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how to do label-free quantification and I cannot find the value from pBulid and the result files. I am wondering if the pfind is capable to do LFQ, and if yes, is the "match between runs" applied and…
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Currently, the IPAW pipeline allows searching of label free data, but no quantification results. [moFF](https://github.com/compomics/moFF) is a MaxQuant equivalent command-line tool for MS1 quantific…
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From crux-users:
"Could someone explain why MS1 intensity-based quantification is not available in Crux? With inconsistent fragmentation being a common feature of label-free shotgun experiments, be…
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Hi,
I was wondering whether it is possible to use xCell to make cell-type enrichment analysis based on proteomics data.
And if so, should one use raw quantification (label-free, for instance) data?
…
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Hi,
I would like to add a new modification: biotinylation in artMS.
I changed the modification name Biotinylation to biotinylation(lowercase) in the evidence.txt.
And the modification:PTM:K:biotiny…
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Greetings,
I am working on data analysis projects using OpenMS to search mass spectrometry data collected on a Fusion with a Thermo Fisher FAIMS device on the front end of the instrument.
We ha…
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Hi @Jianguo99,
I am new to conformal prediction, and I have a multitask, multi-output model that performs both classification and regression for a specific problem. Is it possible to use this kind …
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Hello,
When I was using the label-free quantification by the CMD.exe, I found a little problem. If the spectra file repository contains more raw files than that are in the "ExperimentalDesign.tsv" …
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**Describe the bug**
Hello,
I am currently using MaxQuant for data analysis and have encountered an issue after updating from version 2.0.3.0 to 2.5.2.0. Previously, the Peptides.txt file used to …
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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…