quantms
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bigbio
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
### Description of feature Would be good to test for multiple datasets the impact of the parameter `num_hits`. The idea would be seen how this parameter will affect the identification...
### Description of the Feature During the benchmark of quantms using LFQ and MBR (issues #300 #301 #287) we developed a new probabilistic algorithm based on SVM that control the...
### Description of feature A new version of comet has been released `Comet v2024.01.0` https://github.com/UWPR/Comet/releases. The new version includes some major changes, including the way to define the precursor tolerances...
### Description of the bug @jpfeuffer @timosachsenberg @daichengxin I found one dataset that we search using msgf, here the command: ``` #!/bin/bash -euo pipefail MSGFPlusAdapter \ -protocol automatic \ -in...
### Description of feature Dear all, we're currently considering making use of the msquant pipeline for processing of large sample cohort DIA data. Testing the DIA-NN GUI I took note...
### Description of feature @daichengxin #contributors With the support of SAGE by quantms, we have opened the possibility to support a quantms open-search workflow. I recommend the following steps: -...
### Description of the bug ``` nf-core/quantms execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: 1. The full error message was:...
### Description of the bug ``` nf-core/quantms execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: 8. The full error message was:...
### Description of feature @daichengxin, @jpfeuffer: When running multiple datasets, I have found that it would be good to have some logic to configure memory and CPU depending on the...
### Description of feature Now, due to make things as parallelisable as possible, Thus, step 2 consists of analysing each run separately with the in silico library generated in step...
