Download A SPANISH HUMAN PROTEOME PROJECT - SpHPP

A Spanish Human Proteome
Project (sHPP)
La Cristalera, Miraflores de la Sierra,
Madrid, August 28-29th, 2012
Juan P Albar, ProteoRed-ISCIII, CNB-CSIC
A SPANISH HUMAN PROTEOME PROJECT (SHPP)
Preliminary proposal
Index
1.Introduction
International context
Chromosome/gene centric approach
The HPP technological pillars
Protein annotation and database compilation
2.The Spanish Participation in the Human Proteome Project
3.General and Specific Aims
General aims
Specific aims
4.Members of the Spanish Consortium
Description of the groups
ProteoRed presence in the Spanish consortium
5.Working Plan
Work package list
Work package description
6.Financing
7.Spanish Consortium Structure
8.Benefit for Spain
Spanish HPP Consortium:
Current Developments on the
Characterization of the Proteins Encoded by
the Chromosome 16"
5th C-HPP Consortium Workshop
The Chromosome-Centric Human Proteome Project
May 5, 2012, Beijing
Juan-Pablo Albar (Chair)
Francisco Blanco (Co-Chair)
Fernando Corrales (Co-Chair)
A Spanish Human Proteome
Project (sHPP)
Preliminary proposal
San Sebastian, July 9th, 2012
Juan P Albar, ProteoRed-ISCIII, CNB-CSIC
The
Human
Proteome
Project Launch
Sydney HUPO2010
23 September 2010
Geneva HUPO2011
12 September 2011
Sydney September 23
Human Proteome Project
The Mission of the HPP
HPP will deliver a comprehensive map of the
human proteins in their biological context.
HPP will provide tools for the scientific
community that will allow each scientist to
design experiments in a better way, as the
Human Genome Project did.
HPP will inspire, beyond the scientific
community, other stakeholders for diagnosis,
prevention, therapy and cure of diseases and
improved health worldwide.
Sydney September 23
Human Proteome Project
A gene-centric proteome project
Map the human proteins (gene by gene):
• Molecular (isoforms)
• Sub-cellular (localization)
• Cells, tissues and organs (expression)
• Interaction networks
• Plasma/serum (abundance)
Use all available technology platforms:
• Mass spectrometry
• Antibodies (immunotechnologies)
• Gene fusions (GFP)
Sydney September 23
Human Proteome Project
C-HPP teams by April 24th, 2012. The C-HPP Consortium internal information
HPP technologic pillars
Legrain et al. MCP 2011
Flow of the overall procedures of the C-HPP work
Spanish HPP Consortium:
Current Developments on the
Characterization of the Proteins Encoded by
the Chromosome 16"
5th C-HPP Consortium Workshop
The Chromosome-Centric Human Proteome Project
May 5, 2012, Beijing
Juan-Pablo Albar (Chair)
Francisco Blanco (Co-Chair)
Fernando Corrales (Co-Chair)
Chromosome 16
Chromosome 16 general aims
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 SOP
7. Development of bioinformatic environment.
8. Biobanking.
9. Configuration of the B-D pilar for the Spanish HPP consortium.
Top 15 Biofunctions represented in
chromosome 16. IPA analysis
Genes on Chromosome 16
UNKNOWN,
111
NON PROTCODING, 485
KNOWN, 751
ENSEMBL
UNIPROTKB
•
Protein coding genes (n=862)
•
GPMDB
Unknown proteins are
present neither in
UNIPROT nor in GPMDB.
GPMDB threshold was
loge<-5
600
Protein coding genes (n=862)
400
300
200
100
0
Entries
B-lymphocyte
538
T-lymphocyte
244
Leukocyte
263
Epithelium
491
Fibroblast
329
More than 85 % of protein coding genes of chromosome
16 are expressed in lymphoid cells, epitelial cells and
fibroblasts.
