Annie Ha

Sorry, wrong repository posted, will repost this on Fragpipe.

Thanks for the reply Vadim! It doesn't seem to be an issue to be too concerned with since it doesn't persist in the peak intensities. I have one more question...

None of the peptides from that protein were present in the psm.tsv. It almost looked like this protein was just completely filtered out...

I have sent the data to your email with a google drive link!

The decoys was generated using the TPP tool decoyFastaGenerator.pl . The same fasta file was used to analyze the DDA files, and that the high abundant proteins were there. I...

I will give it a try. The first trial was with the entire cohort, and then i took a subset of 10 files from the cohort to perform DDA search...

Sorry for the confusion! I meant that the results from the analyzes of subsets had the protein, but the results from the entire cohort did not.

The issue is that i see the protein in the intermediate proteins, but it's not in the result files.... the psm.tsv, protein.tsv, protein.fas, and the library.tsv. I can upload these...

sorry i mean intermediate files, bad typo... I am using v18.0 fragpipe with the DIA_speclib pipeline, but this seems to be a consistent problem on my end :\

Maybe i will re-install the latest Fragpipe version and the dependencies and run it again.