MaxQuant

A brief introduction and Users guide

Protein

Peptide

Parent mass

Daughter masses

=

Peptide Sequence

Work Flow of the program

QuantQuant

QuantQuant

QuantQuant

Mascot DaemonMascot Daemon

.par file

.msm file

Mascot DaemonMascot Daemon

Mascot DaemonMascot Daemonhttp://mascot.proteomics.dundee.ac.uk/cgi/master_results.pl?file=../data/20090210/F030383.dat

http://mascot.proteomics.dundee.ac.uk/data/20090210/F030383.dat

IdentifyIdentifyOriginal .raw files

Generated .dat files

IdentifyIdentify

Peptide selection

All Peptides- as it suggests it identifies proteins using all peptides.

Unique Peptides- uses peptides which are not common in more than one protein.

Razor and Unique peptides-

Ockham's Razor theory: “the explanation of any phenomenon should make as few

assumptions as possible, eliminating those that make no difference in the observable

predictions of the explanatory hypothesis or theory.” Searches all peptides, noting which ones occur in more than one protein- and

suggests the most likely protein that peptides came from and uses that protein

for quantification calculations.

ResultsResults

Making sense of it all!Making sense of it all!A couple of pointers to stop you feeling over-whelmed:

•Keep in mind the group of proteins you are interested in (i.e. kinases, chromatin binding proteins etc.)

•Remember your high school statistics- p values of >0.05 are statistically insignificant etc. This may cut down the information

some what

•Less than 2 peptides used to Identify a protein should be approached with caution.

•Graphing values of interest and noting trends may clarify the situation in a global analysis.

Normalised Ratios (SILAC triple labeling)

0

10

20

30

40

50

60

70

Cofilin

-1;Cofi

lin, n

on-m

uscle

isofo

rm;18

kDa p

hosp

hopro

tein;p

18

Thior

edox

in;Trx;

ATL-de

rived

facto

r;ADF;S

urfac

e-ass

ociat

ed su

lphyd

ryl pr

otein;

SASP;Thio...

Galecti

n-1;Le

ctin g

alacto

side-b

inding

solub

le 1;B

eta-ga

lactos

ide-bi

nding

lecti

n L-14

-I;Lac

t...

Small nu

clear

ribon

ucleo

prote in

Sm D1;s

nRNP co

re pro

tein D

1;Sm-D

1;Sm-D

autoa

ntige

n

Destrin

;Actin-d

epoly

merizin

g fac

tor;A

DF

Filamin-

A;Alpha-f

i lamin;

Filamin-

1;End

otheli

al ac

tin-bi

nding

prote

in;Acti

n-bind

ing pr

otein

2...

Uncha

racter

ized p

rotein

ENSP00

0003

47049

;HCG20

0459

3;60S

ribos

omal p

rotein

L17;L

2...

Uncha

racter

ized p

rotein

RPL3

0;60S

ribos

omal

protei

n L30

Clathri

n hea

vy ch

ain 1;

CLH-17

BolA-lik

e prot

ein 2

Tropom

yosin

alph

a-3 ch

ain;Trop

omyo

sin-3;

Tropo

myosin

gamma;h

TM5;T

ropom

yosin

3;T...

Fatty

acid

synth

ase;[

Acyl-c

arrier

-prote

in] S-ac

etyltran

sferas

e;[Acy

l-carr

ier-pr

otein]

S-m

alon..

.

Small nu

clear

ribon

ucleo

protein

Sm D3;s

nRNP co

re pro

tein D

3;Sm-D

3

6-pho

spho

fructo

kinas

e typ

e C;P

hosp

hofru

ctokin

ase 1

;Pho

spho

hexo

kinas

e;Pho

spho

fructo

...

Smal l nu

clear

ribon

ucleo

protei

n G;sn

RNP-G;Sm pr

otein

G;Sm-G

;SmG

Nucleo

side d

iphos

phate

kina

se;N

ucleo

side d

iphos

phate

kina

se B

;NDK B;

NDP kina

se B;...

Protei

n S10

0-A6;S

100 c

alcium

-bind

ing pr

otein

A6;Calc

yclin;

Prolac

tin re

cepto

r-ass

ociated

...

