3 rd Spanish Human Proteome Project ( spHPP ) Workshop

3rd Spanish Human Proteome Project (spHPP) Workshop

La Cristalera, Miraflores de la Sierra, Madrid, December 10-11th, 2012

Juan P Albar, ProteoRed-ISCIII, CNB-CSIC

The Human Proteome Project Launch

Sydney HUPO2010 23 September 2010

Geneva HUPO201112 September 2011

Sydney September 23 Human Proteome Project

Gil’s comments on the Resources Issues: A good example of a resource we should make known to all C-HPP and B/D-HPP investigators is the Chr 16 team's library of 11,000 expression vectors for SRM assays (www.dnasu.org,www.plasmid.med.harvard.edu) as stated in the Chr 16 manuscript. I think we should collect such offers from the manuscripts of the Special Issue of JPR and make them known within HPP. We could also tabulate them in the Overview article. This information could make a good article in HUPOST, if we have the capacity to make information and resources available more widely. In addition, the Chr 16 team highlighted their interest in the B/D-HPP; we need to think about how best to capture and stimulate the chromosome teams to contribute their datasets and possibly their specimens to interested colleagues throughout the B/D-HPP. They identify projects in cancers, obesity, infectious, neurodegenerative, cardiovascular, and rheumatoid and osteoarthritis disease categories. The leader/corresponding author is Fernando Corrales, Pamplona, [email protected].

Dataset Submission Guidelines for the Human Proteome Project Version 1.0 (2012 October 30): Based on discussions at the HUPO Proteomics Standards Initiative (PSI) workshop (2012 Mar 12-14), the ProteomeXchange workshop (2012 Mar 15-16), the World HUPO Congress in Boston (2012 Sept 9-13), follow-on emails, and review and approval by the HPP-EC. Gel images Gel images accompanying MS/MS datasets should be uploaded as supporting raw data with the MS/MS dataset. There is a possibility that Swiss2DPage or ProteoRed may be able to serve as a Gel image repository, but this is not yet confirmed.

Steering Committee

AnalyticalGene/chromosome centric

ResearchDisease centric

Bioinformatics

MS and Ab based quantitative methods

Open access repositories

Hallmarks of diseasePotential biomarkers and

therapeutic targets

Clinical devices

Personalized medicine

Design of prototypesQuantitation of target proteins

MICINN

PharmasISCIII

Biotechs

MICINN ISCIII

CNB-CSICPCM-UCMCIB-CSICFJD/HNPCIC bioGUNECIMAUAB-CSICUVPCBVHIOUSALUPV-EHUINIBICBioDoHM

CHROMOSOME 16 at PeptideAtlas SITE

1616

1. Bioinformatic analysis of chromosome 16.2. Cell type(s) selection. Trascriptomic and proteomic detailed analysis.3. Expression, purification and characterization of proteins encoded by

chromosome 16 that have not been described so far.4. Development of MRM methods for the quantification of the most abundant

protein species encoded by each of the chromosome 16 genes.5. Identification, characterization and quantification of protein variants from

chromosome 16 genes.6. Definition of SOP7. Development of bioinformatic environment.8. Biobanking.9. Configuration of the B-D pilar for the Spanish HPP consortium.

Chromosome 16 general aims

2015 2016 2017

Biobanking

Validation of MRM assays (3 groups, immunoreagents, correlation with gene expression)

Clinical samples. Disease-related changes on protein abundance. Biomarkers

Bioinformatic study

MRM for 184 proteins MRM for 339 proteins

SOP, bioinformatic procedures, formats, data banks, etc.

