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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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From https://sentry.galaxyproject.org/share/issue/da466f63ec5541e58db2ce827ada3918/.
I can't see any use of `$protein` in the configfile, but this is not easy to read.
These were the selection optio…
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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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Here are my comments/suggestions for the new web interface of the modules. Feel free to disagree/comment on all these points :). I go tab by tab.
Tab **“module description”**: I don’t think that w…
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I have a model gemma 2 9B. I quantized this with AWQ-4bit. Size of model is 5.9GB. I set the kv_cache_free_gpu_mem_fraction to 0.01 and run triton on one A100. But triton takes 10748MiB of ram. I expe…
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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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Quantitative Behavior of Mass Spectrometers
To apply the theory we learnt in the last chapters of this unit to quantitative analyses with mass spectrometers, we need to think about the limitations th…
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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" …