I've had this problem with a variety of tools and their handling .wiff data file from Analyst, and now having gotten msconvert to work (thanks Matt) I was hoping that msconvert did it "right".
Unfortunately, it doesn't seem so. I believe that the scan number and retention times should increase monotonically in the mzXML file and in a tandem mass-spectrometry experiment, I expect the MS1 scan to be immediately followed by the MS/ MS scans whose precursors are derived from the MS1 scan. A number (n >= 2) of converters (msconvert & ABI's) for .wiff files do not respect this file structure and output the spectra by experiment and cycle, with all experiment 1 (MS1 spectra) first, then all experiment 2 (MS/MS from first selected precursor peak from each MS1 spectrum), then all experiment 3, etc. In the msconvert mzXML output, there isn't even any reference in the MS2 spectra to assist in determining the correct MS1 spectrum to associate with the MS2 spectrum. It is possible to use various tricks to try and determine cycle, experiment, and MS1/MS2 relationships but at the least these require sorting (globally) on retentionTime, an expensive proposition for large mzXML files. I'd be happy to provide an example mzXML output to demonstrate the issue. - n -- 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.
