1. Proteomics Informatics – Databases, data repositories and standardization (Week 6)

2. Protein Sequence Databases

3. RefSeq http://www.ncbi.nlm.nih.gov/books/NBK21091/ Distinguishing Features of the RefSeq collection include: non-redundancy explicitly linked nucleotide and protein sequences updates to reflect current knowledge of sequence data and biology data validation and format consistency ongoing curation by NCBI staff and collaborators, with reviewed records indicated

4. Ensembl http://www.ensembl.org/ genome information for sequenced chordate genomes. evidenced-based gene sets for all supported species large-scale whole genome multiple species alignments across vertebrates variation data resources for 17 species and regulation annotations based on ENCODE and other data sets.

5. UniProt http://www.uniprot.org/ The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

6. Species-Centric Consortia For some organisms, there are consortia that provide high-quality databases: Yeast (http://yeastgenome.org/) Fly (http://flybase.org/) Arabidopsis (http://arabidopsis.org/)

7. FASTA http://en.wikipedia.org/wiki/FASTA_format RefSeq: >gi|168693669|ref|NP_001108231.1| zinc finger protein 683 [Homo sapiens] MKEESAAQLGCCHRPMALGGTGGSLSPSLDFQLFRGDQVFSACRPLPDMVDAHGPSCASWLCPLPLAPGRSALLACLQDL DLNLCTPQPAPLGTDLQGLQEDALSMKHEPPGLQASSTDDKKFTVKYPQNKDKLGKQPERAGEGAPCPAFSSHNSSSPPP LQNRKSPSPLAFCPCPPVNSISKELPFLLHAFYPGYPLLLPPPHLFTYGALPSDQCPHLLMLPQDPSYPTMAMPSLLMMV NELGHPSARWETLLPYPGAFQASGQALPSQARNPGAGAAPTDSPGLERGGMASPAKRVPLSSQTGTAALPYPLKKKNGKI LYECNICGKSFGQLSNLKVHLRVHSGERPFQCALCQKSFTQLAHLQKHHLVHTGERPHKCSVCHKRFSSSSNLKTHLRLH SGARPFQCSVCRSRFTQHIHLKLHHRLHAPQPCGLVHTQLPLASLACLAQWHQGALDLMAVASEKHMGYDIDEVKVSSTS QGKARAVSLSSAGTPLVMGQDQNN Ensembl: >ENSMUSP00000131420 pep:known supercontig:NCBIM37:NT_166407:104574:105272:-1 gene:ENSMUSG00000092057 transcript:ENSMUST00000167991 MFSLMKKRRRKSSSNTLRNIVGCRISHCWKEGNEPVTQWKAIVLGQLPTNPSLYLVKYDGIDSIYGQELYSDDRILNLKVL PPIVVFPQVRDAHLARALVGRAVQQKFERKDGSEVNWRGVVLAQVPIMKDLFYITYKKDPALYAYQLLDDYKEGNLHMIPD TPPAEERSGGDSDVLIGNWVQYTRKDGSKKFGKVVYQVLDNPSVFFIKFHGDIHIYVYTMVPKILEVEKS UniProt: >sp|Q16695|H31T_HUMAN Histone H3.1t OS=Homo sapiens GN=HIST3H3 PE=1 SV=3 MARTKQTARKSTGGKAPRKQLATKVARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLMREIAQDFK TDLRFQSSAVMALQEACESYLVGLFEDTNLCVIHAKRVTIMPKDIQLARRIRGERA

8. PEFF - PSI Extended Fasta Format >sp:P06748 \ID=NPM_HUMAN \Pname=(Nucleophosmin) (NPM) (Nucleolar phosphoprotein B23) (Numatrin) (Nucleolar protein NO38) \NcbiTaxId=9606 \ModRes=(125|MOD:00046)(199|MOD:00047) \Length=294 >sp:P00761 \ID=TRYP_PIG \Pname=(Trypsin precursor) (EC 3.4.21.4) \NcbiTaxId=9823 \Variant=(20|20|V) \Processed=(1|8|PROPEP)(9|231|CHAIN) \Length=231 http://www.psidev.info/node/363

9. Sample-specific protein sequence databases Protein DB Identified and quantified peptides and proteins MS Samples Peptides

10. Sample-specific protein sequence databases Next-generation sequencing of the genome and transcriptome Sample-specific Protein DB Identified and quantified peptides and proteins MS Samples Peptides

11. Sample-specific protein sequence databases Next-generation sequencing of the genome and transcriptome Sample-specific Protein DB Identified and quantified peptides and proteins MS Samples Peptides

12. Data Repositories

13. ProteomeExchange http://www.proteomeexchange.org/

14. PRIDE http://www.ebi.ac.uk/pride/

15. PeptideAtlas http://www.peptideatlas.org/

16. Chorus Key Aspects: Upload and share raw data with collaborators Analyze data with available tools and workflows Create projects and experiments Select from public files and (re- )analyze/visualize Download selected files

17. MassIVE Key Aspects: Upload files Spectra and Spectrum libraries, Analysis Results, Sequence Databases, Methods and Protocol) Perform analysis using available tools Browse public datasets Download data

18. The Global Proteome Machine Databases (GPMDB) http://gpmdb.thegpm.org

19. Comparison with GPMDB Most proteins show very reproducible peptide patterns

20. Comparison with GPMDB Query Spectrum Best match In GPMDB Second best match In GPMDB

21. GPMDB Data Crowdsourcing Any lab performs experiments Raw data sent to public repository (TRANCHE, PRIDE) Data imported by GPMDB Data analyzed & accepted/rejected General community uses information and inspects data Accepted information loaded into public collection

