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The ProteomicsLFQ tool performs protein inference and FDR filtering of peptide/protein IDs (before quantification). It would be helpful to have an optional output (idXML file) of the IDs after these s…
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Hi Vadim,
I am searching diaPASEF data for quantification against a sample specific spectral library. The spectral library contains 11973 protein groups and I am identifying 10606 of these protein …
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For new term requests, please provide the following information:
## Preferred term label
protein-DNA complex
## Synonyms
DNA-protein complex
## Textual definition
A macromolecular complex …
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There is a new paper criticizing featureCount for not being able to quantify lncRNA expression effectively. Here is my summary of their paper:
1. featureCount under-estimated lncRNA expression compar…
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Hi,
I need decoys to run the protein quantification tool Triqler. Is there a way to get DIA-NN to output the decoy peptides?
Best,
Patrick
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### Description of feature
In the DDA/label-free workflow (perhaps in others as well), it would be useful to get an output of the identification results at the end of the search/inference/filtering p…
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Now that we have separated the phosphoproteomics data, we no longer need to duplicate the gene symbols.
. When I run the raw data …
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Dear Vadim,
I have some issues with identifying high confidence proteins from SWATH data acquired on ZenoTOF 7600.
I am using fasta predicted library. The SWATH data should contain about ~100 pr…
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Hi,
I follow the [tutorial ](https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/download_prepare.html)and run the codes below:
```
query