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Re: [Psidev-pi-dev] mzIdentML 1.2.0 - determining "donor" of cross-linked peptide
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From: Jones, A. <And...@li...> - 2017-01-18 12:51:45
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Good suggestion David, I will add that to the specifications. Best wishes Andy -----Original Message----- From: Oliver Kohlbacher [mailto:oli...@un...] Sent: 17 January 2017 20:09 To: David Hollenstein <hol...@gm...> Cc: psi...@li... Subject: Re: [Psidev-pi-dev] mzIdentML 1.2.0 - determining "donor" of cross-linked peptide 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 > > > ---------------------------------------------------------------------- > -------- Check out the vibrant tech community on one of the world's > most engaging tech sites, SlashDot.org! > http://sdm.link/slashdot______________________________________________ > _ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev --- 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 email oli...@un... / oli...@tu... WWW kohlbacherLab.org twitter @OKohlbacher phone +49 7071 29 70457 fax +49 7071 29 5152 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