2012 2013 2014

Biobanking

MRM for 339 proteins

Validation of MRM assays (3 groups, immunoreagents, correlation with gene expression)

Clinical samples. Disease-related changes on protein abundance. Biomarkers

1616 Chromosome 16 workplan

Chromosome 16

ENSEMBL v68UniProtKB v2012_06

GPMDB v101012HPA v10.0

2316 genes870 protein coding genes305 unknown proteins

110 OMIM hitsObesityNeurodegenerative diseasesCancer

Coverage of 75% gene products inLymphoid cellsEpitelial cellsFibroblasts Shotgun

Proteomic analysis

Transcriptomicanalysis

486 HPA antibodies for Chr16 proteins, 121 for unknown

Protein profile Gene expression profileData integration

Global and cell type specific outcomesCorrelation proteome/transcriptomeProteome coverage and chromosome distributionChr16 proteome coverage

Protein expression vectors for 58 Chr16 unknown proteins

Workflow Scheme

• Characterize the transcriptome to define the actual chr16’s gene set expressed and most importantly which genes are not expressed in the three selected cell types.

• Detailed characterization of the proteome: Shotgun approaches for maximum protein coverage. • Expression, purification, and characterization of 22 unknown proteins available in NAPPA collection.• Development of SRM quantitative assays.

Protein genes (870) has been distributed in known (565) and unknown groups (305) and the study will be performed along 3 years, starting in 2012 (214 proteins).

Protein packs has been assigned to each of the 8 MRM groups (24), including equal proportion of known (20, with different range of theoretical difficulty) and unknown proteins (4).

Unknown proteins have been first searched by targeted discovery (TD) and relevant information resulting from these studies will be used to design MRM assays. TD groups (9) will analyze 54 proteins during the first year.

Each group will use the master sample. TD will be done in all three selected cell lines. Decision on using a pool or a particular cell line for the unknown proteins will be taken in light of the results from TD.

Validated by 2 additional groups. • Definition of Bioinformatic standards and SOPs.• Definition of Biobanking strategy, standards... in collaboration with the Spanish Biobanking Platform.

1616 Workplan proposal

As lymphocytes express more than 75% Chr16 protein coding genes, periferal blood lymphocyte (PBL), or lymphoid cell lines are proposed. Epithelial cell lines and/or fibroblasts might complement.

Once decided the biological source:

• Prepare a master sample to distribute to all participating labs (CIMA, CIB, VHIO, others).• Characterize the transcriptome to define the actual chr16’s gen set expressed and most

importantly which genes are not expressed (CIMA).• Characterize the proteome in detail (protein sequencing teams). It may require

fractionation.• Expression, purification, and characterization of 22 unknown proteins available in NAPPA

collection (CIC, sequencing team...).

1616 Workplan proposal for 2012

External repositories

Development of bioinformatic environment: Spanish HPP will join the different resources to provide a unique enquiring system

PAtlasNProt

GPMDB

PRIDE

UProtUpcoming

Proteomics results

Data standards submission

(ProteomeXchange)+ +Emsembl

Raw data• Analyst®

TF Software (AB SCIEX)

.mgf format• Mascot

General File

• Peak View

UniProtKB/ SwissProt (v2012_06)DB NEWT 9606• Human• 36852 proteins• Mascot Server

mzIdentML

• Mascot results are exported as mzIdentML

MIAPE MS MIAPE MSI

ProteoRed MIAPE web repository

MIAPE Comparison Project• MIAPE Extractor Software

Raw data .mgf format

UniProtKB/ SwissProt database

NEWT 9606mzIdentML

MIAPE MS MIAPE MSI

ProteoRed MIAPE web repository

Metadata

PRIDE XML

Profiling the Chromosome 16 by high-resolution data-dependent Mass Spectrometry

Board of Directors: Principal investigators (PIs) Council

Project Manager

1st Deputy Director 2nd Deputy Director

WG 1

RU 1a

WG n

RU 1x RU na RU nx

Executive Committee

. . . . . . . . . . . . . . . . .

. . . . . . . .

