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.
thermorawfileparser=1.4.5 quantms-utils=0.0.12 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...
We recently reimplemented quantms-rescoring to generate the features for MS2PIP and DeepLC for quantms. This issue is to trace the benchmark performance within quantms and the gold-standard datasets we use....
### Description of the bug Reported here: https://nfcore.slack.com/archives/C02Q3FL29PD/p1728424167422049 ``` Command error: 2024-10-08 21:43:49,054 [mztab_prh] - Calculating protein coverage (bottleneck)... 2024-10-08 21:44:04,074 [mztab_prh] - Getting ambiguity members... 2024-10-08 21:44:04,087 [mztab_prh] -...
### Description of the bug Plus 28 more processes waiting for tasks… Execution cancelled -- Finishing pending tasks before exit -[nf-core/quantms] Pipeline completed with errors- ERROR ~ Error executing process...
### quantms 1.4 phosphoproteomics In version 1.4 of quantms phosphoproteomics experiments can be done using the Luciphor2 tool. Phosphoproteomics experiments are analysed in the following way: - Every search engine...
### Description of feature This issue is to control some important tasks that should be done in OpenMS core related to the current pipeline: - [x] Support for common enzymes...
### Description of feature Currently, @timosachsenberg @jpfeuffer comet only support 'Asp-N,Chymotrypsin,CNBr,no cleavage,unspecific cleavage,Trypsin,Arg-C,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase' However comet has a way to pass a definition of more enzymes https://uwpr.github.io/Comet/parameters/parameters_202301/search_enzyme_number.html using a parameter...
### Description of feature @MaLLLiYA @timosachsenberg @jpfeuffer @daichengxin : We have been analysing some of the datasets and we found some interesting unexpected PTMs (mass shits), most of them are...
### Description of feature Is it possible to run a search with multiple enzymes, or to add a custom enzyme (in this case with the appropriate cleaving locations expected for...
