defining protease combination in Fragpipe

[talpa25]

Describe the problem

• I'm submitting a:

  • [ ] problem running the software
  • [ ] bug report
  • [ ] feature request
  • [x] question

• My MSFragger use case:

  • [x] Closed search (standard small precursor mass tolerance)
  • [x] Open search (large precursor mass tolerance)

  put your general problem description here Dear developer,

i have done a consequtive protease digestion of Trypsin and Glu-C, How do i specify the cutting sites (KRE) in the Fragpipe Box?

Best Roman

System info

You can find that printed on the Config tab.

• OS and version: your response here
• Java version: your response here

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Describe your experiment

Genral proteomics experiment description

e.g. "TMT, Human, full cell lysate with Trypsin" , "AP-MS pulldowns, mouse, liver tissue"

...

Input data files

e.g. "fractionated HeLa, 5 samples, 3 bio replicates, 2 technical replicates" or "ten 3 hour LC gradients, full cell lysate, fruit fly" or or at least "5 mzml files 1.5Gb each"

Sequence database

your response here, preferably a link or at least name, organism etc.
Size of the either in proteins or in megabytes

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Attach fragger.params file

You can find it in the output directory you specified for analysis.

Run log output

** copy text from the text console in the gui here **

[fcyu]

Thanks for your interest in FragPipe and MSFragger. I think you can set the parameter like

In order to let PeptideProphet recognize the enzyme (it only supported limited enzymes), you need to fill "Trypsin" in the "Enzyme name" entry.

Best,

Fengchao

[sarah-haynes]

Hi Roman, For best results, the enzyme name and cleavage rules used in your search should match those used by PeptideProphet. We recommend that you specify "trypsin_gluc" and the corresponding rules (cut DEKR, no cuts P) as shown in the list at the bottom of this page.

Regards, Sarah