Getting modified peptides into skyline | Jan Refsgaard | 2013-02-14 04:27 | |||||||||||||||||||||
I have converted some Thermo rawfiles to mzML (with msconvert.exe), and subsequently altered the <binary>fields to only contain the peaks identified by maxquant and updated the checksum, all 'pointers' and the 3 'array length' attributes accordingly, for none modified peptides I can build a library by supplying skyline with my modified mzML file and a ssl file (build from max quants msms.txt), but for some reason I cannot get skyline to accept modifications snippet of my SSL file: file scan charge sequence modifications ... 20130204_QE5_LC3_KBE_QC_MNT_HELA_01_filtered.mzML 2006 3 AGMTHIVREVDR AGM[+15.994914]THIVREVDR ... How do I tell skyline that the modication of weight +15.994 is an oxygen? I have also looked at the sql tables of the biblospeck files generated by skyline to compare my constructed library with 'custom libraries' and even there I cannot see which column maps the weight to modification... I could of course spend a week or two writing a parser to convert MaxQuant files into *.mzid files and then everything should work (I think)... but there must be a simpler way :) Thanks for your help, keep up the good work Jan, the confused bioinformatician :) |
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