Number of proteins
Entries
500
900
800
700
600
500
400
300
200
100
0
Absent
NAPPA
602
HPA
431
UNIPROT
238
GPMDB
164
Present
260
431
624
698
Diseases mapping
on Chromosome 16
DISEASERELATED, 116
OMIM
Non DISEASERELATED, 746
CANCER
OBESITY
NEURODEGENERATIVE
AUTOINMUNE DISEASES
Metabolism
Mitochondria
Inflammation
ensembl_gene_id
ENSG00000005339
ENSG00000008710
ENSG00000033011
ENSG00000039068
ENSG00000039068
ENSG00000039068
ENSG00000039068
ENSG00000039068
ENSG00000051523
ENSG00000062038
ENSG00000062038
ENSG00000063854
ENSG00000065427
ENSG00000067955
ENSG00000069329
ENSG00000070729
ENSG00000070729
ENSG00000070915
ENSG00000072864
ENSG00000077238
ENSG00000077238
ENSG00000083093
ENSG00000083093
ENSG00000083093
ENSG00000083093
ENSG00000083799
ENSG00000083799
ENSG00000083799
ENSG00000087237
ENSG00000087237
ENSG00000087245
ENSG00000088682
ENSG00000089280
ENSG00000089280
ENSG00000090581
ENSG00000090861
ENSG00000091262
ENSG00000091262
ENSG00000091651
ENSG00000099377
ENSG00000099769
ENSG00000102878
ENSG00000102893
ENSG00000102967
ENSG00000103005
ENSG00000103051
ENSG00000103089
ENSG00000103126
ENSG00000103126
ENSG00000103150
ENSG00000103197
ENSG00000103197
ENSG00000103197
ENSG00000103227
ENSG00000103241
ENSG00000103249
ENSG00000103249
ENSG00000103313
ENSG00000103313
ENSG00000103449
ENSG00000103489
ENSG00000103494
ENSG00000103494
ENSG00000103494
ENSG00000103522
ENSG00000103546
ENSG00000121270
ENSG00000125124
ENSG00000126603
ENSG00000127554
ENSG00000127688
ENSG00000129910
ENSG00000133392
ENSG00000135697
ENSG00000140650
ENSG00000140675
ENSG00000140678
ENSG00000140718
ENSG00000140718
ENSG00000140836
ENSG00000140873
ENSG00000140905
ENSG00000141012
ENSG00000141076
ENSG00000149922
ENSG00000149925
ENSG00000154099
ENSG00000154118
ENSG00000155719
ENSG00000156873
ENSG00000159723
ENSG00000162009
ENSG00000162065
ENSG00000166546
ENSG00000166548
ENSG00000166548
ENSG00000166828
ENSG00000166828
ENSG00000166828
ENSG00000167207
ENSG00000167207
ENSG00000167207
ENSG00000167207
ENSG00000167207
ENSG00000167397
ENSG00000167397
ENSG00000167513
ENSG00000167522
ENSG00000167972
ENSG00000168434
ENSG00000168447
ENSG00000168447
ENSG00000168447
ENSG00000169344
ENSG00000169344
ENSG00000169344
ENSG00000169896
ENSG00000175595
ENSG00000175595
ENSG00000176387
ENSG00000176692
ENSG00000176692
ENSG00000176692
ENSG00000176715
ENSG00000177455
ENSG00000178573
ENSG00000178952
ENSG00000179583
ENSG00000179583
ENSG00000179583
ENSG00000183044
ENSG00000183196
ENSG00000183454
ENSG00000186153
ENSG00000187741
ENSG00000188536
ENSG00000188536
ENSG00000188536
ENSG00000188536
ENSG00000188603
ENSG00000188827
ENSG00000189067
ENSG00000196155
ENSG00000196155
ENSG00000196296
ENSG00000196557
ENSG00000197912
ENSG00000198211
ENSG00000198211
ENSG00000198650
ENSG00000198848
ENSG00000198931
ENSG00000205336
ENSG00000206172
ENSG00000206172
ENSG00000206172
ENSG00000206172
ENSG00000213380
ENSG00000213398
ENSG00000213398
ENSG00000213918
ENSG00000225614
ENSG00000257017
ENSG00000258839
ENSG00000258839
ENSG00000258839
ENSG00000258839
ENSG00000258839
ENSG00000258839
ENSG00000258947
ENSG00000258947
external_gene_id
CREBBP
PKD1
ALG1
CDH1
CDH1
CDH1
CDH1
CDH1
CYBA
CDH3
CDH3
HAGH
KARS
CBFB
VPS35
CNGB1
CNGB1
SLC12A3
NDE1
IL4R
IL4R
PALB2
PALB2
PALB2
PALB2
CYLD
CYLD
CYLD
CETP
CETP
MMP2
COQ9
FUS
FUS
GNPTG
AARS
ABCC6
ABCC6
ORC6
HSD3B7
IGFALS
HSF4
PHKB
DHODH
C16orf57
COG4
FA2H
AXIN1
AXIN1
MLYCD
TSC2
TSC2
TSC2
LMF1
FOXF1
CLCN7
CLCN7
MEFV
MEFV
SALL1
XYLT1
RPGRIP1L
RPGRIP1L
RPGRIP1L
IL21R
SLC6A2
ABCC11
BBS2
GLIS2
GFER
GAN
CDH15
MYH11
BCMO1
PMM2
SLC5A2
ITGAX
FTO
FTO
ZFHX3
ADAMTS18
GCSH
GALNS
CIRH1A
TBX6
ALDOA
DNAAF1
JPH3
OTOA
PHKG2
AGRP
SSTR5
TBC1D24
