I am working with Waters Xevo GS-2 Q-TOF mass spectrometer in MSe mode to analyze and identify tryptic peptides. are progenesis QI for proteomics or waters PLGS the only software that can analyze MSe data? are there any open source software for this purpose or any converstion tool to convert them to mzml or mgf...?
Have a look at ProteoWizard, it will convert your files for you. Depending on what you want to do Skyline may be able to help. Skyline is about quantitation, not identification. How well they work with MSe data, I can't say as I've never actually tried this.
http://proteowizard.sourceforge.net/
https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view
Hello Peter,
Skyline is not going to help me in this situation, i want first to identify peptides in the mixture. Proteowizard does not support MSe files
Hi Bassel, Actually, that's why we have just released versions of Byonic and Byologic which process Waters MS^E data alongside data from Thermo, Bruker, Agilent and SCiex. Our customers wanted that capability. There's a link on our updates page which has an example of that data processing in Anna Schwendeman's lab in Michigan, which processed SYNAPT data ; https://www.linkedin.com/company/protein-metrics-inc-?trk=co-feed-recent-comments. There's a peer-reviewed paper out shortly, so I can't send that yet, sorry.
You can get FREE trial downloads here: http://www.proteinmetrics.com/contact-us/request-demo/
I used to work at Waters and was involved in the development of those packages you mention, feel free to ask me on [email protected].
Regards
St John
Hello St John, great! i would try the software. I think in my case Byonic would be helpful becasue i want to use it for identification
Hi,
Have a look at Progenesis from Waters. The software is quite expensive but supports MSe data analysis. If you ask for a demo, you might be able to try it first and see if it helps. Personally, I treat MSe data in MassLynx only for confirmation purposes (ID validation of small metabolites). Good luck.
P.
Hi Pierre, yes progenesis is auite expensive. i need to identify peptides so Masslynx alone is not enough
Hi Bassel,
You could try DIA-Umpire (http://diaumpire.sourceforge.net). Should be able to handle MSe data.
Regards
Robert
Hi,
Anyone with experience using the DIA-Umpire? What are the recommended PC specifications?
We have been using Progenesis but recently having memory-related problems and it keeps getting stuck
will appreciate any thoughts on this...
Osnat
Hi,
Somebody knows if we can treated the MSe data from Waters machine with Masquant sofware ?
Best regards
José
Hi Jose,
Do you mean Mascot? As far as I know for .raw MSe files you must use the waters software (Progenesis or PLGS)
Thank you,
Yes Mascot or other freeware. Can we treated our .raw MSe files to used other free software (MasQuant or other) ?
I have the same problem... so far I could not find any software to process my files, only the waters one. It depends on your acquisition mode... DDA or DIA, with the latter only compatible with Waters software.
Hope this helps
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