Working Groups

Research Units

CHROMOSOME-16 CONSORTIUM STRUCTURE

3rd SpHPP Workshop, La Cristalera, Dec 2012

WG 1.-Protein Expression & Peptide Standard Team

WG 1.-Protein Expression & Peptide Standard Team

RU1a (Protein Micro Array)

M. FuentesCIC/IBMCC (USAL/CSIC), Salamanca

RU1a (Protein Micro Array)

M. FuentesCIC/IBMCC (USAL/CSIC), Salamanca

RU1c (Peptide Standard Team)

JP. AlbarCNB-CSIC, ProteoRed-ISCIII, Madrid

RU1c (Peptide Standard Team)

JP. AlbarCNB-CSIC, ProteoRed-ISCIII, Madrid

Scientific Researchers:M. GonzálezN. DasilvaP. DíezM. Perez de Andrés

Scientific Researchers:M. GonzálezN. DasilvaP. DíezM. Perez de Andrés

Scientific Researchers:M. LombardíaScientific Researchers:M. Lombardía

RU1b(Protein Expression Team)

C. GilUCM-PCM, ProteoRed-ISCIIIMadrid

RU1b(Protein Expression Team)

C. GilUCM-PCM, ProteoRed-ISCIIIMadrid

Scientific Researchers:L. MonteolivaA. PitarchE. Marín

Scientific Researchers:L. MonteolivaA. PitarchE. Marín

RU1d(m-RNA Expression Analysis Team)

FJ. CorralesCIMA-UN, ProteoRed-ISCIII, Pamplona

RU1d(m-RNA Expression Analysis Team)

FJ. CorralesCIMA-UN, ProteoRed-ISCIII, Pamplona

Scientific Researchers:M. MolinaScientific Researchers:M. Molina


WG 2.-S/MRM-Protein Platform Team WG 2.-S/MRM-Protein Platform Team

RU2aJP. AlbarCNB-CSIC, ProteoRed-ISCIII, Madrid


RU2bFJ. CorralesCIMA-UN ProteoRed-ISCIII, Pamplona

RU2bFJ. CorralesCIMA-UN ProteoRed-ISCIII, Pamplona

RU2cF. CanalsV.H.I.O.ProteoRed-ISCIII, Barcelona

RU2cF. CanalsV.H.I.O.ProteoRed-ISCIII, Barcelona

RU2dC. GilPCM-UCMProteoRed-ISCIII, Madrid


RU2eM. Sanchez del PinoUVProteoRed-ISCIII, Valencia

RU2eM. Sanchez del PinoUVProteoRed-ISCIII, Valencia

RU2fF. Vivanco / ME. BarderasFJD,Madrid/HNP, Toledo

RU2fF. Vivanco / ME. BarderasFJD,Madrid/HNP, Toledo

RU2gFJ. BlancoINIBIC, ProteoRed-ISCIII, La Coruña

RU2gFJ. BlancoINIBIC, ProteoRed-ISCIII, La Coruña

RU2hS. BarcelóIACS, ProteoRed-ISCIII, Zaragoza (Provisional)

RU2hS. BarcelóIACS, ProteoRed-ISCIII, Zaragoza (Provisional)

Scientific Researchers:M. MarcillaS. GharbiA. AlpízarC. González

Scientific Researchers:M. MarcillaS. GharbiA. AlpízarC. González

Scientific Researchers:ML. HernáezF. ClementeD. Cáceres

Scientific Researchers:ML. HernáezF. ClementeD. Cáceres

Scientific Researchers:L. ValeroO. Antúnez R.Argamasilla L. Cantero

Scientific Researchers:L. ValeroO. Antúnez R.Argamasilla L. Cantero

Scientific Researchers:G. AlvarezM. PosadaM. MartínL. González F. de la CuestaL. MouriñoV. MoralG. BarrosoLR. Padial

Scientific Researchers:G. AlvarezM. PosadaM. MartínL. González F. de la CuestaL. MouriñoV. MoralG. BarrosoLR. Padial