BEAN1
TK2
TK2
SCNN1G
SCNN1G
SCNN1G
NOD2
NOD2
NOD2
NOD2
NOD2
VKORC1
VKORC1
CDT1
ANKRD11
ABCA3
COG7
SCNN1B
SCNN1B
SCNN1B
UMOD
UMOD
UMOD
ITGAM
ERCC4
ERCC4
HSD11B2
FOXC2
FOXC2
FOXC2
ACSF3
CD19
MAF
TUFM
CIITA
CIITA
CIITA
ABAT
CHST6
GRIN2A
WWOX
FANCA
HBA2
HBA2
HBA2
HBA2
CLN3
SLX4
LITAF
PLEKHG4
PLEKHG4
ATP2A1
CACNA1H
SPG7
TUBB3
TUBB3
TAT
CES1
APRT
GPR56
HBA1
HBA1
HBA1
HBA1
COG8
LCAT
LCAT
DNASE1
ZNF469
HP
MC1R
MC1R
MC1R
MC1R
MC1R
MC1R
RP11-566K11.2
RP11-566K11.2
mim_morbid_accession
180849
173900
608540
114480
137215
167000
176807
608089
233690
225280
601553
614033
613641
601626
614203
268000
613767
263800
614019
147050
609423
114480
227650
610832
613348
132700
601606
605041
143470
152430
259600
607426
608030
612160
252605
613287
177850
264800
613803
607765
601489
116800
261750
263750
604173
613489
612319
114550
607864
248360
191100
606690
613254
246650
265380
166600
611490
134610
249100
107480
264800
216360
611560
611561
147050
604715
117800
209900
611498
613076
256850
612580
132900
115300
212065
233100
152700
601665
612938
176807
608454
605899
253000
604901
610265
611881
613193
606438
607039
613027
601665
102200
605021
117210
251880
609560
177200
264350
613071
181000
186580
266600
607507
609464
122700
607473
613804
148050
610921
608779
177200
211400
264350
162000
603860
609886
609939
278760
610965
218030
153200
153300
153400
614265
613493
610202
610678
126200
180300
209920
613163
217800
613971
133239
227650
140700
141800
604131
613978
204200
613951
601098
117210
600223
601003
611942
607259
600638
614039
276600
114835
102600
606854
140700
141800
604131
613978
611182
136120
245900
152700
229200
614081
155600
203200
226300
266300
613098
613099
600638
614039
mim_morbid_description
RUBINSTEIN-TAYBI SYNDROME 1; RSTS1
POLYCYSTIC KIDNEY DISEASE 1; PKD1
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ik; CDG1K
BREAST CANCER
GASTRIC CANCER, HEREDITARY DIFFUSE; HDGC
OVARIAN CANCER
PROSTATE CANCER
ENDOMETRIAL CANCER
GRANULOMATOUS DISEASE, CHRONIC, AUTOSOMAL RECESSIVE, CYTOCHROME b-NEGATIVE
EEM SYNDROME
HYPOTRICHOSIS, CONGENITAL, WITH JUVENILE MACULAR DYSTROPHY; HJMD
HYDROXYACYL GLUTATHIONE HYDROLASE DEFICIENCY
CHARCOT-MARIE-TOOTH DISEASE, RECESSIVE INTERMEDIATE B; CMTRIB
LEUKEMIA, ACUTE MYELOID; AML
PARKINSON DISEASE 17; PARK17
RETINITIS PIGMENTOSA; RP
RETINITIS PIGMENTOSA 45; RP45
GITELMAN SYNDROME
LISSENCEPHALY 4; LIS4
IgE RESPONSIVENESS, ATOPIC; IGER
HUMAN IMMUNODEFICIENCY VIRUS TYPE 1, SUSCEPTIBILITY TO
BREAST CANCER
FANCONI ANEMIA, COMPLEMENTATION GROUP A; FANCA
FANCONI ANEMIA, COMPLEMENTATION GROUP N; FANCN
PANCREATIC CANCER, SUSCEPTIBILITY TO, 3
CYLINDROMATOSIS, FAMILIAL
TRICHOEPITHELIOMA, MULTIPLE FAMILIAL, 1
BROOKE-SPIEGLER SYNDROME; BRSS
HYPERALPHALIPOPROTEINEMIA 1; HALP1
LONGEVITY 1
TORG-WINCHESTER SYNDROME
COENZYME Q10 DEFICIENCY
AMYOTROPHIC LATERAL SCLEROSIS 6, WITH OR WITHOUT FRONTOTEMPORAL DEMENTIA;
HISTIOCYTOMA, ANGIOMATOID FIBROUS
MUCOLIPIDOSIS III GAMMA
CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2N; CMT2N
PSEUDOXANTHOMA ELASTICUM, FORME FRUSTE
PSEUDOXANTHOMA ELASTICUM; PXE
MEIER-GORLIN SYNDROME 3; MGORS3
BILE ACID SYNTHESIS DEFECT, CONGENITAL, 1; CBAS1
INSULIN-LIKE GROWTH FACTOR-BINDING PROTEIN, ACID-LABILE SUBUNIT; IGFALS
CATARACT, LAMELLAR
GLYCOGEN STORAGE DISEASE IXb; GSD9B
POSTAXIAL ACROFACIAL DYSOSTOSIS; POADS
POIKILODERMA WITH NEUTROPENIA; PN
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIj; CDG2J
SPASTIC PARAPLEGIA 35, AUTOSOMAL RECESSIVE; SPG35
HEPATOCELLULAR CARCINOMA
CAUDAL DUPLICATION ANOMALY
MALONYL-CoA DECARBOXYLASE DEFICIENCY
TUBEROUS SCLEROSIS 1; TSC1
LYMPHANGIOLEIOMYOMATOSIS; LAM
TUBEROUS SCLEROSIS 2; TSC2
