MIAPEs in ProteoRed Multicentric Experiments

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MIAPEs in ProteoRed
Multicentric

Experiments

1
st

Session:
MultiCenter

Projects. Collaborative environment



Salvador Martínez de Bartolomé

Bioinformatics

working

group

-

ProteoRed

National

Center
for

Biotechnology



CSIC

Madrid
-

Spain

Overview


Introduction


What is MIAPE?


Why is MIAPE important for you?


MIAPE generator tool


ProteoRed
Multicentric

Experiments (PME)


Overview


Introduction


What is MIAPE?


Why is MIAPE important for you?


MIAPE generator tool


ProteoRed
Multicentric

Experiments (PME)


Need of standards in Proteomics


No
standardized reporting
,
not standard database
submission



Proteomics data is generated at a high rate, and lost at a
high rate



Experiments are repeated unnecessarily, the
field
advances
slower than necessary

HUPO PSI



Open community initiative




Involve
data producers, database providers, software
producers, publishers

Proteomics Standards
Initiative

http://psidev.info

The Proteomics Standards Initiative (PSI) aims to define
community standards for data representation in proteomics
and to facilitate data comparison, exchange and verification


Proteomics

2003,

3

(7): The proteomics standards initiative.

Orchard,S.

,

Hermjakob,H.

,

Apweiler,R.


HUPO PSI

Proteomics Standards
Initiative

http://www.psidev.info

HUPO
-
PSI

PSI deliverables



Formats to store proteomics data



Controlled Vocabularies



MIAPE
documents

HUPO
-
PSI

PSI deliverables



Formats to store proteomics data



Controlled Vocabularies



MIAPE
documents

Overview


Introduction


What is MIAPE?


Why is MIAPE important for you?


MIAPE generator tool


ProteoRed
Multicentric

Experiments (PME)


Sufficiency and practicability


• Unambiguous description of the
experimental context

• Allow
understanding

of the results and their interpretation

• Sufficient to permit a
critical evaluation

• In principle allow
recreation of the work

MIAPE:
M
inimum
I
nformation
A
bout a
P
roteomics
E
xperiment

Taylor, C.F., Paton, N.W., Lilley, K.S., Binz, P.A., Julian, R.K., Jr., Jones, A.R., Zhu, W., Apweiler, R., Aebersold, R., De
uts
ch,
E.W., Dunn, M.J., Heck, A.J., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T.A., Patterson, S.D., Ping, P., Seymou
r,
S.L., Souda, P., Tsugita, A., Vandekerckhove, J., Vondriska, T.M., Whitelegge, J.P., Wilkins, M.R., Xenarios, I., Yates, J.R.
, 3
rd
and Hermjakob, H. (2007)

The minimum information about a proteomics experiment (MIAPE).

Nat Biotechnol
25: 887
-
893.





It is:



Describing a list of information and data to
provide when an experiment is reported (it is a
content descriptor
)


Peptide
sequence
, scores, modifications, mass
errors
, etc.




Helping to assess
quality control


Number of replicates, expected error rate

MIAPE

guidelines

P.A Binz


It is not:



Describing
the way to run an experiment

• does not specify the use of a search engine in particular

• does not force the use of one
protocol




Describing the
data representation

• Use excel to create a table with these five following columns
:…




Including any
quality
judgment

• need 30% sequence coverage to identify a protein

• “The absence of thorough validation of both analytical and
biological results, including error analysis should result in rejection”

• “Authors should justify the use of a very small database or
database that excludes common contaminants, since this may
generate misleading assignments”

MIAPE

guidelines

P.A Binz



MIAPE Gel Electrophoresis (GE) v1.4



MIAPE Gel Informatics (GI)
v1.0



MIAPE Mass Spectrometry (MS)
v2.24



MIAPE Mass Spectrometry Informatics (MSI)
v1.1



MIAPE Column Chromatography (CC) v1.0



MIAPE Capillary Electrophoresis (CE)
v1.0



MIAPE Sample Preparation and handling (SP) v0.2



MIAPE Molecular Interactions (MI)
v1.1.2



MIASSPE Sample Preparation for
Phosphoproteomics

Experiments (v0.91)

Overview


Introduction


What is MIAPE?


Why is MIAPE important for you?