Scientific Researchers:P. FernandezV. CalamiaC. RuizC. Fernandez

Scientific Researchers:P. FernandezV. CalamiaC. RuizC. Fernandez

Scientific Researchers:Scientific Researchers:


Scientific Researchers:MI. MoraL. OdriozolaC. MiqueoR. Martínez

Scientific Researchers:MI. MoraL. OdriozolaC. MiqueoR. Martínez

Scientific Researchers:I. OreraM. Strunk

Scientific Researchers:I. OreraM. Strunk

Scientific Researchers:N. ColoméJJ.Bech-Serra

Scientific Researchers:N. ColoméJJ.Bech-Serra


WG 3.-Protein Sequencing TeamWG 3.-Protein Sequencing Team

RU3fJM. ArizmendiUPVProteoRed-ISCIII, Bilbao

RU3fJM. ArizmendiUPVProteoRed-ISCIII, Bilbao

RU3eI. CasalCIB-CSIC, ProteoRed-ISCIII, Madrid

RU3eI. CasalCIB-CSIC, ProteoRed-ISCIII, Madrid

RU3dE. de OliveiraPCB, ProteoRed-ISCIII, Barcelona

RU3dE. de OliveiraPCB, ProteoRed-ISCIII, Barcelona

RU3cM. Sánchez del PinoUV, ProteoRed-ISCIII, Valencia

RU3cM. Sánchez del PinoUV, ProteoRed-ISCIII, Valencia

RU3bJ. AbianIIBB-CSIC ProteoRed-ISCIII, Barcelona

RU3bJ. AbianIIBB-CSIC ProteoRed-ISCIII, Barcelona

RU3aJM. Mato / F. ElortzaCIC-BioGUNE, ProteoRed-ISCIII, Bilbao

RU3aJM. Mato / F. ElortzaCIC-BioGUNE, ProteoRed-ISCIII, Bilbao

RU3g JP. AlbarCNB-CSIC, ProteoRed-ISCIII, Madrid

RU3g JP. AlbarCNB-CSIC, ProteoRed-ISCIII, Madrid


Scientific Researchers:A. OdenaR. Díaz

Scientific Researchers:A. OdenaR. Díaz



Scientific Researchers:A. ParadelaR. Navajas

Scientific Researchers:A. ParadelaR. Navajas

Scientific Researchers:M. CarrascalJ. VillanuevaO. Gallardo

Scientific Researchers:M. CarrascalJ. VillanuevaO. Gallardo

Scientific Researchers:M. Azkargorta E. RodriguezI. IloroI. Escobes

Scientific Researchers:M. Azkargorta E. RodriguezI. IloroI. Escobes

Scientific Researchers:A. FullaondoM. J. OmaetxebarriaG. PrietoK. AloriaJ. Beaskoetxea

Scientific Researchers:A. FullaondoM. J. OmaetxebarriaG. PrietoK. AloriaJ. Beaskoetxea

Scientific Researchers:M. MendesM.Fernandez

Scientific Researchers:M. MendesM.Fernandez

Scientific Researchers:L. ValeroO. Antúnez R. Argamasilla L. CanteroV. Rejas

Scientific Researchers:L. ValeroO. Antúnez R. Argamasilla L. CanteroV. Rejas


WG 4.-Bioinformatics TeamWG 4.-Bioinformatics Team



RU4bFJ. CorralesCIMA-UNProteoRed-ISCIII, Pamplona

RU4bFJ. CorralesCIMA-UNProteoRed-ISCIII, Pamplona

RU4cJ. AbianIIBB-CSIC ProteoRed-ISCIII, Barcelona

RU4cJ. AbianIIBB-CSIC ProteoRed-ISCIII, Barcelona

RU4eJM. ArizmendiUPVProteoRed-ISCIII, Bilbao

RU4eJM. ArizmendiUPVProteoRed-ISCIII, Bilbao



Scientific Researchers:A. MedinaS. M-Bartolomé

Scientific Researchers:A. MedinaS. M-Bartolomé

Scientific Researchers:V. SeguraE. GuruceagaM. Braga

Scientific Researchers:V. SeguraE. GuruceagaM. Braga

Scientific Researchers:

