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Hello Fragpipe team,
I am trying to analyze results from a mass-offset search. In the psm.tsv output, there are some PSMs with a reported 'Modified Peptide' but no 'Assigned Modification'. These on…
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Hi Vadim,
There is something fishy with the cpu cores allocation, we have noticed that if we process with absolutely the same parameters a number of 6 sciex wiff swath files, it allocates 64 cores.…
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Hiya!
Thanks for such a wonderful package. I'm working with a lot of peptides that I order from GenScript. A lot of these have modifications or are non-natural amino acids (see [here](https://www.g…
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Hello DiaNN team,
I have been using DiaNN to analyze histone modifications. The peptides we are analyzing are first derivatized using propionic anhydride, so many of the modifications are combinati…
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Hi,
I want to analyze LFQ-DIA global proteome and phospho-enriched proteome data separately on DIA-NN. Just want to make sure that we need two different libraries for these two different searches, r…
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I really like pepquery and have found this to be a valuable tool. However, I would also love to be able to search for specific modifications using the web version. Is there a way to input a peptide to…
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Hi,
I am interested in modifying FragFold to support custom tiling offsets for fragment generation. For example, a 3 aa increment when generating fragments could speed up peptide binding prediction…
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Hope it finds you well.
I'm using DIA-NN 1.9 and Skyline (64 bit) 24.1.
I'm trying to use following skyline visualiation function.
_Skyline. To visualise chromatograms/spectra in Skyline, analy…
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Hi Vadim and team,
I have done 3 plex dimethyl labeling on samples and am now trying to analyze them following the steps outlined in the plexDIA section. But as you can see below, after finished wi…
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It would be nice if the user could specify modifications (in brackets) when the peptide is specified on the command line.
Kaipo, can you comment on how difficult this would be to do?