LIPASE DEFICIENCY, COMBINED
ALVEOLAR CAPILLARY DYSPLASIA WITH MISALIGNMENT OF PULMONARY VEINS;
OSTEOPETROSIS, AUTOSOMAL DOMINANT 2; OPTA2
OSTEOPETROSIS, AUTOSOMAL RECESSIVE 4; OPTB4
FAMILIAL MEDITERRANEAN FEVER, AUTOSOMAL DOMINANT
FAMILIAL MEDITERRANEAN FEVER; FMF
TOWNES-BROCKS SYNDROME; TBS
PSEUDOXANTHOMA ELASTICUM; PXE
COACH SYNDROME
JOUBERT SYNDROME 7; JBTS7
MECKEL SYNDROME, TYPE 5; MKS5
IgE RESPONSIVENESS, ATOPIC; IGER
ORTHOSTATIC INTOLERANCE
APOCRINE GLAND SECRETION, VARIATION IN
BARDET-BIEDL SYNDROME; BBS
NEPHRONOPHTHISIS 7; NPHP7
MYOPATHY, MITOCHONDRIAL PROGRESSIVE, WITH CONGENITAL CATARACT, HEARING
GIANT AXONAL NEUROPATHY 1; GAN1
MENTAL RETARDATION, AUTOSOMAL DOMINANT 3; MRD3
AORTIC ANEURYSM, FAMILIAL THORACIC 4; AAT4
HYPERCAROTENEMIA AND VITAMIN A DEFICIENCY, AUTOSOMAL DOMINANT
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ia; CDG1A
RENAL GLUCOSURIA; GLYS1
SYSTEMIC LUPUS ERYTHEMATOSUS; SLE
OBESITY
GROWTH RETARDATION, DEVELOPMENTAL DELAY, COARSE FACIES, AND EARLY
PROSTATE CANCER
KNOBLOCH SYNDROME 2; KNO2
GLYCINE ENCEPHALOPATHY; GCE
MUCOPOLYSACCHARIDOSIS TYPE IVA
NORTH AMERICAN INDIAN CHILDHOOD CIRRHOSIS; NAIC
DEAFNESS, AUTOSOMAL RECESSIVE 67; DFNB67
GLYCOGEN STORAGE DISEASE XII; GSD12
CILIARY DYSKINESIA, PRIMARY, 13; CILD13
HUNTINGTON DISEASE-LIKE 2; HDL2
DEAFNESS, AUTOSOMAL RECESSIVE 22; DFNB22
GLYCOGEN STORAGE DISEASE IXc; GSD9C
OBESITY
PITUITARY ADENOMA, GROWTH HORMONE-SECRETING
MYOCLONIC EPILEPSY, FAMILIAL INFANTILE; FIME
SPINOCEREBELLAR ATAXIA 31; SCA31
MITOCHONDRIAL DNA DEPLETION SYNDROME 3 (HEPATOCEREBRAL TYPE); MTDPS3
MITOCHONDRIAL DNA DEPLETION SYNDROME 2 (MYOPATHIC TYPE); MTDPS2
LIDDLE SYNDROME
PSEUDOHYPOALDOSTERONISM, TYPE I, AUTOSOMAL RECESSIVE; PHA1B
BRONCHIECTASIS WITH OR WITHOUT ELEVATED SWEAT CHLORIDE 3; BESC3
SARCOIDOSIS, SUSCEPTIBILITY TO, 1; SS1
BLAU SYNDROME
INFLAMMATORY BOWEL DISEASE 1; IBD1
PSORIATIC ARTHRITIS, SUSCEPTIBILITY TO
SARCOIDOSIS, EARLY-ONSET
COUMARIN RESISTANCE
VITAMIN K-DEPENDENT CLOTTING FACTORS, COMBINED DEFICIENCY OF, 2; VKCFD2
MEIER-GORLIN SYNDROME 4; MGORS4
KBG SYNDROME; KBGS
SURFACTANT METABOLISM DYSFUNCTION, PULMONARY, 3; SMDP3
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIe; CDG2E
LIDDLE SYNDROME
BRONCHIECTASIS WITH OR WITHOUT ELEVATED SWEAT CHLORIDE 1; BESC1
PSEUDOHYPOALDOSTERONISM, TYPE I, AUTOSOMAL RECESSIVE; PHA1B
HYPERURICEMIC NEPHROPATHY, FAMILIAL JUVENILE, 1; HNFJ1
MEDULLARY CYSTIC KIDNEY DISEASE 2; MCKD2
GLOMERULOCYSTIC KIDNEY DISEASE WITH HYPERURICEMIA AND ISOSTHENURIA
SYSTEMIC LUPUS ERYTHEMATOSUS, SUSCEPTIBILITY TO, 6; SLEB6
XERODERMA PIGMENTOSUM, COMPLEMENTATION GROUP F; XPF
XFE PROGEROID SYNDROME
APPARENT MINERALOCORTICOID EXCESS; AME
LYMPHEDEMA, HEREDITARY, II
YELLOW NAIL SYNDROME
LYMPHEDEMA-DISTICHIASIS SYNDROME
COMBINED MALONIC AND METHYLMALONIC ACIDURIA; CMAMMA
IMMUNODEFICIENCY, COMMON VARIABLE, 3; CVID3
CATARACT, PULVERULENT, JUVENILE-ONSET
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 4; COXPD4
MULTIPLE SCLEROSIS, SUSCEPTIBILITY TO; MS
RHEUMATOID ARTHRITIS; RA
BARE LYMPHOCYTE SYNDROME, TYPE II
GABA-TRANSAMINASE DEFICIENCY
MACULAR DYSTROPHY, CORNEAL, 1; MCDC1
EPILEPSY WITH NEURODEVELOPMENTAL DEFECTS; EPND
ESOPHAGEAL CANCER
FANCONI ANEMIA, COMPLEMENTATION GROUP A; FANCA
HEINZ BODY ANEMIAS
HEMOGLOBIN--ALPHA LOCUS 1; HBA1
ALPHA-THALASSEMIA
HEMOGLOBIN H DISEASE; HBH
CEROID LIPOFUSCINOSIS, NEURONAL, 3; CLN3
FANCONI ANEMIA, COMPLEMENTATION GROUP P; FANCP
CHARCOT-MARIE-TOOTH DISEASE, DEMYELINATING, TYPE 1C; CMT1C
SPINOCEREBELLAR ATAXIA 31; SCA31
SPINOCEREBELLAR ATAXIA 4; SCA4
BRODY MYOPATHY
EPILEPSY, CHILDHOOD ABSENCE, SUSCEPTIBILITY TO, 6; ECA6
SPASTIC PARAPLEGIA 7, AUTOSOMAL RECESSIVE; SPG7