O.Gallardo


O.Gallardo

Scientific Researchers:V. Vialás

Scientific Researchers:V. Vialás


RU4fM. Sánchez del PinoUV, ProteoRed-ISCIII, Valencia

RU4fM. Sánchez del PinoUV, ProteoRed-ISCIII, Valencia

Scientific Researchers:J. Ortíz

Scientific Researchers:J. Ortíz

Scientific Researchers:G. Prieto

Scientific Researchers:G. Prieto


WG 5.-Clinical Health Care & Biobanking Team (B/D-SpHPP)

WG 5.-Clinical Health Care & Biobanking Team (B/D-SpHPP)

RU5gM. MorenteSNBN, CNIO, Madrid(considered for inclusion in the consortium)

RU5gM. MorenteSNBN, CNIO, Madrid(considered for inclusion in the consortium)

RU5dA. López de MunainInst. BiodonostiaS. Sebastian

RU5dA. López de MunainInst. BiodonostiaS. Sebastian

RU5cL. Rodríguez Padial/ F. Vivanco /M.E BarderasFJD, Madrid/HNP, Toledo

RU5cL. Rodríguez Padial/ F. Vivanco /M.E BarderasFJD, Madrid/HNP, Toledo

RU5aFJ. BlancoINIBIC, ProteoRed-ISCIII, La Coruña

RU5aFJ. BlancoINIBIC, ProteoRed-ISCIII, La Coruña


B. CilleroJ. MateoB. Rocha

L. Lourido


B. CilleroJ. MateoB. Rocha

L. Lourido


Scientific Researchers:G. AlvarezM. PosadaM. MartínL. González F. de la CuestaL. MouriñoV. MoralG. Barroso

Scientific Researchers:G. AlvarezM. PosadaM. MartínL. González F. de la CuestaL. MouriñoV. MoralG. Barroso

Scientific Researchers:Scientific Researchers: Scientific

Researchers:F. de Luna MC. Marín

Scientific Researchers:F. de Luna MC. Marín

RU5fC. GilPCM-UCMProteoRed-ISCIII, Madrid

RU5fC. GilPCM-UCMProteoRed-ISCIII, Madrid

RU5eF. CorralesCIMA-UN ProteoRed-ISCIII, Pamplona

RU5eF. CorralesCIMA-UN ProteoRed-ISCIII, Pamplona

Scientific Researchers:A. MorenoE. Bigaud

Scientific Researchers:A. MorenoE. Bigaud

Scientific Researchers:L.MonteolivaA.PitarchE. Marín

Scientific Researchers:L.MonteolivaA.PitarchE. Marín

Scientific Researchers:J.M. ArizmendiA. FullaondoMJ. OmaetxebarriaG. PrietoK. AloriaJ. Beaskoetxea

Scientific Researchers:J.M. ArizmendiA. FullaondoMJ. OmaetxebarriaG. PrietoK. AloriaJ. Beaskoetxea

RU5bF. Bonilla/ I. Casal /C. BeldaHospital Puerta de Hierro, CIB Madrid

RU5bF. Bonilla/ I. Casal /C. BeldaHospital Puerta de Hierro, CIB Madrid

Scientific Researchers:C. PeñaS. TorresM. Mendes

Scientific Researchers:C. PeñaS. TorresM. Mendes


WG5-Clinical Health Care & Biobanking TeamRU5a-Dr. Francisco BlancoInstituto de Investigacion Biomedica (INIBIC), ProteoRed, La CoruñaRU5b-Dr. Felix Bonilla/ Dr Ignacio CasalHospital Puerta de Hierro, CIB-CSIC MadridRU5c-Dr. Rodriguez Padial/Dr. Fernando Vivanco/ Dr. ME BarderasJimenez Díaz Foundation (FJD), Madrid /National Paraplegics Hospital, ToledoRu5d-Dr. Adolfo López de MunainInstituto Biodonostia, San SebastianRU5e-Dr. Fernando Corrales/J. PrietoCIMA-University of Navarra RU5f-Dr. Concha GilPCM-Computensis University (PCM-UCM), ProteoRed, MadridRU5g-Dr. Manuel Morente (considered for inclusion in the consortium), Spanish National BioBank Network- ISCIII. CNIO, Madrid”

