Hi everyone!
My name is Debora, and I am a Ph.D. student. I work with protein analysis by mass spectrometry. I use the bottom-up strategy in my project.
I am doing some tests, and I can see that in many MS2 spectra the precursor ion still with a significant relative abundance. I am searching for some informatic tool to extract this information from the spectra files. I do not want to remove them from the spectra, actually in my mind I thought in to get this information in some text or csv file. Like to export the intensity of the precursor ion in the MS2 spectrum in a table.
Please, does anyone knows if some tool like this is available?
Thank you
Hi Debora,
You can use a free software called "ProteoWizard" ; it is downloadable at:
http://proteowizard.sourceforge.net/
After you download, you can use the MSConvert function to generate a peak list (mgf) from a mass spec file which contains MS1 and MS2 the intensity of the corresponding ions.
If you have Thermo mass spectrometers which will come with the data analysis software, you can use Proteome Discoverer software to design the workflow to generate the same, "mgf" file.
Good luck!
Hediye.
Hi Hediye,
Thank you so much! I will follow your suggestion =).
Best regards,
Débora
Mrs/Miss Silva,
Please pay attention to the following discussion:
https://www.researchgate.net/post/Are_my_final_S2_or_S3_or_S4_compound_pure_of_S1,
with the associated attachments and the reference section. The postings deals with the topic of MS quantification of intensity.
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