Closed uhaifabioinfo closed 8 years ago
mvaudel
commented
8 years ago Hi David,
It looks like PeptideShaker has troubles extracting the information it needs from the Morpheus files. It would be really great if you could share the mzid file with us!
Many thanks,
Marc
uhaifabioinfo
commented
8 years ago Hi Marc,
I've uploaded the Morpheus output, MGF and FASTA files onto google drive: https://drive.google.com/open?id=0B4n6EGpYOGYGR1VlRFZVR09JRUE
Please let me know if there is anything else I can supply you with.
Many thanks! David.
mvaudel
commented
8 years ago Hi again,
Thanks, this should be more than enough :) Will come back to you once we have looked into it - hopefully in August :)
Best regards,
Marc
hbarsnes
commented
8 years ago Hi David,
Here's a beta version that should allow you to load Morpheus pepXML files: https://www.dropbox.com/s/5524z8cc7zpbch9/PeptideShaker-1.13.0-beta.zip?dl=0
The Morpheus mzid files are a bit more complicated as raw files (or mzIdentML?) are used as input instead of mgf files. We're therefore loosing the connection between the PSMs and the spectra in the mgf file. It may be possible to find a way around this, but this will not happen in the short term. So for now I hope you can use the pepXML files when importing into PeptideShaker?
Best regards, Harald
uhaifabioinfo
commented
8 years ago will do, thank you very much!
David.
On Thu, Jul 28, 2016 at 1:01 AM, Harald Barsnes notifications@github.com wrote:
Hi David,
Here's a beta version that should allow you to load Morpheus pepXML files:
https://www.dropbox.com/s/5524z8cc7zpbch9/PeptideShaker-1.13.0-beta.zip?dl=0
The Morpheus mzid files are a bit more complicated as raw files (or mzIdentML?) are used as input instead of mgf files. We're therefore loosing the connection between the PSMs and the spectra in the mgf file. It may be possible to find a way around this, but this will not happen in the short term. So for now I hope you can use the pepXML files when importing into PeptideShaker?
Best regards, Harald
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/peptide-shaker/issues/192#issuecomment-235735280, or mute the thread https://github.com/notifications/unsubscribe-auth/APVYifb1et3JKZq9lfkPrwT92saVmtxvks5qZ9VWgaJpZM4JRuH8 .
David Morgenstern, PhD University of Haifa Bioinformatics Service Unit, Director Multipurpose Bldg, Room 148 University of Haifa, Mount Carmel, Haifa, Israel 04-664-7978 (internal 7178) uhaifabioinfo@gmail.com http://uhaifabioinfo.wix.com/bioinfoserviceunit
hbarsnes
commented
8 years ago Hi David,
PeptideShaker v1.13.0 has just been released which should now allow you to load Morpheus pepXML files as long as mgf is used as the spectrum input format. If this is not the case please let us know and we'll reopen the issue.
Best regards, Harald
uhaifabioinfo
commented
8 years ago Thanks!
From: Harald Barsnes [mailto:notifications@github.com] Sent: Sunday, August 14, 2016 12:22 AM To: compomics/peptide-shaker Cc: uhaifabioinfo; Author Subject: Re: [compomics/peptide-shaker] Support Morpheus pepXML and/or mzid (#192)
Hi David,
PeptideShaker v1.13.0 has just been released which should now allow you to load Morpheus pepXML files as long as mgf is used as the spectrum input format. If this is not the case please let us know and we'll reopen the issue.
Best regards, Harald
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/peptide-shaker/issues/192#issuecomment-239642186 , or mute the thread https://github.com/notifications/unsubscribe-auth/APVYiQkvPrVfs0WUAPuJL2JzsNui-L_9ks5qfjVugaJpZM4JRuH8 .
uhaifabioinfo
commented
8 years ago Hi,
Embarrassing to admit, but I’ve got to look at it only just now… Morpheus accepts only MzML, RAW or .d (Agilent)…. :P
Sorry for the very late reply…
Cheers,
David.
From: Harald Barsnes [mailto:notifications@github.com] Sent: Sunday, August 14, 2016 12:22 AM To: compomics/peptide-shaker Cc: uhaifabioinfo; Author Subject: Re: [compomics/peptide-shaker] Support Morpheus pepXML and/or mzid (#192)
Hi David,
PeptideShaker v1.13.0 has just been released which should now allow you to load Morpheus pepXML files as long as mgf is used as the spectrum input format. If this is not the case please let us know and we'll reopen the issue.
Best regards, Harald
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/peptide-shaker/issues/192#issuecomment-239642186 , or mute the thread https://github.com/notifications/unsubscribe-auth/APVYiQkvPrVfs0WUAPuJL2JzsNui-L_9ks5qfjVugaJpZM4JRuH8 . https://github.com/notifications/beacon/APVYiUtp8s43tipWYJKAlhdPKd44AP10ks5qfjVugaJpZM4JRuH8.gif
hbarsnes
commented
8 years ago Hi David,
Embarrassing to admit, but I’ve got to look at it only just now… Morpheus accepts only MzML, RAW or .d (Agilent)…. :P
Ok, we'll get back to it when we get the time to support raw files as input then. Not sure when that will happen though.
Best regards, Harald
uhaifabioinfo
commented
8 years ago Thanks!
From: Harald Barsnes [mailto:notifications@github.com] Sent: Tuesday, September 20, 2016 3:43 PM To: compomics/peptide-shaker Cc: uhaifabioinfo; Author Subject: Re: [compomics/peptide-shaker] Support Morpheus pepXML and/or mzid (#192)
Hi David,
Embarrassing to admit, but I’ve got to look at it only just now… Morpheus accepts only MzML, RAW or .d (Agilent)…. :P
Ok, we'll get back to it when we get the time to support raw files as input then. Not sure when that will happen though.
Best regards, Harald
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/peptide-shaker/issues/192#issuecomment-248289954 , or mute the thread https://github.com/notifications/unsubscribe-auth/APVYiTqNII5HGSE_aFSiLmXj77FE28Vtks5qr9TcgaJpZM4JRuH8 . https://github.com/notifications/beacon/APVYibgfhsCDs-pXY9afma-RvsmJl4f1ks5qr9TcgaJpZM4JRuH8.gif
Hi, 210716PSbug report.txt
I'm trying to import results searched by Morpheus into peptideshaker, without much success - looks like failure to import data. the files are quite big so I can upload them via file sharing, and I'm attaching the report txt file.
Thanks! David.