22. Information for including a data set in GPMDB 1.MS/MS data (required) 1.MS raw data files 2.ASCII files: mzXML, mzML, MGF, DTA, etc. 3.Analysis files: DAT, MSF, BIOML 2.Sample Information (supply if possible) 1.Species : human, yeast 2.Cell/tissue type & subcellular localization 3.Reagents: urea, formic acid, etc. 4.Quantitation: SILAC, iTRAQ 5.Proteolysis agent: trypsin, Lys-C 3.Project information (suggested) 1.Project name 2.Contact information

23. How to characterize the evidence in GPMDB for a protein? High confidence Medium confidence Low confidence No observation

24. Star t EndN-2-3-4-5-6-7-8-9-10-11SkewKurt 2142485390.150.180.220.170.150.070.030.01 0.00-0.01-2.01 24926710100.040.090.130.16 0.140.130.060.040.05-0.08-1.89 1821968320.090.150.200.190.180.130.050.010.00 -0.12-1.84 25026740.250.000.250.000.250.00 0.250.48-2.28 1242690.100.12 0.170.12 0.140.04 0.03-0.33-0.88 2465510.22 0.200.140.060.000.040.080.020.040.47-1.62 661013340.090.080.11 0.090.110.090.130.080.120.10-1.21 249273600.020.000.200.100.130.250.200.070.030.000.45-1.36 214242100.000.100.00 0.300.20 0.54-1.39 214239320.030.060.16 0.090.220.090.160.000.030.20-0.99 1111201170.090.200.150.260.290.010.00 0.62-1.36 251267160.00 0.130.250.190.13 0.060.000.24-0.60 214241140.00 0.070.290.210.070.290.000.070.87-0.97 1591741000.300.250.310.030.070.030.010.00 0.99-1.07 68101100.00 0.200.10 0.30 0.86-0.91 235248300.000.030.00 0.300.200.230.130.030.070.81-0.82 Statistical model for 212 observations of TP53

25. Statistical model for observations of DNAH2

26. Statistical model for observations of GRAP2

27. DNA Repair

29. TP53BP1:p, tumor protein p53 binding protein 1

31. Sequence Annotations

32. TP53BP1:p, tumor protein p53 binding protein 1

34. Peptide observations, catalase Peptide SequenceObservations FSTVAGESGSADTVR2633 FNTANDDNVTQVR2432 AFYVNVLNEEQR1722 LVNANGEAVYCK1701 GPLLVQDVVFTDEMAHFDR1637 LSQEDPDYGIR1560 LFAYPDTHR1499 NLSVEDAAR1400 FYTEDGNWDLVGNNTPIFFIR1386 ADVLTTGAGNPVGDK1338

35. Peptide Sequenceω FSTVAGESGSADTVR0.08 FNTANDDNVTQVR0.07 AFYVNVLNEEQR0.05 LVNANGEAVYCK0.05 GPLLVQDVVFTDEMAHFDR0.05 LSQEDPDYGIR0.04 LFAYPDTHR0.04 NLSVEDAAR0.04 FYTEDGNWDLVGNNTPIFFIR0.04 ADVLTTGAGNPVGDK0.04 Peptide frequency (ω), catalase

36. ω Peptide sequences Global frequency of observation (ω), catalase

37. For any set peptides observed in an experiment assigned to a particular protein (1 to j ): Omega (Ω) value for a protein identification

38. Protein IDΩ (z=2)Ω (z=3) SERPINB10.880.82 SNRPD10.880.59 CFL10.810.87 SNRPE0.80.81 PPIA0.790.64 CSTA0.790.36 PFN10.760.61 CAT0.710.78 GLRX0.660.8 CALM10.620.76 FABP50.570.17 Protein Ω’s for a set of identifications

39. Retention Time Distribution

40. Mass Accuracy

41. GO Cellular Processes

42. KEGG Pathways

43. Open-Source Resources

44. ProteoWizard http://proteowizard.sourceforge.net

45. Protein Prospector http://prospector.ucsf.edu/

46. PROWL http://prowl.rockefeller.edu/

47. Proteogenomics - PGx http://pgx.fenyolab.org/

48. UCSC Genome Browser http://genome.ucsc.edu/

49. Slice - Scalable Data Sharing for Remote Mass Informatics Most mass spectrometry data is acquired in discovery mode, meaning that the data is amenable to open-ended analysis as our understanding of the target biochemistry increases. In this sense, mass spectrometry based discovery work is more akin to an astronomical survey, where the full list of object-types being imaged has not yet been fully elucidated, as opposed to e.g. micro-array work, where the list of probes spotted onto the slide is finite and well understood. openslice.fenyolab.org Developed by Manor Askenazi

50. Standardization

51. Standardization - MIAPE

52. Standardization – MIAPE-MSI

53. Standardization – XML Formats mzML - experimental results obtained by mass spectrometric analysis of biomolecular compounds mzIdentML - describe the outputs of proteomics search engines TraML - exchange and transmission of transition lists for selected reaction monitoring (SRM) experiments mzQuantML - describe the outputs of quantitation software for proteomics mzTab - defines a tab delimited text file format to report proteomics and metabolomics results. MIF - decribes the molecular interaction data exchange format. GelML - describes the processing and separations of proteins in samples using gel electrophoresis, within a proteomics experiment.

54. Standardization - mzML

55. Standardization - mzIdentML

56. Proteomics Informatics – Databases, data repositories and standardization (Week 6)