Retreats Spring2014 ProteinInference

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Knut Reinert edited this page Mar 28, 2014 · 16 revisions

Protein inference discussion (Hendrik, Lars, George, Canan, Xiao, Rabia, Jens)

Protocol

Knut explains Xiaos project: We want to implement a bayesain appraoch that takes into account not only peptide ID lists but additional information from the MS1 map. He mentions PIA (Bochum)
Hendrik: we would need a good protein inference in OpenMS now. Mentions Fido which is a C++ library with MIT license and could go into contrib.
Lars: mentions the Huang He comprison paper (Knut adds Claasens paper). He thinks ProteonProhet would be a standard to beat and nice to have. (T. Huang and Z. He, Bioinformatics vol. 28 no. 22 (2012) 2956)
George: Mayu from Claasen is more for FDR not protein inference
Jens: Proteoypicity has to be on the whole genome. Also in the implementation it would be nice to have a container that encapsulates all evidence for a ProteinID so other approaches could use it.
All: We discussed getting a possible "good" real data set. People should talk to experimental partners whether they could provide protein sets (antibodies?. commericla prtoeins (form synthesized peptides)? )

Action items

Hendrik will look at possible integration of Fido into OpenMS contrib.
Evaluation pipeline will be coordinated between Freiburg (Lars) and Berlin (Xiao) with KNIME/Galaxy
Think about integrating quantitation information, when having a labelled experiment. (Peptides originating from same protein expected to show similar fold changes.)
Think about aopying the consenus ID approach (possible MSc thesis)
Look at what MaxQuant does => see http://bit.ly/1dz8g3S

Questions

how do we go about pepXML? (Fido, ProteinProhet, Jens (dnmso) still need it)
pepXML(generated from peptideProphet) doesn't go through external/TPP_ProteinProhet in TOPPAS, problem with absolut paths in pep.xml files.
pepXML(converted by IDfileconverter) can not be processed in PeptideProphet (OpenMS-ms-general mailing list Feb 12)

Misc

Oliver might get data of whole protein measurements that could be combined with different fragmentation technologies (ETD, HCD, CID).