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First of all, thank you for developing this wonderful package. It makes the MaxLFQ intensity calculating and report generating much easier and faster.
However, it seems to have issues when the col…
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Hi, I tried running one DIA raw file with DIA_DIA-Umpire_SpecLib_Quant and got the error below.
I processed the file with Spectronaut and it completed fine.
Thanks,
Yishai
Info: 31 redundant …
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Dear Vadim,
I would like to allow N-terminal acetylation in my library-free searches. I tried to enter the respective var mod in the additional commands field (Unimod:1) with lower-case amino acid …
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I think Fragpipe cannot handle DIAs with windows, which are too wide. I am trying to repeat on my EvosepOne-FAIMS-Exploris 480 system the work of Erwin M. Schoof: "Enhancing single-cell proteomics thr…
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Hi,
I tried to process a batch of .peprec files in ms2pip (those that Ralf generated for me in issue #61), to create predicted output files in spectronaut.csv format instead of just csv. I noticed…
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I tried to process 2 DIA PASEF files (data type defined as either DIA or DIA-Quant - I tried both), together with 60 short DDA PASEF runs (fractions) as auxiliary files for spectral library building, …
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Thanks for this very interesting and easily accessible work!
Unfortunately my first attempt to reprocess a mixed proteome standard (Human/Ecoli -> 1:1 vs1:3) processed via DIA-NN only with default …
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Hi Alex,
First, thank you for the amazing you have done with this plugin.
I wanted to use your plugin for some phospho-enrichment vs total-proteomics DIA acquisitions that were searched with DIA…
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**Is your feature request related to a problem? Please describe.**
Due to its high specificity, trypsin is the enzyme of choice in shotgun proteomics. Nonetheless, several publications do report the …
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**Is your feature request related to a problem? Please describe.**
I have to admit that I am quite overwhelmed/annoyed by the largely unstructured, list-like arrangement of the settings for a new exp…