I provided a more general tool for organics. I don't know about one that
works for peptides. It'd be fairly easy to make though. I agree that MW is
not THAT useful in determining the sequence but it can be helpful. Very
helpful.
For example
If you had MW you could generate a big set of peptides that matches it
within some error.
Then if you had some knowledge of AAs (from MS/MS, derivatives or something)
you could constrain that big list.
Then if you had MS/MS you could constrain further - (perhaps require
existence of some AAs(low mass immonium ions), and sequence 'tags').
>From that you might not have that many choices left.
Actually same applies to small organics. DNA sequences are more strongly
constrained. For small ones you can say how many ACGT 'atoms' there are.
No sequence though. But it may help with some problems. I have solved a
few 'unsolvable' problems through this approach of application of multiple
constraints.
Matt Sweeney
mattsweeney@earthlink.net
Mass Spec Consulting
Training/Operations/Consulting/Method Development
LC/MS Pharmacokinetics, Peptides, Proteins, Metabolism,
Maintenance Classes, Specialist in Finnigan Equipment and Software
-----Original Message-----
From: Marekov, Lyuben (NIAMS) <marekovl@mail.nih.gov>
To: Recipients of ABRF List <abrf@aecom.yu.edu>
Date: Wednesday, April 26, 2000 7:42 PM
Subject: RE: Atomic composition calculator software
> Juhani
>I assume you are talking about peptides.
>While theoretically possible, I believe such a program will not be of much
>practical use.
>Consider a sequence: H-GKSRRVR-OH with a composition C34, H67, N17, O9
>and a sequence: H-KAKMPKR-OH with a composition C37, H71, N13, O8, S1
> The MW difference is 0.0039DA, a little over 4 ppm
> I do not think it is possible to determine MW so accurately and
reliably.
>And when you go to higher MW the combinations are increasing (and the
>accuracy goes down)
> Lyuben
>
>Lyuben Marekov
>NIAMS, Bldg6, Room 128
>Phone 301-496-7190
>e-mail: marekovl@mail.nih.gov
>
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