FIBROSIS OF EXTRAOCULAR MUSCLES, CONGENITAL, 3A, WITH OR WITHOUT EXTRAOCULAR
CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS; CDCBM
TYROSINEMIA, TYPE II
CARBOXYLESTERASE 1; CES1
ADENINE PHOSPHORIBOSYLTRANSFERASE; APRT
POLYMICROGYRIA, BILATERAL FRONTOPARIETAL
HEINZ BODY ANEMIAS
HEMOGLOBIN--ALPHA LOCUS 1; HBA1
ALPHA-THALASSEMIA
HEMOGLOBIN H DISEASE; HBH
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIh; CDG2H
FISH-EYE DISEASE; FED
LECITHIN:CHOLESTEROL ACYLTRANSFERASE DEFICIENCY
SYSTEMIC LUPUS ERYTHEMATOSUS; SLE
BRITTLE CORNEA SYNDROME 1; BCS1
ANHAPTOGLOBINEMIA; AHP
MELANOMA, CUTANEOUS MALIGNANT; CMM
ALBINISM, OCULOCUTANEOUS, TYPE II; OCA2
ENTEROPATHY, PROTEIN-LOSING
SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2
INCREASED ANALGESIA FROM KAPPA-OPIOID RECEPTOR AGONIST, FEMALE-SPECIFIC
MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 5; CMM5
FIBROSIS OF EXTRAOCULAR MUSCLES, CONGENITAL, 3A, WITH OR WITHOUT EXTRAOCULAR
CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS; CDCBM
Development of bioinformatic environment:
Spanish HPP will join the different resources to provide
an unique enquiring system
NProt
PAtlas
Proteomics
results
+
PRIDE
External repositories
+
Emsembl
Upcoming
UProt
GPMDB
Data standards
submission
(ProteomeXchange)
Workplan proposal
•
•
•
•
•
Characterize the transcriptome to define the actual chr16’s gen set expressed and most
importantly which genes are not expressed in the three selected cell types.
Characterize the proteome in detail.
Expression, purification, and characterization of 22 unknown proteins available in NAPPA
collection.
Development of SRM quantitative assays.
 Proteins (862) will be distributed in known (562) and unknown groups (300) and
the study will be performed along 3 years, starting in 2012 (214 proteins).
 Protein packs will be 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 will be first searched by targeted discovery (TD) and relevant
information resulting from this studies will be used to design MRM assays. TD
groups (9) will analyze 54 proteins the first year.
 Each group will use the master sample (this might require the use of synthetic
peptides during the refinement steps). TD will be done in all three selected cell
lines. Regarding MRM, a pool of the three cell lines will be used for the 20 known
proteins. Decision on using a pool or a particular cell line for the unknown proteins
will be taken in light of the results from TD.
 Once developed, the assays will be validated by 2 additional groups. Finally, the
quantitative assay will be set up using heavy peptides.
Definition of Bioinformatic standards and SOPs.
Chromosome 16 timeline
2012
2013
2014
Bioinfirmatic study
Master sample
Transcriptomic study
Targeted discovery (300 proteins)
MRM for 204 proteins
MRM for 329 proteins
MRM for 329 proteins
SOP, bioinformatic procedures, formats, data banks, etc.
Validation of MRM assays (3 groups, immunoreagents, correlation with gene expression)
Clinical samples. Disease-related changes on protein abundance. Biomarkers
Biobanking
2015
2016
Validation of MRM assays (3 groups, immunoreagents, correlation with gene expression)
Clinical samples. Disease-related changes on protein abundance. Biomarkers
Biobanking
2017
SHPP-16
Platform
BD-HPP
Platform
C-HPP
BIOBANK/ISCIII
Proteo-Red/ISCIII
111 Unknow Proteins
735 Know Proteins
Biology
Diseases:
Cells/Tissues
Pathogenesis
Diagnostic
Prognosis
Treatment
http://www.proteored.org
Who we are
• ProteoRed, an initiative for the coordination, integration and
development of 20 proteomics facilities placed all over Spain.