WG5-Clinical Health Care & Biobanking TeamRU5a-Dr. Francisco BlancoInstituto de Investigacion Biomedica (INIBIC), ProteoRed, La CoruñaRU5b-Dr. Felix Bonilla/ Dr Ignacio CasalHospital Puerta de Hierro, CIB-CSIC MadridRU5c-Dr. Rodriguez Padial/Dr. Fernando Vivanco/ Dr. ME BarderasJimenez Díaz Foundation (FJD), Madrid /National Paraplegics Hospital, ToledoRu5d-Dr. Adolfo López de MunainInstituto Biodonostia, San SebastianRU5e-Dr. Fernando Corrales/J. PrietoCIMA-University of Navarra RU5f-Dr. Concha GilPCM-Computensis University (PCM-UCM), ProteoRed, MadridRU5g-Dr. Manuel Morente (considered for inclusion in the consortium), Spanish National BioBank Network- ISCIII. CNIO, Madrid”

WG4-Bioinformatics TeamRU4a-Dr. Juan P AlbarNational Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, MadridRU4b-Dr. Fernando CorralesCIMA-University of Navarra ProteoRed, PamplonaRU4c-Dr. Joaquin AbianIIBB, CSIC, ProteoRed, BarcelonaRU4d-Dr. Concha GilPCM-Computensis University (PCM-UCM), ProteoRed, MadridRU4e-Dr. Jesus M. ArizmendiBasque Country University, ProteoRed, BilbaoRU4d-Dr. Manuel Sanchez del PinoUniversity of Valencia, ProteoRed, Valencia

WG4-Bioinformatics TeamRU4a-Dr. Juan P AlbarNational Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, MadridRU4b-Dr. Fernando CorralesCIMA-University of Navarra ProteoRed, PamplonaRU4c-Dr. Joaquin AbianIIBB, CSIC, ProteoRed, BarcelonaRU4d-Dr. Concha GilPCM-Computensis University (PCM-UCM), ProteoRed, MadridRU4e-Dr. Jesus M. ArizmendiBasque Country University, ProteoRed, BilbaoRU4d-Dr. Manuel Sanchez del PinoUniversity of Valencia, ProteoRed, Valencia

WG2-S/MRM-Protein Platform TeamRU2a-Dr. Juan P AlbarNational Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, MadridRU2b-Dr. Fernando CorralesCIMA-University of Navarra, ProteoRed, PamplonaRU2c-Dr. Francesc CanalsVall d'Hebron Institut d'Oncologia (V.H.I.O.),ProteoRed, BarcelonaRU2d-Dr. Concha GilMadrid Science Park-Computensis University (PCM-UCM), ProteoRed, MadridRU2e-Dr. Manuel Sanchez del PinoFelipe Princess Research Center (CIPF), ProteoRed, ValenciaRU2f-Dr. Fernando Vivanco / Dr. ME BarderasJimenez Díaz Foundation (FJD), Madrid /National Paraplegics Hospital, ToledoRU2g-Dr. Francisco BlancoInstituto de Investigacion Biomedica (INIBIC), ProteoRed, La CoruñaRU2h-Dr Silvia BarcelóAragón Health Sciences Institute (IACS), ZaragozaRU2i- Dr. Eduard SabidóCentre de regulació Genómica (CRG-UPF), ProteoRed, Barcelona

