The result of the LFQ of proteomics

Hi, all
Now I have the final of the workflow of the workflow. But about the MzTabReader, I have two question.
First, the table of PSM section and the Peptide section is different, so which I choose so that I can compare the different groups.
Secondly, the Peptide section has the columns containing rt, m/z and Peptide_abundance_study_variable. Is the abundance samilar to the intensity?
The table of PSM section also has many information.
If I want to analysis the table what should I depend on one table or the two table?
Finally, I also want to the result is wright or not.
Thank you!


For a general overview of the format, please read the mztab specification:

To your questions:

  • The PSM section is mostly for identification information. Multiple PSMs can map to a peptide.
  • The peptide (PEP) section is more for quantification. And yes, abundance = intensity.
  • What you need, depends on your use case. I cannot answer that for you. As mentioned, the tables represent different things. Therefore they contain different values. It looks to me like you should concentrate on the peptide section first. And if this does not contain all information, you may need to join it with the PSM section.

So I understand that the PSM and the Peptide can join in a table according the experiments.

I should based on the Peptide and the PSM is an supplement information.

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