Hi Brian, thanks for your reply. I have just uploaded the mzxml and wiff files on Insilico's ftp server; filename: wiff_mzxml_comparison_complete- upload.zip. 1214-CCM.mzxml is "as expected" whereas "OS_G2...mzxml" has this zig- zag characteristic.
Thanks for your help! Oliver On Feb 16, 5:12 pm, "Brian Pratt" <[email protected]> wrote: > 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 > toftp://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 -~----------~----~----~----~------~----~------~--~---
