Added by Nuno Bandeira, last edited by Nuno Bandeira on Jun 05, 2016  (view change)

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ProteoSAFe Demo (part 2)

ASMS 2016, Bioinformatics of Protein Identification

Configuring a restricted search with PTMs from blind modification search

MODa: search allowing for one vs 2+ unexpected PTMs per peptide

Selected mass shifts for follow-up restricted database search for identification of Peptide-Spectrum Matches (PSMs)

PTM Mass shift Site Most likely explanation
Oxidation 15.994915 M Artifact
Pyroglutamate -17.026549 NTerm-Q Artifact
Phosphorylation 79.966331 S PTM
Carbamylation 43.005814 NTerm Artifact
Acetylation 42.010565 NTerm PTM
Deamidation 0.984016 N,Q Artifact
Dioxidation 31.989829 W Artifact
Sodium adducts 21.981943 * Artifact
Dehydration -18.010565 STE Artifact
Methylation -43.005814 C PTM
Dimethylation 28.031300 K PTM
Methylation 14.01565 H PTM
Carboxymethyl 58.005479 K, NTerm Artifact
Carboxyethyl 72.021129 K PTM
Unknown 55 R Unknown
Unknown 30 S Unknown

MS-GFDB: searching for 17 PTMs with 1 PTM per peptide vs 2 PTMs per peptide

Search #PTMs #PTMs/pep FDR #PSMs URL
MS-GFDB, w/single blind 17 1 5% 8,915 http://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=8da3fa0bd3c94cca9cf2ce3e770f4739
MS-GFDB, w/two single blind 17 2 5% 7,042 http://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=84108cd67da2477c9273d87261f6e20c

Localization of PTM sites

Methylation of Cysteine is a known modification in cataractous lens samples and, because Cysteines were reduced/alkylated in this sample, it shows up as "C-43". In particular, protein gi|557548 in this MS-GFDB search is identified to have multiple cysteine modifications on different sites.

Exercise: Use ProteoSAFe's results filter interface to determine whether the results support multiple Cysteine methylation sites in the 3 Cysteines in YDCDCDCADFHTYLSR

  • Filter the "Peptide" column by entering "ADFHTYLSR.C" in the "Peptide" column header and clicking filter at on the top-left
  • You can also sort the table rows by peptide sequence using the Up/Down arrows to the right of "Peptide" in the column header