MIAPE generator tool


ProteoRed
Multicentric

Experiments (PME)



Editors from the main proteomics journals are now interested
in the acceptance of common MIAPE guidelines, as recently
discussed in the last HUPO Joint PSI/Publication
Committees:


Second Joint HUPO publication and Proteomics Standards
Initiative workshop.
Orchard S, Binz PA, Hermjakob H.
Proteomics. 2009 Oct;9(19):4426
-
8.



Once these formatting problems are solved, journal submission

guidelines for proteomics data are expected to become similar for all

journals
.

Tutorial for Proteomics
DataSubmission
.

Molecullar

and Cellular Proteomics.

MIAPE importance

MIAPE importance


MIAPE and journals:


It is recommended to follow MIAPE guidelines in the
most important proteomics journals:


Proteomics
(
Wiley

InterScience
)


Journal of Proteomics
(
Elsevier
),


Molecular and Cellular Proteomics,


Nature Biotechnology,


Journal of Proteomics Research
(ACS
Publications
)


Journal of Proteomics and Bioinformatics
(OMICS publishing group)

Provision of information according to the more detailed “
Minimum Information
About a Proteomics Experiment”
recommendations
(
http://www.psidev.info/MIAPE) is encouraged
.

Instructions to authors

Proteomics
(
Wiley

InterScience
)

MIAPE importance


MIAPE and journals:


In a short term, it is expected to be mandatory to follow
MIAPE guidelines for publishing proteomics
experiments.

Overview


Introduction


What is MIAPE?


Why is MIAPE important for you?


MIAPE generator tool


ProteoRed
Multicentric

Experiments (PME)


MIAPE generator tool

Semi
-
automatic

tool

to

describe,
store

and compare
proteomics

experiments

based

on

MIAPE
compliant

reports
.

Martínez
-
Bartolomé, S., Medina
-
Aunon
, J.A., Jones, A.R., Albar, J.P.

Proteomics
. 2010
Jan

13. [
Epub

ahead

of
print
]

Aim:


Implement a tool to
make easy writing MIAPE compliant reports
.


The tool serves also as a
MIAPE repository




Allows to generate:


MIAPE Gel Electrophoresis,


MIAPE Gel Informatics,


MIAPE Mass Spectrometry and


MIAPE Mass Spectrometry Informatics documents





It is publicly available for scientific community:

http://
www.proteored.org/MIAPEtool.asp



MIAPE generator tool

http://www.proteored.org

http://
www.proteored.org/MIAPEtool.asp

MIAPE generator tool

MIAPE
Reports

Generate XML

Generate report

Delete document

Edit document

Dynamic improvement

Users get lost in the document





Navigation tree


A way to compare MIAPE documents





MIAPE comparator tool


A way to share MIAPE documents





Sharing documents and projects


Comparing

experiments

with

the

MIAPE
generator

tool

Last improvements

MIAPE generator tool



Controlled vocabulary mapping to MIAPE
information

100173

TOF

T.O.F.

time of flight

time
-
of
-
flight

Controlled Vocabularies (CVs) in MIAPE
information

What is a CV?

Last improvements

MIAPE generator tool



Controlled vocabulary mapping to MIAPE
information

Avoid heterogeneity in the stored MIAPE information

Allow the mapping of MIAPE information to standard XML
files

Controlled

Vocabularies

(
CVs
) in MIAPE
information

Controlled

Vocabularies

(
CVs
) in MIAPE
information

Controlled Vocabularies (CVs) in MIAPE
information

Controlled Vocabularies (CVs) in MIAPE
information

Controlled Vocabularies (CVs) in MIAPE
information

Controlled Vocabularies (CVs) in MIAPE
information

Controlled

Vocabularies

(
CVs
) in MIAPE
information

All information stored in the database is already mapped
(as possible) to the

HUPO
-
PSI ontologies (mainly SEP and MS)

gif

CV: sep:00049

DB

preferred

name
:
graphics

interchange

format


exact

synonym
:
gif

definition
:
A graphics interchange format is an image file format that supports
animated images. Supports only 255 colors per frame, so requires
lossy

quantization for
full
-
color photos (dithering); using multiple frames can improve color precision.

