A graph-based approach for modification site assignment in proteomics
Background In proteomics, the most probable localizations of post-translational modifications are assessed by localization scores evaluating the likelihood of a given modification to occupy a site on a peptide sequence. When identifying highly modified peptides, localization scores for different modifications can return conflicting results, stacking modifications on the same amino acid. Here, we propose a graph-based approach that assigns modifications to sites in a way that maximizes localization scores while avoiding conflicting assignments. Results The algorithm is implemented as both a standalone Python program and in the compomics-utilities Java library. Our graph-based approach showed the ability to match complex combinations of modifications and acceptor sites, allowing the processing of thousands of peptides in a few seconds. Conclusions Our graph-based approach to modification site assignment allows distributing multiple modifications in a way that maximizes individual localization scores. Having an optimal modification site assignment is important for spectrum annotation and biological interpretation.
Code (1)
Similar Papers 제목 키워드 기반
PhosNetVis: a web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data
Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphoryl…
Cysteine post-translational modifications: ten years from chemical proteomics to bioinformatics
As the only thiol-bearing amino acid, cysteine (Cys) residues in proteins have the reactive thiol side chain, which is susceptible to a series of post-translational modifications (PTMs). These PTMs participate in a wide …
Proteomics Standards Initiatives ProForma 2.0 Unifying the encoding of Proteoforms and Peptidoforms
There is the need to represent in a standard manner all the possible variations of a protein or peptide primary sequence, including both artefactual and post-translational modifications of peptides and proteins. With tha…
Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, …
Graph Matching via Optimal Transport
The graph matching problem seeks to find an alignment between the nodes of two graphs that minimizes the number of adjacency disagreements. Solving the graph matching is increasingly important due to it's applications in…
Graph Matching