Quantifying the unknown on MS1 level. UnbeQuant allows the quantification of measured ions without identification annotations in a DDA setting for mass spectrometry proteomics data from Bruker or Thermo mass spectrometers. To achieve this it uses identification results and sets same identifications across runs as anchors to align multiple runs, providing a mixture of the following: Identified ions with quantitative values, only some identified ...

ProGFASTAGen

The ProGFASTAGen (Protein-Graph-FASTA-Generator or ProtGraph-FASTA-Generator) repository contains workflows to generate so-called precursor-specific-FASTAs (using the precursors from MGF-files) including feature-peptides, like VARIANTs or CONFLICTs if desired, or global-FASTAs (as described in ProtGraph). The single workflow scripts have been implemented with Nextflow-DSL-2 ...