User
interface

database

GIF

Imagen gif

gif format

.gif

Last improvements

MIAPE generator tool



Controlled vocabulary mapping to MIAPE
information



Validation of MIAPE Gel Electrophoresis
information for
GelML

requirements.

The Gel electrophoresis
Markup

language (
GelML
) from the
Proteomics Standards
Initiative.

Frank Gibson F., Christine
Hoogland
, Salvador Martinez
-
Bartolomé, J.
Alberto Medina
-
Aunon

JA, Juan Pablo Albar,
Gyorgy

Babnigg
, Anil
Wipat
,
Norman W
Paton and
Andrew R
Jones
.

Proteomics.
Submited
.



MIAPE GE to
GelML

export.

Validation of MIAPE Gel Electrophoresis for
GelML

requirements

conversor

Last improvements

MIAPE generator tool



Controlled vocabulary mapping to MIAPE
information



Validation of MIAPE Gel Electrophoresis for
GelML

requirements.



Validation of MIAPE Gel Electrophoresis for
GelML

requirements.



MIAPE GE to
GelML

export.



MIAPE API: automation for MIAPE generation
comes!!!

MIAPE API

Automation for MIAPE generation comes!!!

Standard
XML file

MIAPE DB

PRIDE XML

mzML

mzIdentML

gelML

Emilio Salazar’s talk:

New improvements in MIAPE
generation: MIAPE API.
At
11:45




Overview


Introduction


What is MIAPE?


Why is MIAPE important for you?


MIAPE generator tool


ProteoRed
Multicentric

Experiments (PME)


2006:
PME1. Test 2DE Electrophoresis study (November 2006)


2007:
PME2 & 3. PMF & 2DE study (MIAPEs) (October 2007)


2008:
PME4. 2DE differential proteomic reproducibility study (Sept
-
Oct 2008)


2009
-
2010:
PME5
.
Quantitative

Proteomics

Methods

(
Nov

2009
-
Feb 2010)


ProteoRed
Multicentric

Experiments (PME)


From

2006
to

2010

Participations in ABRF
sPRG

studies

MIAPEs

in PME2,3

October

(2007)

Public

available

in
project


ProteoRed
multicenter

assays

2007
” ID: 277

6 MIAPE GE

6 MIAPE GI

4 MIAPE MS

4 MIAPE MSI

20 MIAPE
were

generated

from

6
experiments


Others

were

documented

in
excel

spreadsheets

MIAPEs

in PME4

October

(
2008)

Public

available

in
project


ProteoRed
multicenter

assays

2008
” ID: 286

14 MIAPE GE

16 MIAPE GI

22 MIAPE MS

20 MIAPE MSI

72 MIAPE
were

generated

from

18
experiments


Online MIAPE questionnaire

http://
www.proteored.org/MIAPE_Survey_Results_Nov08.html

In November 2008, before the presentation of the results of the ProteoRed
Multicenter Experiment 2008 (PME4), we elaborated this survey in order to
evaluate two aspects:











-

the MIAPE generator tool







-

the MIAPE guidelines











The survey was completed by 31 proteomic experts from 17 Proteomics
facilities:





Bilbao: CIC
BioGune
, UPV







Pamplona: CIMA







Valencia: CIPF, UV







Madrid: CNB, CBM, PCMUCM







Barcelona: HUVH, CSICUAB, PCB, UPF, IBBUAB, UB





Alicante: UA







La Coruña: INIBIC







Geneva: SIB

1

Yes: 95%

No: 5%

2

3

MIAPEs

in PME5

March

(2010)

Public

available

in
project


ProteoRed
multicenter

assays

2010
” ID: 364

3 MIAPE GE

3 MIAPE GI

21 MIAPE MS

18 MIAPE MSI

53 MIAPE
have

been

generated

from

18
experiments




Raw

data and
peak

lists

stored

in a
repository



Web page http://www.proteored.org/PME5_main.asp



MIAPEs

in PME5

Summary



ProteoRed as the first multi
-
centric organization involved in the
MIAPE generation



MIAPE generator tool: A useful method to generate reports. Allows to
contrast protocols from different facilities



Current developments allow the automation in MIAPE generation




PME2, PME3, PME4 and PME5 experiment reports available at:
http://www.proteored.org/MIAPEtool.asp