• ProteoRed use to organize and participate in multi-centric
studies that aims to evaluate the robustness and
reproducibility of different proteomics workflows.
• ProteoRed organization has played an active role in the HUPOPSI activities, always in close relation with the developments
and reviews of different MIAPE modules.
Geographical organization
Node 2
J. Mato - CIC-bioGUNE
F. Corrales – CIMA
JM. Arizmendi - UPV
Assoc. to node 4
F.J. Blanco - INIBIC
*
.
Node 3
J. Abian - LP-CSIC/UAB
J. Arribas - HUVH
S. Martínez - PCB
D. Andreu - UPF
FX. Avilés - IBB UAB
O. Bachs - UB
Node 4
X. Bustelo - CIC
*
Central Structure
JP. Albar - CNB
J. Mato - CIC-bioGUNE
J. Abian - LP-CSIC/UAB
Geneva
Jean Charles Sanchez - UG
Portugal
Ana Coelho - ITQB
Deborah Penque - ProCura
Node 1
JP. Albar - CNB
C. Gil - PCM-UCM
A. Marina - CBMSO
Assoc. to Node 1
I. Casal - CIB
Node6
JA. Bárcena - UCO
-
Node 5
M. Sánchez del Pino – CIPF
R. Bru - UA
Assoc. To Node 5
P. Carrasco - UV
SHPP-16
BD-HPP Platform
Coordinator: Francisco J. Blanco
Clinical Research
Biomarkers (D/P/P/T)
1st Phase: Known Proteins
2nd Phase: Unknown Proteins
BIOBANK/ISCIII
Neurologic Disorders
Chair: A. Lopez- Munain
Co-chair:JM Arizmendi
Cancer
Chair:
Co-Chair: I. Casal)
Cardiovascular Diseases:
Chair: L Rodriguez-Padial
Co-Chair: F. Vivanco
CIBERNed
RETIC of
Cancer
Rheumatic Diseases:
Chair: FJ. Blanco
Co-Chair: JP Albar
CAIBER/ISCIII
Obesity
Chair: J Prieto
Co-Chair: F. Corrales
Infectiious Diseases:
Chair: J Fortun
Co-Chair: C. Gil
RETIC of
Rheumatic
CIBERObesity
RETICCardiov.
HOSPITALES
INSTITUTOS DE
INVESTIGACIÓN
NEUROLOGICAL
DISEASES
Dr A. LOPEZ DE
MUNAIN
SPANISH NATIONAL
BIOBANK NETWORK-ISCIII
Dr M. MORENTE
CARDIOVASCULAR
DISEASES
Dr F. VIVANCO & JLR:
PADIAL
CENTROS DE
INVESTIGACIÓN
RHEUMATIC &
MUSCLOSKELETAL
DISEASES
Dr. F. BLANCO
REDES
COOPERATIVAS
OBESITY/LIVER
DISEASES
Drs J. PRIETO & F.
CORRALES
Chr16-HPP
Proteomics
Platforms
CANCER
Drs C. BELDA & I.
CASAL
INFECTIOUS DISEASES
Drs C. GIL & J. FORTÚN
HOSPITALES
ASOCIACIONES
DE PACIENTES
FARMAINDUSTRIA
INSTITUTOS DE
INVESTIGACIÓN
CENTROS DE
INVESTIGACIÓN
PLATAFORMAS
PROTEÓMICAS
REDES
COOPERATIVAS
MINISTERIO DE
ECONOMIA Y
COMPETITIVIDAD
MINISTERIO DE
INDUSTRIA
HPP
ASEBIO
EMPRESAS
AFINES
INVERSIÓN
PRIVADA
MINISTERIO DE SANIDAD
MINISTERIO DE
EDUCACIÓN
COMUNIDADES
AUTÓNOMAS
MINECO
Steering Committee
Analytical (C-HPP)
ISCIII
B-D initiatives
Bioinformatics
Gene/chromosome centric
MS and Ab based
quantitative methods
Disease centric
Hallmarks of disease
Open access repositories
Potential biomarkers and
therapeutic targets
Biotechs
MINECO
Design of prototypes
Quantitation of target proteins
Pharmas
ISCIII
Clinical devices
Personalized medicine
CNB
UCM
CIB
FJD
CicBiogune
CIMA
CIPF
UAB
PCB
Vall D’Hebron
USAL
La Paz
INIVIC
CHROMOSOME-16 CONSORTIUM STRUCTURE
Board of Directors
Project Manager
Executive Committee
Technical Director
Finance Director
WG 1
WG 2
WG 3
WG 4
WG 5
Working Groups
RU1a/1b
RU 2a/2h
RU 3a/3g
RU 4a/4e
RU 5a/5g
Research Units
WG 1.-Protein Micro Array &
Peptide Standard Team
RU1a
RU1b
(Protein Micro Array and Protein Expression Team)
(Peptide Standard Team)
Dr. Manuel Fuentes
CIC/IBMCC (USAL/CSIC),
Salamanca
Dr. Juan P Albar
CNB-CSIC,
ProteoRed, Madrid
Scientific Researchers:
Scientific Researchers:
F. Roncal
M. Lombardía
WG 2.-S/MRM-Protein Platform Team
RU2a
RU2b
RU2c
RU2d
RU2e
RU2f
RU2g
Dr.
