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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Threads and midification #1893

Open Li5459000 opened 23 hours ago

Li5459000 commented 23 hours ago

Hi,

I want to compare the analysis speed between DIA-NN and MSFragger-DIA.

For DIA-NN, I set the threads to 16. For MSFragger-DIA, how should I configure the settings?

In the global settings, I noticed options for RAM and parallelism, but I’m not sure how to configure them to match the 16 threads used in DIA-NN.

Also, how should I configure the Methionine excision (N-term)? Should I set it to [^ -131.0405?

fcyu commented 13 hours ago

Set parallelism to 16.

Also, how should I configure the Methionine excision (N-term)? Should I set it to [^ -131.0405?

Peptide N-term or protein N-term? For peptide N-term n^ -131.0405, for protein N-term [^ -131.0405.

Best,

Fengchao

anesvi commented 13 hours ago

If they asked about protein N-terminal M removal, we already have that box checked by default. No extra changes are needed.