Thank You all for your helpful input.
Actually the problem came from the lab nex door, they have a
molecule that has molecular weight in the region of 160 Da, with a
very peculiar NMR spectra and they have a relatively accurate mass,
determined by FT-ICR MS. In this case a mass alone can be used to
give a suggestion of the atomic composition for the molecule.
For petide analysis, I agree to stick with good old MSMS analysis
using my nice little Q-TOF.
Thank you!
-Juhani
***************************
> From: "MSweeney" <mattsweeney@earthlink.net>
> Subject: Re: Atomic composition calculator software
> Date: Wed, 26 Apr 2000 22:36:34 -0700
> To: Recipients of ABRF List <abrf@aecom.yu.edu>
> 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
> >
>
>
Juhani Saarinen
Protein Chemistry Laboratory
Institute of Biotechnology
University of Helsinki, Finland
e-mail jksaarin@operoni.helsinki.fi
Phone +358-9-708 59 414
Fax +358-9-708 59 416
Street adress:
Viikinkaari 9
FIN-00014, Helsingin yliopisto
PL 56
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