Manuel
Sanchez
del Pino
Dr.
Fernando
Vivanco /
Dr. M.E
Barderas
Dr.
Francisco
Blanco
Dr.
Juan P.
Albar
Dr.
Fernando
Corrales
Dr.
Francesc
Canals
Dr.
Concha
Gil
CNB-CSIC,
ProteoRed,
Madrid
CIMA-UN
ProteoRed,
Pamplona
V.H.I.O.
ProteoRed,
Barcelona
PCM-UCM
ProteoRed
, Madrid
Scientific
Researchers:
M. Marcilla
S. Gharbi
A.Alpízar
C. González
Scientific
Researchers:
Scientific
Researchers:
Scientific
Researchers:
UV
ProteoRed
, Valencia
Scientific
Researchers:
FJD,Madrid/
HNP, Toledo
Scientific
Researchers:
INIBIC,
ProteoRed,
La Coruña
Scientific
Researchers:
RU2h
Dr. Silvia
Barceló
IACS,
Zaragoza
(Provisional)
Scientific
Researchers:
WG 3.-Protein Sequencing Team
RU3a
RU3b
RU3c
RU3d
RU3e
RU3f
RU3g
Dr. José M.
Mato / Dr.
Félix
Elortza
Dr. Joaquin
Abian
Dr. Manuel
Sanchez
del Pino
Dr.
Eliandre
de Oliveira
Dr. Ignacio
Casal
Dr. Jesus
M.
Arizmendi
Dr.
Juan P. Albar
UV,
ProteoRed,
Valencia
PCB,
ProteoRed,
Barcelona
Scientific
Researchers:
Scientific
Researchers:
CICBioGUNE,
ProteoRed,
Bilbao
Scientific
Researchers:
IIBB-CSIC
ProteoRed,
Barcelona
Scientific
Researchers:
CIB-CSIC,
ProteoRed,
Madrid
Scientific
Researchers:
UPV
ProteoRed,
Bilbao
Scientific
Researchers:
CNB-CSIC,
ProteoRed,
Madrid
Scientific
Researchers:
A.Paradela
R. Navajas
WG 4.-Bioinformatics Team
RU4a
RU4b
RU4c
RU4d
RU4e
Dr. Juan P
Albar
Dr. Fernando
Corrales
Dr. Joaquin
Abian
Dr. Concha
Gil
Dr. Jesus M.
Arizmendi
CNB-CSIC,
ProteoRed,
Madrid
CIMA-UN
ProteoRed,
Pamplona
IIBB-CSIC
ProteoRed,
Barcelona
PCM-UCM
ProteoRed,
Madrid
UPV
ProteoRed,
Bilbao
Scientific
Researchers:
A.Medina
S. MBartolomé
Scientific
Researchers:
Scientific
Researchers:
Scientific
Researchers:
Scientific
Researchers:
WG 5.-Clinical Health Care & Biobanking
Team (S_B/D-HPP)
RU5a
RU5b
RU5c
RU5d
RU5e
RU5f
RU5g
Dr.
Francisco
Blanco
INIBIC,
ProteoRed,
La Coruña
Dr. Cristobal
Belda
FSB, La Paz
Hospital,
Madrid
(Provisional)
Dr. Rodríguez
Padial/ Dr.
Fernando
Vivanco / Dr.
M.E Barderas
FJD,
Madrid/HNP,
Toledo
Dr. Adolfo
López de
Munain
Inst.
Biodonostia
S. Sebastian
Dr.
Fernando
Corrales
CIMA-UN
ProteoRed,
Pamplona
Dr. Concha
Gil
PCM-UCM
ProteoRed,
Madrid
Dr. Manuel
Morente
SNBN, CNIO,
Madrid
Scientific
Researchers:
Scientific
Researchers:
Scientific
Researchers:
Scientific
Researchers:
Scientific
Researchers:
Scientific
Researchers:
(considered for
inclusion in the
consortium)
Scientific
Researchers:
WG1-Protein Micro Array & Peptide Standard Team
RU1a (Peptide standardization Team):Dr. Manuel Fuentes
Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), Salamanca
RU1b (Protein Micro Array and Protein expression Team): Dr. Juan P
Albar
National Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, Madrid
WG2-S/MRM-Protein Platform Team
RU2a-Dr. Juan P Albar
National Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, Madrid
RU2b-Dr. Fernando Corrales
CIMA-University of Navarra, ProteoRed, Pamplona
RU2c-Dr. Francesc Canals
Vall d'Hebron Institut d'Oncologia (V.H.I.O.),ProteoRed, Barcelona
RU2d-Dr. Concha Gil
Madrid Science Park-Computensis University (PCM-UCM), ProteoRed, Madrid
RU2e-Dr. Manuel Sanchez del Pino
Felipe Princess Research Center (CIPF), ProteoRed, Valencia
RU2f-Dr. Fernando Vivanco / Dr. ME Barderas
Jimenez Díaz Foundation (FJD), Madrid /National Paraplegics Hospital, Toledo
RU2g-Dr. Francisco Blanco
Instituto de Investigacion Biomedica (INIBIC), ProteoRed, La Coruña
RU2h-Dr Silvia Barceló
Aragón Health Sciences Institute (IACS), Zaragoza
WG4-Bioinformatics Team
RU4a-Dr. Juan P Albar
National Center for Biotechnology-CSIC (CNB-CSIC),
ProteoRed, Madrid
RU4b-Dr. Fernando Corrales
CIMA-University of Navarra
ProteoRed, Pamplona
RU4c-Dr. Joaquin Abian
IIBB, CSIC, ProteoRed, Barcelona
RU4d-Dr. Concha Gil