WG2-S/MRM-Protein Platform TeamRU2a-Dr. Juan P AlbarNational Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, MadridRU2b-Dr. Fernando CorralesCIMA-University of Navarra, ProteoRed, PamplonaRU2c-Dr. Francesc CanalsVall d'Hebron Institut d'Oncologia (V.H.I.O.),ProteoRed, BarcelonaRU2d-Dr. Concha GilMadrid Science Park-Computensis University (PCM-UCM), ProteoRed, MadridRU2e-Dr. Manuel Sanchez del PinoFelipe Princess Research Center (CIPF), ProteoRed, ValenciaRU2f-Dr. Fernando Vivanco / Dr. ME BarderasJimenez Díaz Foundation (FJD), Madrid /National Paraplegics Hospital, ToledoRU2g-Dr. Francisco BlancoInstituto de Investigacion Biomedica (INIBIC), ProteoRed, La CoruñaRU2h-Dr Silvia BarcelóAragón Health Sciences Institute (IACS), ZaragozaRU2i- Dr. Eduard SabidóCentre de regulació Genómica (CRG-UPF), ProteoRed, Barcelona

WG1-Protein expression & Peptide Standard TeamRU1a (Protein Micro Array and Protein Expression Team):Dr. Manuel FuentesCentro de Investigación del Cáncer/IBMCC (USAL/CSIC), SalamancaRU1b (Peptide standardization Team): Dr. Juan P AlbarNational Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, Madrid

WG1-Protein expression & Peptide Standard TeamRU1a (Protein Micro Array and Protein Expression Team):Dr. Manuel FuentesCentro de Investigación del Cáncer/IBMCC (USAL/CSIC), SalamancaRU1b (Peptide standardization Team): Dr. Juan P AlbarNational Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, Madrid

WG3-Protein Sequencing Team RU3a-Dr. José M. Mato / Dr. Félix ElortzaCIC-BioGUNE, ProteoRed, BilbaoRU3b-Dr. Joaquin AbianIIBB, CSIC ProteoRed, BarcelonaRU3c-Dr. Manuel Sanchez del PinoUniversity of Valencia, ProteoRed, ValenciaRU3d-Dr. Eliandre de OliveiraParc Científic de Barcelona (PCB), ProteoRed, BarcelonaRU3e-Dr. Ignacio CasalBiology Research Center-CSIC (CIB-CSIC), ProteoRed, MadridRU3f-Dr. Jesus M. ArizmendiBasque Country University ProteoRed, BilbaoRU3g-Dr. Juan P AlbarNational Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, Madrid

WG3-Protein Sequencing Team RU3a-Dr. José M. Mato / Dr. Félix ElortzaCIC-BioGUNE, ProteoRed, BilbaoRU3b-Dr. Joaquin AbianIIBB, CSIC ProteoRed, BarcelonaRU3c-Dr. Manuel Sanchez del PinoUniversity of Valencia, ProteoRed, ValenciaRU3d-Dr. Eliandre de OliveiraParc Científic de Barcelona (PCB), ProteoRed, BarcelonaRU3e-Dr. Ignacio CasalBiology Research Center-CSIC (CIB-CSIC), ProteoRed, MadridRU3f-Dr. Jesus M. ArizmendiBasque Country University ProteoRed, BilbaoRU3g-Dr. Juan P AlbarNational Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, Madrid


2013 SpHPP HALLMARKS

• 1. European Bioinformatics cross analysis of Jurkat cells LC-MS/MS data.

