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Page 1

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

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