Reagents and resources
Michael Tiemeyer
Monday, 28 July 2008 01:19 UTC
Several other of the CFG subgroups have initiated topics that allow subgroup members to request or offer key reagents. If you have a resource or reagent that you think might be particularly useful for glycoproteomic analysis, why not let others know about it? Or, if you’re looking for a thing, this might be the place to ask….
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Replies
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A series of oligosaccharide standards may soon be available to the community for the purpose of investigating structure-to-structure differences in fragmentation patterns, molar response factors, and other analytical parameters. I’ve pasted a recent e-mail, sent from Jim Paulson to several glycobiologists (with permission of the sender and the primary receiver, see below), that describes some aspects of the origin and potential usefulness of this material. Perhaps we could discuss and make suggestions regarding the best use of this material and the sorts of questions that would be most valuable to address. For instance, I would like to know how different the molar response factors are for permethylated oligosaccharides and whether it is realistic to expect that MS and MSn analysis of permethylated glycans can be made quantitative by reference to standards over a practical concentration range. Any other interests or concerns?
Text of e-mail from Jim Paulson to Lance Wells under the subject line: Opportunity for Glyco Standards, (7/16/08):
Lance,
The short answer is yes, standards will be available shortly. I don’t have a list handy, but it includes about 30 N-linked, O-linked and glycolipids glycans . In addition there are about 100 or so terminal glycan structures (di-dodeca saccharides) that were prepared in larger amounts that are currently available on request (not being billed as MS standards, but I see no reason not to use these).
Examples of compounds made in the last two quarters, many of which will be offered, are found at this link:
http://www.functionalglycomics.org/static/consortium/resources/timelined2.shtml
And the compounds currenlty offered in 1-5 mg amounts:
http://www.functionalglycomics.org/static/consortium/resources/resourcecored2.shtml#TetraHigh
Let me clarify a bit to set realistic expectations. This is an existing effort of the CFG synthesis Core that was initiated two years ago and will just come ‘online’ in the next month or two. It took a long time to see that the demand was truley there, and a major impetus for this was the NCI request of you and Novotny/Yehia. Then the Core had to modify its practices to set aside compound, and accumulate sufficient compounds to make available. The Core makes 40 glycans per year, and is now setting aside 0.5 mg (or as little as 0.25 mg) of each compound synthesisized to be distributed in 5-10 µg aliquots to any request approved by the Steering Committee in the usual request process. All this activity is approved by the SC, but is not yet a formal milestone of the Core (will be in September this year).
Since it is intended to be distributed to MS labs, it makes terrific sense to me to coordinate activities. Regardless we will be moving forward with the distribution when someone finds time to aliquot them, label them and develop the online list. Since Core D has been doing this on their own, I have no idea at this point if they will be good standards. But I expect they will be useful based on the limited analytical data we have on each of them (mainly TLC, MS and NMR for the ones prepared in larger amounts). So involvement of MS labs to validate them as useful standards (and eliminate any not useful) would be extremely valuable for the community.
Regards,
Jim
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