Upload
reese-byers
View
23
Download
0
Tags:
Embed Size (px)
DESCRIPTION
3 rd 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 HUPO2011 12 September 2011. - PowerPoint PPT Presentation
Citation preview
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
3rd SpHPP Workshop, La Cristalera, Dec 2012
WG 2.-S/MRM-Protein Platform Team WG 2.-S/MRM-Protein Platform Team
RU2aJP. AlbarCNB-CSIC, ProteoRed-ISCIII, Madrid
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
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: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
3rd SpHPP Workshop, La Cristalera, Dec 2012
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:Scientific Researchers:
Scientific Researchers:A. OdenaR. Díaz
Scientific Researchers:A. OdenaR. Díaz
Scientific Researchers:Scientific Researchers:
Scientific Researchers:Scientific Researchers:
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
3rd SpHPP Workshop, La Cristalera, Dec 2012
WG 4.-Bioinformatics TeamWG 4.-Bioinformatics Team
RU4aJP. AlbarCNB-CSIC, ProteoRed-ISCIII, Madrid
RU4aJP. AlbarCNB-CSIC, ProteoRed-ISCIII, Madrid
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
RU4dC. GilPCM-UCMProteoRed-ISCIII, Madrid
RU4dC. GilPCM-UCMProteoRed-ISCIII, Madrid
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
Scientific Researchers:
O.Gallardo
Scientific Researchers:V. Vialás
Scientific Researchers:V. Vialás
Scientific Researchers:Scientific Researchers:
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
3rd SpHPP Workshop, La Cristalera, Dec 2012
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
Scientific Researchers:
B. CilleroJ. MateoB. Rocha
L. Lourido
Scientific Researchers:
B. CilleroJ. MateoB. Rocha
L. Lourido
Scientific Researchers:Scientific Researchers:
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
3rd SpHPP Workshop, La Cristalera, Dec 2012
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
3rd SpHPP Workshop, La Cristalera, Dec 2012
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
3rd SpHPP Workshop, La Cristalera, Dec 2012
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
3rd SpHPP Workshop, La Cristalera, Dec 2012
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
3rd SpHPP Workshop, La Cristalera, Dec 2012
11 de Diciembre (2):