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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Warning! Thermo MSFileReader is not version 3.0 SP2; a crash may result from searching this .raw file #1090

Closed DaliJarboui closed 5 years ago

DaliJarboui commented 6 years ago

there is no mention of having a specific MSFILEReader version anywhere???

DaliJarboui commented 6 years ago

That was the warning message I got when I uploaded RAW files: Warning! Thermo MSFileReader is not version 3.0 SP2; a crash may result from searching this .raw file

rmillikin commented 6 years ago

Hello,

On the main page under "System Requirements" we ask that you have Thermo MSFileReader installed, and the particular version we recommend is v3.0 SP2. We've noticed that other versions of MSFileReader can cause crashes; 3.0 SP2 seems to be the best at not crashing.

You may of course ignore the warning and still "Run all tasks" if you don't want to install that particular version of MSFileReader. That's why it's a warning and not a requirement :)

DaliJarboui commented 6 years ago

thanks couldn't see it in the wiki page. although seems to affect the calibration step. Search and new GTPMD working fine. during the calibration step the error message is that there is not enough MS1 and MS2.

rmillikin commented 6 years ago

There may not be enough high-quality PSMs in your run to calibrate with; how many target PSMs with scores of at least 10 do you observe? Is it low-res MS2 data or a very simple sample (e.g., 1 digested protein)?

DaliJarboui commented 6 years ago

it is actually a complex sample (full cell lysate) run on an Orbitrap Fusion using a topN method, files were searched with Maxquant already and wanted to compare and use morpheus to id some glycos peptides and use LFQ.

rmillikin commented 6 years ago

Are you able to share this data with us? I can try to identify the problem. Please email a download link to rmillikin@wisc.edu . Include your .toml settings for search and calibration, results.txt from your search, your spectra file(s), and database(s). Thanks!

trishorts commented 6 years ago

what were the resolution settings for MS1 and MS2 during acquisition?

DaliJarboui commented 6 years ago

120K on the MS1 and 30K MS2

trishorts commented 6 years ago

that should be perfect. suggest searching one injection where you know protein abundance was high and open the search tolerance for both MS1 (20 ppm) and MS2 (30 or 40 ppm). We sometime see bad calibration resulting in low PSMs. This should only take a couple minutes. If still low, I suggest that you give us access to a file and let us know what organism. We'll search it and get to the bottom of the problem. Let us know, we'll set up a box drive for you to place the file.

DaliJarboui commented 6 years ago

thanks, I used the default settings (15 and 25 ppm), will try to change the settings and see. if not I appreciate your help to do the search as I would like as well to understand how to set the LFQ search to compare between 2 datasets

trishorts commented 6 years ago

we're happy to help. email to mshort@chem.wisc.edu to request the link which will provide you a place to upload your raw file if necessary

rmillikin commented 6 years ago

Hello,

Any update on this? were you able to calibrate your files by opening up the tolerance?

rmillikin commented 6 years ago

I'm going to close this issue due to inactivity; if you can, please email us or comment here to let us know how this turned out.

DaliJarboui commented 6 years ago

Hey there, sorry for the inactivity, the issue is still standing, I'm waiting for new experiments to be run to re-analyze data again, will try with the complete set and see how it goes, thanks for your assistance. regards

On Mon, Apr 23, 2018 at 3:09 PM, rmillikin notifications@github.com wrote:

I'm going to close this issue due to inactivity; if you can, please email us or comment here to let us know how this turned out.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/smith-chem-wisc/MetaMorpheus/issues/1090#issuecomment-383569206, or mute the thread https://github.com/notifications/unsubscribe-auth/AkigwWrmdanYsfl7GFl9Y_XFCDf4viFXks5trdKhgaJpZM4TRZQh .

-- Dr. Mohamed Ali Jarboui, PhD, M.Sc, Eng. University Hospital Tübingen. Department of Preclinical Imaging and Radiopharmacy. Röntgenweg 13, 72076 Tübingen. GERMANY

Office: +49 (7071) 29-83462 Fax: +49 (7071) 29-4451

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http://www.isct.uni-tuebingen.de/wsic/ http://www.isct.uni-tuebingen.de/wsic/group/staff/staff-member/mohamed-ali-jarboui/