InsilicosViewer uses the same parsing library as TPP so if there's a problem with interpreting the files it would be common to both systems (or, of course, the files themselves may be expressing a converter issue).
Perhaps you could zip up an example (input and output) and FTP to ftp://insilicos.serveftp.net/pub ? Brian -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Monday, February 16, 2009 3:31 AM To: spctools-discuss Subject: [spctools-discuss] Problems with mzXML files/ASAPratio Dear spctools community, I would like to ask for some help with a strange phenomena that I observe in some mzxml files. We acquire our LC-MS/MS data from an ABI QSTAR. The wiff files are converted into the mzxml format using mzwiff. Normally the resulting profile of the total ion chromatogram (TIC) in the mzxml file corresponds to the wiff file and is depicted as a continuous line using Insilicos' mzxml viewer. However, we now get wiff files from a different QSTAR in a different facility: Here, the TIC of the mzxml file differs from the wiff file and is depicted as a zig-zag line rather than a continuous line as is seen for the wiff file. These mzxml files still yield a high number of peptide identifications in X!Tandem and can be used for quantization with XPRESS; ASAPratio however fails on these files. In terms of data acquisition, "normal" mzxml files are derived from wiff files where each MS1 scan is followed by 3 MS2 scans whereas "zig- zag" mzXML files are derived from wiff files where each MS1 scan is followed by 4 MS2 scans. I have observed this behavior with both mzSTAR and mzwiff for both profile and centroid mode. Since this behavior seems to interfere with ASAPratio, I would like to ask for some help and guidance. Thanks! Oliver --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