• 2. PM8/QTAPAS Targeted Proteomics Study.• 3. Specific WGs Hallmarks:

- CHPP: Berlin, March 16th, 2013- HUPO-PSI-PX: Liverpool, April 15th-19th, 2013- HUPO: Yokohama, September 2013- 2013 CHPP Report, December 2013

SpHPP Council, La Cristalera, Dec 2012

III Workshop of the Chromosome 16 Consortium Agenda10-11 Dic. 2012, La Cristalera, Miraflores de la Sierra, Madrid 10 de Diciembre (1): 10:30 Bus CNB-Miraflores de la Sierra 11:30-11:45 Bienvenida Juan P. Albar

11:45-13:30 WG 1 Expresión de proteínas. Síntesis de PéptidosIntroducción. Concha Gil. (5´)Síntesis de péptidos. Manuel Lombardía. (15´)Expresión de Proteínas. Estrategia general. Manuel Fuentes. (20´)Análisis de las proteínas expresadas mediante MS. Félix Elortza. (15´)Otras estrategias de expresión. Felipe Clemente y Elvira Marín. (15´) Discusión y participación de otros grupos en el WG1. 15 minPlan de trabajo Junio 2013. Juan Pablo Albar, Concha Gil, Manuel Fuentes. (20´)

13:30-13:45 WG5 Biology and Disease (B/D-HPP)Presentación general. (15´) 13:45-15:15 Comida


15:15-16:15 Consejo de dirección: Reunión de los investigadores principales (IPs)Gestión del proyecto. Posibles escenarios en función de la financiaciónHitos para el 2013. Relación C-HPP con B/D-HPP

16:15-19:30 WG 3 Shotgun proteomics GroupPresentación general. (30’)Fernando Corrales: Comparación de resultados de shotgun y transcriptómica. (15’)Severine Gharbi/Carmen González: Profiling the Chromosome 16 by high-resolution datadependent MS: Extraction/fractionation method evaluation in Jurkat cells. (15´)Óscar Gallardo/Joan Villanueva: Experimentos de shotgun empleando listas de inclusión. Utilización de datos de SEQUEST con MIAPE Extractor. (15’)17:30-18:00 Coffee break Kerman Aloria. Protein Grouping. (15’)Alberto Medina. How and where will I apply the FDR filter? (10')Discusión: (50’)

Estrategias para ampliar la cobertura del cromosoma 16. Utilización de la información de los experimentos shot-gun para el diseño de experimentos de MRM. Información cuantitativa de los datos de shot-gun

Plan de trabajo Junio 2013. (15’) 19:30-20:15 Charla Workshop Speaker Invitado:Juan Antonio Vizcaíno: “PRIDE and the ProteomeXchange consortium: enhancing visibility and accessibility of MS-based proteomics data”. (30’)Discusión. (15’) 3rd SpHPP Workshop, La Cristalera, Dec 2012

11 de Diciembre (1): 9:00-11:15 WG2 Selected Reaction Monitoring Group (S/MRM)Presentación general (30´)MRM data base. Vital Vialas (15').Discusión (60’)

Aspectos a discutir:- Criterios verificación transiciones- péptidos- Validación con péptidos sintéticos: criterios para selección de péptidos- Criterios de "proteotipicidad" - Tratamiento de las isoformas- Factores para establecer un sistema de scores- ranking de péptidos

para cuantificar por SRM (presencia de Met, Cys, modificaciones...) - Optimización de parámetros de adquisición: Energías de Colisión...

- Uso de standards para determinar tiempos de retención relativos - Uso de un standard interno para establecer una escala de intensidad relativa de las señales de SRM

- Planificación validación multi-laboratorio -Objetivos siguiente hito: validación, asignación de nuevas proteínas...Plan de trabajo Junio 2013 (15’). 11:15-11:45 Café


11:45-13:30 WG4 Bioinformatics GroupPresentación general: Bioinformatics pipeline improvements. Alberto Medina (30’)Discusión (60')

Propuestas Logo/Imagen. Actualización BDs Referncia Problemas envío datos MIAPE extractorConsultas datos shotgun para diseño experimentos MRM.

Plan de trabajo Junio 2013 (15’). 13:30-14:45 Conclusiones finales. 15:00-16:00 Comida 16:30 Bus Miraflores-CNB


11 de Diciembre (2):

Documents

3 rd Spanish Human Proteome Project ( spHPP ) Workshop