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M-CHIPS home
FAQs
UNIX
Questions, comments, contributions?
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The mchips server has access to the IPAG storage.
SILAC
1. Please export from MaxQuant
- a protein list (.txt file) OR
- a peptide list (.txt file)
Unfortunately MaxQuant does not use Mascot any more (now Andromeda). The
identification attributes recorded depend on the file type (peptides or proteins)
and are not compatible to the TMT6x and labelfree pipelines (recording pepXML
tags).
2. Put the file(s) to put_MGFs_here.
3. Open a Nx
connection to mchips
4. On mchips (yellow text window) type silac.pl <enter> (or
silac.pl blabla.txt <enter> using <tab> after hacking in
the first few characters of your file name) which
will parse the .txt file (either proteins or peptides). It produces
- blabla.id (identification information, see 1.)
- blabla.quantL (Intensity L column)
- blabla.quantH (Intensity H column)
- blabla.quantM (Intensity M column, when comprised)
7. 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.
n for not label free
1 (number of conditions excl.
control)
not monochannel
y (non-control
measurements and control measurements are both ...)
1
yes (Input filenames from file)
yes (correct sequence, or
change to put first whatever should be the control)
2x (or 3x) 1 (to affiliate the
same run 1 to all measurements)
n after run 1 was sucessfully entered
everywhere
y to start the upload.
Upload may take a while but it does not need any further action from the
user side. After importing the quantification data (.quantL/H/M)
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
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