Yasset Perez-Riverol

Benchmarking of the id dda workflow (ms2rescore, percolator, SNR)

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### PXD001819 Analysis Currently, we have a workflow that can perform peptide identification using: `-> ms2rescore -> SNR + spectrum properties -> percolator` Here the results can be found (https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/PXD001819-id-ms2rescore/)....

### 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] -...

bug in quantms related with parquet and SDRF-pipelines

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### 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...

First Tasks for of improvements of OpenMS and quantms

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### 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...

Defining more enzymes in OpenMS Comet adaptor

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### 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...

OpenMS and frequently mass shifts in Unimod

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### 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...

Test the impact and how the parameter num_hits works

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### 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...

LFQ MBR FDR algorithm needed.

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### 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...

Comet new version has been released Comet v2024.01.0

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### 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...