FragPipe Labile mode search_How to get the matching results of fragment ions(b,y) with labile modification

[Lang5991]

Dear FragPipe Team,

Recently, I am fucosing on labile-mode search with FragPipe. However, I don't know how to get the matching results of fragment ions(b,y) with labile modification

Just like the above picture, Could you kindly help me, thank you.

[KaiLiCn]

Hi,

To get the match result with labile modification like above pic, you need to manually assign a new mass on the amino acid.

Right now, there are two ways to do that in FP-PDV.

1. Generate a mirror spectrum like above.

Click Toolsand then select Check peptide.

Click Addbutton then select Add peptide

A dialog with same peptide will be shown. In this example, there is a modification on C. You could click C in the panel and type any mass in dropdown menu or select other modification. And click Enter key then Addit

2. Change modification mass

Click Toolsand then select Change modifications

A table with original modifications will be shown. Click the cell in New Defined column. Type any mass in dropdown menu or select other modification. And click OK. If you want to reset the mass, click Re-Set in the final column.

Let me know if you meet any issue when you try it.

Kai

[Lang5991]

Hi,

To get the match result with labile modification like above pic, you need to manually assign a new mass on the amino acid.

Right now, there are two ways to do that in FP-PDV.

1. Generate a mirror spectrum like above.

Click Toolsand then select Check peptide.

Click Addbutton then select Add peptide

A dialog with same peptide will be shown. In this example, there is a modification on C. You could click C in the panel and type any mass in dropdown menu or select other modification. And click Enter key then Addit

2. Change modification mass

Click Toolsand then select Change modifications

A table with original modifications will be shown. Click the cell in New Defined column. Type any mass in dropdown menu or select other modification. And click OK. If you want to reset the mass, click Re-Set in the final column.

Let me know if you meet any issue when you try it.

Kai

Dear Kai, Thanks so much for your kind help! I will try the method you provided. But I still have the problem that can we get the MS/MS matching results from output files? I'm desperate to know the actual matching result(real situation of Fragpipe) of fargment ions(b,y) of the matched peptide with labile modification. I look forward to hearing from you! Thanks.

[fcyu]

@Lang5991 unfortunately, the tsv report doesn't have the matched ions information.

Best,

Fengchao

[fcyu]

Same as https://github.com/Nesvilab/FragPipe/issues/719

[Lang5991]

@Lang5991 unfortunately, the tsv report doesn't have the matched ions information.

Best,

Fengchao

Dear Fengchao, I found that In Spec Lib part, we can generate spectral library from search results, and the output file "library.tsv" contains the b,y matching ions information.

I wonder Is this the actual right matching ions information?

[fcyu]

They are matched ions generated by the spectral library generation module, not from MSFragger. Also, it is for precursor, not PSM.

Best,

Fengchao

[fcyu]

Similar to https://github.com/Nesvilab/FragPipe/issues/885

I have implemented the feature to report the matched fragments. Let MSFragger generate the tsv report will have those two new columns. If you want to try the pre-released version, please send an email to yufeATumich.edu (replace AT with @).

Currently, there are some limitations

The reported fragments are not exactly the one used in the scoring because MSFragger does not record such information (to be fast). I let it "re-match" the fragments when generating the report. The fragments are deisotoped by default, so the reported matches only have singly charged. Disabling the deisotoping in the database search will have doubly charged fragments being matched, but the sensitivity is sub-optimal. It only supports closed search now, but I will extend it to open and mass-offset search in the future. Best,

Fengchao