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Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
https://msfragger.nesvilab.org
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Various Workflow for DIA data #279

Closed TeckYewLow closed 1 year ago

TeckYewLow commented 1 year ago

Hi,

I am reading with great interest your paper on "analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform". There were many combinations of methods within the Fragpipe that we could use for DIA data. For example, I am very interested in applying the MSFragger-DIA method. I am wondering if Fragpipe provides step-by-step protocols for analyzing DIA data.

In that paper, methods like FP-MSF, FP-MSF hybrid, FP-DIAU, FP-DIAU hybrid, and DIA-NN library-free were used. I am confused as to how I can ensure the parameters that I choose are correct: (i) which workflow? (ii) should I use a decoy database? (iii) what to select under the Validation tab (iv) Do I need to configure the Advanced Output Options within MSFragger? etc etc.

It would be great if you could enlighten me.

Best,

Teck

fcyu commented 1 year ago

Hi Teck,

Here is the tutorial: https://fragpipe.nesvilab.org/docs/tutorial_DIA.html

Answers to your questions:

  1. Using the DIA_SpecLib_Quant workflow
  2. Should have both target and decoy similar to the DDA analysis 3 and 4. The workflow will take care of them.

Best,

Fengchao