Dear Colleagues,
We have done several label-free proteomics analysis using Thermo Fisher LC/MS/MS and proteome Discoverer software.
I see a problem about the improper peak retention time. From my understanding about the workflow, a peptide is found in sample1 at rention time t1 through peptide search; but in sample 2, such peptide is not found due to low abundance; instead of finding peptide, the software find the peak with feature Q1/Q3 mass of the peptide in sample 2 to find a peak for quantification. For most cases, the peptide peak in sample 1 and Q1/Q3 peak in sample 2 have similar rention time. For many cases, the two peaks have a very big different retention time (like one is at 5 min, and another at 10 min), and the software still regard featured mass peak as the peptide peak for comparative analysis.
I am only the end-user for the proteomics service from a platform. I am not clear how to make software have a better retention time accuracy.
Is there anyone understanding my problem and knowing the solution? Is this due to workflow missing a step or a parameter was not set well? Or, is this common for proteomics study and currently, needing a technical improvement?
Could you please give me some instruction?
Thanks a lot!
Bingyin
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