pcruzparri

PTM Stoichiometry

4

Creating a mzLib method to calculate the stoichiometry (or site-occupancy) of PTMs using the intensity of each quantified peak. The current inputs are the _protein database(s) file(.xml) paths_ and the...

Adds occupancy calculation to MM using peptide intensities from FlashLFQ. Backend calculation currently implemented in the `MzLib.MzLibUtil.PositionFrequencyAnalysis` class. In MM, the updating of the ProteinGroup.ModInfo field with intensity-based stoichiometry is...

Spectral library prediction

3

Created a "Koina" class library to provide an expandable interface to use the deep learning models hosted by the [Koina](https://koina.wilhelmlab.org/) project. This is mostly a WIP-solution for now to get...

Ptm stoichiometry

4

New PR with changes from PR #797 and more. Description: PTM stoichiometry classes created for each structural level (protein group -> protein -> (base) peptide - modification). Probably the most...

Updates to Full Sequence Writing and Parsing of Mods

4

Purpose: 1) ParseModifications was bugged in that it could output negative indices. Updated the regex pattern also to explicitly ignore cation brackets (i.e. [Metal: Calcium[II] on E] will ignore the...