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My raw files were searched with DIA-NN 1.8.1 and the output table "report.pg_matrix.tsv" was used for further analysis. I was confused with the two columns "Protein.Group" and "Protein.Ids". The colu…
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I am just naive here. When comparing the results of MASCOT and and MSGFPlus, some proteins are not identified with MSGFPlus.But lot of other proteins are identified with MSGFPlus. Is this something to…
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Hey, I am attempting to use FragPipe to analyze some proteogenomic data for use in making structural comparisons and am running into some issues with handling instances where the individual is a heter…
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Hi. I want to work with an 8 aminoacids peptide contain Amine and Acetyl group at C and N-terminal, respectively. Before anything, I create amine and acetyl parameters by antechamber and add obtained …
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Hi all !
With BALL and VIEW, I'm trying to colorize some residues really often. I saw that the update() function of the ColorProcessor examples (and my implementation too by the way) rewrite the colo…
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Hi Vadim,
Thanks for this amazing software.
I want to analyze DIA data using a DDA library that was constructed from MSFragger. The actual LC gradient is 40 minutes, but after building the library, …
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Hi
We ran DIA_spec_diaPASEF workflow and DIA NN output protein group files does not have protein name. However, if i run DIA NN without using FragP
[PG_output.xlsx](https://github.com/user-attachme…
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[log_2024-11-26_18-48-29.txt](https://github.com/user-attachments/files/17929728/log_2024-11-26_18-48-29.txt)
**- Upload your log file**
(If a log file hasn't been generated, go to the 'Run' tab i…
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Hi, I have a question about the decoy generation. The method in your paper is "By default, this is done by replacing the fragment ion m/z values of the target precursor assuming the amino acids adjace…