PCM-Computensis University (PCM-UCM), ProteoRed, Madrid
RU4e-Dr. Jesus M. Arizmendi
Basque Country University, ProteoRed, Bilbao
WG3-Protein Sequencing Team
RU3a-Dr. José M. Mato / Dr. Félix Elortza
CIC-BioGUNE, ProteoRed, Bilbao
RU3b-Dr. Joaquin Abian
IIBB, CSIC ProteoRed, Barcelona
RU3c-Dr. Manuel Sanchez del Pino
University of Valencia, ProteoRed, Valencia
RU3d-Dr. Eliandre de Oliveira
Parc Científic de Barcelona (PCB), ProteoRed, Barcelona
RU3e-Dr. Ignacio Casal
Biology Research Center-CSIC (CIB-CSIC), ProteoRed, Madrid
RU3f-Dr. Jesus M. Arizmendi
Basque Country University ProteoRed, Bilbao
RU3g-Dr. Juan P Albar
National Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, Madrid
WG5-Clinical Health Care & Biobanking Team
RU5a-Dr. Francisco Blanco
Instituto de Investigacion Biomedica (INIBIC),
ProteoRed, La Coruña
RU5b-Dr. Cristobal Belda (Provisional)
Severiano Ballesteros Foundation
La Paz Hospital, Madrid
RU5c-Dr. Rodriguez Padial/Dr. Fernando Vivanco/ Dr. ME Barderas
Jimenez Díaz Foundation (FJD), Madrid /National Paraplegics Hospital,
Toledo
Ru5d-Dr. Adolfo López de Munain
Instituto Biodonostia, San Sebastian
RU5e-Dr. Fernando Corrales/J. Prieto
CIMA-University of Navarra
RU5f-Dr. Concha Gil
PCM-Computensis University (PCM-UCM), ProteoRed, Madrid
RU5g-Dr. Manuel Morente (considered for inclusion in the consortium)
Spanish National BioBanking Network
CNIO, Madrid
Aims to achieve in the 1st Chr-16
Consortium Meeting
• Evaluation of the strategy defined in the April
2nd S_HPP Meeting: S/MRM, AIMS, Shotgun,
cell culture, protein expression, data base,
bioinformatics platform, data workflow
• Preparation of JPR manuscript, HUPO-Boston
Posters…
• 2012 Working plan (short and medium term)
HUPO CONGRESS POSTERS (I)
• RE: Abstract log #322 Your abstract entitled Chromosome 16 Consortium:
Current Developments on the Characterization of the Proteins Encoded
by the Chromosome 16" (log #322) is formally accepted for poster
presentation at the HUPO 11th Annual World Congress, September 9-13,
2012 in Boston, MA (USA).
• RE: Abstract log #146 Your abstract entitled Chromosome 16.
Transcriptomic profiling of lymphocyte B Ramos cells, MCF-7 epithelial
cells and CCD18 fibroblasts (log #146) is formally accepted for poster
presentation at the HUPO 11th Annual World Congress, September 9-13,
2012 in Boston, MA (USA).
• RE: Abstract log #368 Your abstract entitled Profiling the Chromosome 16
by high-resolution data-dependent Mass Spectrometry (log #368) is
formally accepted for poster presentation at the HUPO 11th Annual World
Congress, September 9-13, 2012 in Boston, MA (USA).
•
HUPO CONGRESS POSTERS (II)
•
RE: Your abstract log# 758 for the HUPO2012 conference was submitted on
6/30/2012.The log number for your abstract is 758. Chromosome 16 Consortium:
The Spanish B/D-C-HPP Initiative Juan P Albar; Jesus Fortun; Jesus Mari
Arizmendi; Cristobal Belda; Ignacio Casal; Fernando Corrales; Concha Gil; Adolfo
Lopez-Munain; Jesus Prieto; Jesus Rodriguez-Padial; Fernando Vivanco; Francisco J
Blanco . Spanish B/D-HPP Consortium, A Coruña, Spain.
•
•
RE: Abstract log #217 Your abstract entitled Automatic reporting and
reproducibility analysis of ProteoRed participants in the multi-laboratory studies
using the “MIAPE extractor” tool (log #217) is formally accepted for poster
presentation at the HUPO 11th Annual World Congress, September 9-13, 2012 in
Boston, MA (USA).
RE: Abstract log# 785 Your abstract entitled Reporting and connecting
experimental information through proteomics data standards. J. Alberto MedinaAunon; Salvador Martínez de Bartolomé; Miguel A. López; Juan P. Albar Centro
Nacional de Biotecnología - CSIC, Madrid, Spain for the HUPO2012 conference was
submitted on 7/11/2012.