title: Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.
abstract: The proteome informatics research group of the Association of Biomolecular Resource Facilities conducted a study to assess the community's ability to detect and characterize peptides bearing a range of biologically occurring post-translational modifications when present in a complex peptide background. A data set derived from a mixture of synthetic peptides with biologically occurring modifications combined with a yeast whole cell lysate as background was distributed to a large group of researchers and their results were collectively analyzed. The results from the twenty-four participants, who represented a broad spectrum of experience levels with this type of data analysis, produced several important observations. First, there is significantly more variability in the ability to assess whether a results is significant than there is to determine the correct answer. Second, labile post-translational modifications, particularly tyrosine sulfation, present a challenge for most researchers. Finally, for modification site localization there are many tools being employed, but researchers are currently unsure of the reliability of the results these programs are producing.
authors.affiliation: University of California, San Francisco, California;
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Chalkley
authors.forename: Nuno
authors.initials: N
authors.lastname: Bandeira
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Chambers
authors.forename: Karl R
authors.initials: KR
authors.lastname: Clauser
authors.forename: John S
authors.initials: JS
authors.lastname: Cottrell
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Eugene A
authors.initials: EA
authors.lastname: Kapp
authors.forename: Henry H N
authors.initials: HH
authors.lastname: Lam
authors.forename: W Hayes
authors.initials: WH
authors.lastname: McDonald
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Neubert
authors.forename: Rui-Xiang
authors.initials: RX
authors.lastname: Sun
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D045424:Complex Mixtures / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology; D006801:Humans; D010455:Peptides / Q000737:chemistry / Q000302:isolation & purification* / Q000378:metabolism; D011499:Protein Processing, Post-Translational / Q000235:genetics*; D020543:Proteome; D020539:Sequence Analysis, Protein
chemical_list: D045424:Complex Mixtures; D010455:Peptides; D020543:Proteome