Dear Matt, thanks for your answer. I do not know what the Agilent API does or not to the data, but what I can tell is that the scan are indeed *consecutively* numbered (from 1 till 5'000 or more) in the raw data when you browse them with the Agilent MassHunter Qual software. So my guess is that there might still be something fishy about msconvert here. My understanding was that the former converter (Trapper from Natalie Tasman) was actually relying on the same Agilent API as well! Maybe Natalie could comment on that. And since Trapper was conserving the proper numbering of the scan as in the raw data, something might have changed upon switching to msconvert.
My problem (and others' from our lab) is that, with the current version of msconvert, you almost cannot do anything with the converted Agilent data. For example, MzXML2Search splits out a "segmentation fault" error message as soon as one scan number exceed 27'219 (i.e. if scan>27'220 it crashes; this probably has something to do with single/ double integers stuff?). Second, our Sequest server (Sage-Sorcerer) also crashes on those files (the number of .dta files created from the mzXML are again very much limited to a well defined scan number limit and therefore very few spectra are actually searched). I don't know if I make myself clear but here are my comments: 1) could you verify why msconvert is behaving differently than Trapper (while they supposedly use the same Agilent libraries) when exporting the scan numbers (Trapper performing the correct conversion by conserving the same scan numbering as the raw file) 2) If that's not possible for you to fix msconvert in that respect, would it be possible to provide an option in msconvert in order to renumber the scan consecutively from 1 till the end. I guess such option may anyway one day be useful for other people for other applications. Thanks a lot for your help, Best, Ludovic -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
