Data acquisition mode of the proteomics workflow

Hi, all
The acquisition mode is SWATH. I want to ask the workflow is suitable for the workflow.

Thank you!


No, for SWATH you should use the OpenSWATHWorkflow node.

Ok,I see. Thank you!

Hi,Now I got the result of the LFQ_proteomics, Now I have some question for you.
a. I processed the pep results to screen for differential proteins.Then, I identify them
b. because some protentions of the sequence and accession are null, So I refer to the PSM, but not any protentions are identified.(the yellowed are pep,other are PSM)
c. I consider that the FDR(0.01,0.05) of PSM and the protention are relation to this result. Or I should change other nodes parameters.
Thank you for your answer.

Rows in the PEP section are from quantitative features. If they do not have an ID, the sequence will be “null”.
PSM rows are all the IDs for the MS2 spectra in your file. They do not necessarily need to be associated with a PEP row.

FDR is fine. It depends on how strict you want to be.

Ok, Thank you for your answer.
Then I refer to the pep intensity to screen the different pep,or refer to the protein.
Do the protention intensity combine the pep intensity accoring the same accseeion?
such as protention=pep A+pep B+…

If you are interested in proteins, you need to use the PRT section.
The protein quantities are by default aggregated by a top3-sum approach. For anything more elaborate we suggest using MSstats downstream.

Ok,By the way is the MSstats a software?

Yes, an R software. Please see our blog workflow.

Hi,The abundance of PRT section is mull.

You need to run ProteinInference and ProteinQuantifier to calculate protein quantities. But I would honestly try to start from a ready-made workflow on the hub.

Ok,I download this but The ID node is null,So do I refer to theLFQ_proteomics to link the node?

Sorry, what do you mean by “null”? Everything looks green and therefore correct, as far as I can see on the screenshots.

yeah,my meaning is that I download the protein quantification workflow,but the ID (meta node)node this doesn‘t have node.
Thank you!