to proteomics data in the PRIDE database

Transcription

1 Interactive and computational access to proteomics data in the PRIDE database Daniel RIOS PRIDE software developer PRIDE team, Proteomics Services Group PANDA group European Bioinformatics Institute Hinxton, Cambridge United Kingdom BSPR/EBI EBI is an Outstation of the European Molecular Biology Laboratory.

2 Overview PRIDE: what do we store? Accessing the data: BioMart DAS DASTY client

3 PRIDE

4 MS proteomics: overall workflow peptides proteins 100 % sequence database MS analysis 100 % m/z fragmentation MS/MS analysis P R O T O C O L m/z 7 th Joint BSPR/EBI Proteomics meeting

5 PRIDE database ( peptides 100 MS/MS analysis proteins 100 % sequence database MS analysis % m/z fragmentation m/z PRIDE stores: 1) Peptide IDs 2) Protein IDs 3) Mass spectra as peak lists 4) Valuable additional metadata 7 th Joint BSPR/EBI Proteomics meeting

6 PRIDE: why is it there? Repository to support publications (proteomics MS derived data) Source of proteomics data for other data resources PRIDE: reliable source of MS proteomics data for other resources 7 th Joint BSPR/EBI Proteomics meeting

7 PRIDE growth Count Date 7 th Joint BSPR/EBI Proteomics meeting

8 BIOMART Interface ( 7 th Joint BSPR/EBI Proteomics meeting

9 BioMart A collaboration European Bioinformatics Institute (EBI) Cold Spring Harbor Laboratory (CSHL) Ontario Institute for Cancer Research (OICR) Aim To develop a structured data query engine that works for biological research All benefits of structured data in the relational database but with Queries without the knowledge of the table structure Scales for big datasets Solves integration

10 PRIDE BioMart (

11 PRIDE BioMart

12 PRIDE BioMart

13 The spectacular bit: across-biomart queries! Question: Which proteins, identified in PRIDE, in blood plasma, are transcribed from genes located in chromosome 11 PRIDE Ensembl

14 DAS ( 7 th Joint BSPR/EBI Proteomics meeting

15 Distributed Annotation System DASTY

16 PRIDE DAS server

17 DASTY3 client ( 7 th Joint BSPR/EBI Proteomics meeting

18 DASTY client Dasty, a web client which retrieves, integrates and visualizes protein annotations. It collects data from different DAS sources and then merge it to provide the user with a unified view of the sequence-annotated features.

19 PRIDE DAS server: Dasty example (1) (

20 PRIDE DAS server: Dasty example (2) (

21 PRIDE AND OTHER REPOSITORIES: ProteomeXchange Juan A. Vizcaíno BSPR/EBI Educational Workshop Hinxton, 16 July 2010

22 Large-scale submissions -Protein IDs -Peptide IDs -Peak lists -Metadata -Instrument output files (raw data, ) PeptideAtlas NCBI Peptidome Individual submission EBI PRIDE Tranche GPMDB Users Other DB s Large-scale submissions ProteomeXchange Consortium Juan A. Vizcaíno juan@ebi.ac.uk BSPR/EBI Educational Workshop Hinxton, 16 July 2010

23 The PRIDE Team Attila Csordas Juan Vizcaino Richard Côté Florian Reisinger Henning Hermjakob Rui Wang Joe Foster (Ph.D. student) Andreas Schonegger (Trainee)

24 Special thanks, collaborations and funding Rafael Jimenez Jose Villaveces PRIDE collaborators Funding

25 Thank you! Questions? 7 th Joint BSPR/EBI Proteomics meeting