Glyco-peptide
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Current revision
2008-08-22 RA proposes effort to generate peptide lists for dirty peptide synthesis. Tentative deadline is 08-29.
Links:
Glyco-peptide TODO list Export questions discussion list
2008-08-22 [late] emailed the following people, seeking data
Simon
- responded. Does not have any relevant data. Has database of existing transitions and ordered peptides, perhaps this can be used to filter list.
Safia
- responded. She has already given me 2 large sets of data from Breast Cancer cell lines/tissue. The first is part of the existing GlycoAtlas build,
the second will be incorporated.
Yong (Z)
- responded. He had already contributed some data, but has additional urine (1800 peptides) and ovarian cell glycocapture (400 peptides) samples. Sent
sample information, will incorporate into new build.
Kelly
- responded. Has given a pancreas dataset in the past, may have generated data in set that Julian gave to Eric. Contributed breast-cancer IEF samples. Has now also contributed an additional pancreas dataset.
Hamid
- responded. Contributed several test datasets created while testing HPINs technology. These use a large serum glycocapture sample prepared by Kelly.
Julian
- responded. Had recently given dataset to Eric, which will be incorporated.
Bernd (W)
- responded. Created a separate list from his cell surface data, will be responsible for merging and prioritizing the lists from Jingchun, himself, and me.
Johan
- responded. Has contributed large serum (IEF) datasets in the past, no new data.
Ralph
- responded. Has only mouse data, has contributed in the past and is basis for mouse glyco build.
Ruth
- responded. Has only mouse data, will transfer to ftp servers. Suggested using mouse/human ortholog data.
Silvia
- responded, contributed Colon cancer data.
2008-08-26 Jingchun announces he has generated list of 3464 glycopeptides from putative cancer biomarkers.
2008-08-27 Bernd announces he has generated a list of peptides from surface proteins, proposes common export format.
2008-08-28 Discuss export details with Bernd
2008-08-28 Discover that Breast cancer search not compatible with Atlas Build, will research with XTandem.
2008-08-28 Received last of human data
2008-08-31 Received one batch of mouse glyco data, more to come?
2008-09-01 Finished global ProteinProphet, started build proper
2008-09-01 Ran export script against unipep data, send email to Bernd.
