta
str
uctu
res
da
ta f
orm
at
ab
str
actio
n
utility
ma
thp
ars
ing
en
co
din
gte
stin
g
da
ta
extr
actio
np
ea
k
de
tectio
n 2
msa
cce
ss
msp
ictu
re
Hig
h le
vel a
rch
itec
ture
of
Pro
teo
Wiz
ard
Hyperl
inks
to
various
exam
ple
docum
ents
on
the
mzM
L d
eve
lopm
ent w
eb s
ite.
A s
am
ple
snip
pet
of
an e
xam
ple
mzM
L d
ocum
ent, s
how
ing
the top h
eader
port
ion o
f th
e f
ile.
Part
of
the
HT
ML
docum
enta
tion
page
for
mzM
L,
show
ing
the
availa
ble
docum
enta
tion for
the <
sourc
eF
ile>
ele
men
t.
Title
page
of
the
full
mzM
L
Specific
ation D
ocum
ent
Na
tive
IDre
fere
nces b
ack t
o the
ori
gin
al sca
n r
efe
ren
ce
s in
th
e
so
urc
e d
ata