hydroxylated residues

[hcadr...@gmail.com]

Hi Anton, Lev,

I just stumbled across your retention time calculator. Looks interesting but due to an analytical problem that I am confronted with at the moment there immediately came up a question: Would it be possible to also include other PTMs as allowed modifications (besides pSTY), such as hydroxylation (on PKND...) or acetylation, methylation etc. Could be quite useful when dealing with peptides that are heavily modified.

Best,

Hannes

[Lev Levitsky]

Hi Hannes,

you can add new chemical groups to a ChemicalBasis object and then predict retention times, as described in this section of the docs. The main problem would be to find the optimal binding energy for the modified residue, which you would have to set. BioLCCC currently does not provide tools to optimize the binding energy of newly added chemical groups, but you can try varying it and fitting to some experimental data. With enough data, it should be possible to optimize some kind of a penalty function (such as residual sum of squares) and find the best binding energy.

Best regards,

Lev

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Lev Levitsky
Institute for Energy Problems of Chemical Physics RAS
Laboratory of Physical and Chemical Methods for Structure Analysis
Leninsky pr. 38, bld. 2 119334 Moscow Russia
tel: +7 499 1378257 fax: +7 499 1378257, +7 499 1378258