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FAQs

UNIX

Questions, comments, contributions?

The mchips server has access to the IPAG storage.

    label free

    1. Please export from Progenesis (do not filter beforehand)
    • protein list
    • all identification export as aie.csv (fixed name)
    and export from Mascot the according (!) result. Click export (Error message: In the adressbar delete the "i" in "idata"), Export format: pepXML, p<0.05, select Description and Mass, deselect pI. Save the .xml file in put_MGFs_here (takes a while, too) and grant read access to ipag(Unix Group\ipag). If it is too big to export via webserver, do this. Now as a third file you have the
    • pepXML file


    2. Put all three files to put_MGFs_here.

    3. Open a Nx connection to mchips

    4. On mchips (yellow text window) type pid.pl <enter> which will parse the .xml file. For label free (in contrast to TMT6x) pid.pl will also read the aie file. Beware: warning messages will be displayed in case of filtering in Progenesis or when the aie and XML files do not match. But the skript will not stop because of this! An .id file will be produced (that should be verified to have a considerable size).

    7. On mchips type the following two lines, each followed by <enter>:
    cd put_MGFs_here
    mchips

    8. Click Data Import, Upload Experiment, (evt. the table family to upload to),yellow textwindow: type n<enter>, click define new experiment and provide an experiment name in the text window.

    y for label free and provide the name of your .id file (from step 4, e.g. 000101_SFB_fp_A.id), then your protein list (e.g. 000101_SFB_fp_A_protein_list.csv).

    Upload may take a while but it does not need any further action from the user side. After importing the quantification data (.csv) and the identification data (.id file) it will display

    -- SUCCESSFUL COMPLETION :-) --

    Data are uploaded in all-or-none fashion, i.e. when there was a problem any time during the upload, the database remains completely unchanged.

    2011-02-14