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I am using the FragPipe software for database searches, and the output file combined_ion.tsv is used for quantification with directLFQ. I plan to perform differential expression analysis using DEqMS, …
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### Current Behavior
Some MetaProteomics records have non-compliant values in the the `best_protein` and `all_protein` slots. The range of these slots is a `GeneProduct`, which have a range of `id` …
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Hi all,
I can't understanding why all the peptides are quantified to zero intensity when using labile-phosphor default workflow despite the flag ionquant.run-ionquant=true in the workflow file. (W…
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Hi,
Thanks for providing this tool, I'm using it, and it is very fast and flexible in usage.
I wanted to ask you if you think would be possible to use it for functional annotation and quantificat…
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In the iq package, we use the following code to compare protein quantification between iq and MaxQuant?
Line1: w1
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Dear Vadim,
So great help in our analysis of DIA worflow!!! I have some details during my AP-MS analysis
1) If I need no-normalized quantification, could I replace "Precursor.Normalised" with "Pr…
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Something I noticed in our production server timeline. A user has successfully edited a sample sheet, but them clicking on "finish sheet editing" to return to browsing mode and saving a sheet version …
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Hi All,
I'm working on this project where I add light and heavy-labeled peptides together, mix them and run on an Orbitrap, using LC-DIA.
Interestingly, when I create my own peptide library usi…
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Hi, Vadim,
If I want to extract peptide quantification as following, could I also got their protein names?
peptides.maxlfq
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Maybe I missed it.
Can one use TMT quantification with metamorpheous?