Re: [Psidev-pi-dev] mzIdentML 1.2.0 - determining "donor" of cross-linked peptide

[Oliver K. <oli...@un...>]

I like that idea.

Cheers,
  O.

> On 17 Jan 2017, at 17:14, David Hollenstein <hol...@gm...> wrote:
> 
> Hi, I was at the EuBIC winter school last week and heard from Gerhard Mayer about the upcoming update of the mzIdentML format.
> 
> Since I'm interested in the inclusion of cross-linked peptides I read the current draft for version 1.2.0. I'm very happy about this modification. However, I have one suggestion to make the selection of the donor peptide less ambiguous. Currently the draft contains the following text passage:
> 
> It is RECOMMENDED that the “donor” peptide SHOULD be the longer peptide or the one with the higher molecular weight if the same length.
> 
> There are various possibilites when two peptides have the same length and the same molecular weight, but not exactly the same sequence. One example is when they have the same amino acid composition but a different order, for example: AADITSLYK and YLSTIDAAK
> 
> In order to make these cases unambiguous and to avoid the need to calculate the molecular mass for determining the donor and acceptor peptides, I would suggest to use the alphabetical order, not considering any modifications, if both peptides are equally long.
> 
> Best regards
> David Hollenstein
> 
> 
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---
Oliver Kohlbacher
Professor, Center for Bioinformatics, Dept. of Computer Science, & Faculty of Medicine
Director, Quantitative Biology Center, University of Tuebingen, Germany
Fellow, Max Planck Institute for Developmental Biology

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