ADP/ATP tra

nsloc

ase 1

;Adenin

e nuc

leotid

e tran

sloca

tor 1;

ANT 1;ADP,ATP

carrie

r prot

ein...

Profilin

-2;Prof

ilin II

Protein

RCC2;Telo

phas

e disk

prote

in of

60 kD

a;RCC1-l

ike pr

otein

TD-60

Elong

ation

facto

r 2;EF-2

60S rib

osom

al pro

tein L

19

Ketosa

mine-3-

kinas

e;Fruc

tosam

ine-3-

kinas

e-rela

ted pr

otein

Heat sh

ock c

ogna

te 71

kDa p

rotein

;Hea

t sho

ck 70

kDa p

rotein

8;Hea

t sho

ck 70

kDa p

rotein

..

Riboso

mal pro

tein L1

0;60S

ribos

omal

protei

n L10

;QM pr

otein;

Tumor

supp

resso

r QM;La

min..

40S rib

osom

al pro

tein S

9;RPS9 p

rotein

Crk-lik

e prot

ein

Protein

argin

ine N-m

ethylt

ransfe

rase 5

;Shk

1 kina

se-bi

nding

prote

in 1 h

omolo

g;SKB1Hs;J

...

40S rib

osom

al pro

tein S

11

Glutath

ione S

-tran

sferas

e Mu 3

;GST

M3-3;G

ST clas

s-mu 3

;hGSTM

3-3;B

rain ty

pe m

u-glut

a...

Pheny

lalany

l-tRNA sy

ntheta

se al

pha c

hain;

Pheny

lalan

ine-- t

RNA ligas

e alph

a cha

in;Phe

R...

Probab

le ub

iquitin

carbo

xyl-te

rmina

l hyd

rolas

e FAF-X

;Ubiq

uitin

thioe

steras

e FAF-X;U

biquit

...

Kerat

in, ty

pe I c

ytosk

eletal

17;Cyto

kerat

in-17

;CK-17

;Keratin

-17;K1

7;39.1

;Unc

harac

terize

d ...

40S rib

osom

al pro

tein S

6;Pho

spho

protei

n NP33

;Ribo

somal

protei

n S6;Ribo

somal

protei

n S..

Keratin

, type

II cy

toske

letal

8;Cyto

kerat

in-8;C

K-8;Kera

tin-8;

K8

Tubu

lin be

ta-2C

chain

;Tubuli

n beta

-2 ch

ain;cD

NA FLJ7

7784

;HCG1983

504,

isofor

m CRA_f

Gem-as

socia

ted pr

otein

5;Gem

in5

Tubu

lin al

pha-4

A chain

;Tubulin

alph

a-1 ch

ain;A

lpha-t

ubuli

n 1;Tes

tis-sp

ecific

alph

a-tub

ulin..

.Vim

entin

Surviva

l moto

r neuro

n prot

ein;C

ompo

nent

of ge

ms 1;G

emin-

1

Gem-as

socia

ted pr

otein

7;Gem

in-7;S

IP3

Probab

le ATP

-depe

nden

t RNA he

licase

DDX20

;DEAD box p

rotein

20;D

EAD box p

rotein

..

Gem-as

socia

ted pr

otein

8;Prot

ein FAM

51A1

Proteins

Ratio

Ratio M/L NormalizedRatio H/L NormalizedRatio H/M Normalized

Peptide Statistics (Unique/Razor)

0

1

2

3

4

5

6

7

8

40S rib

osom

al prot

ein S11

40S rib

osom

al prot

ein S14

40S rib

osom

al prot

e in S15

a40

S ribos

omal

protein

S23

40S rib

osom

al prot

e in S26

;40S rib

osom

al pro

tein..

40S rib

osom

al prot

e in S3a

;Unc

haracte

rized

prote

40S rib

osom

al prot

ein S6;P

hosp

hopro

tein N

P33;.

40S rib

osom

al prot

e in S9;R

PS9 prot

e in60

S ribos

omal

protein

L19

60S rib

osom

al prot

e in L2

7a

Protein Name

Num

ber o

f Pep

tides

Peptides (seq)Peptides (seq/mod/labels)Razor Peptides (seq/mod/labels)Unique Peptides (seq/mod/labels)