msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease.
Bioinformatics
; 40(7)2024 07 01.
Article
de En
| MEDLINE
| ID: mdl-38944032
ABSTRACT
SUMMARY:
Identification and quantification of phosphorylation sites are essential for biological interpretation of a phosphoproteomics experiment. For data independent acquisition mass spectrometry-based (DIA-MS) phosphoproteomics, extracting a site-level report from the output of current processing software is not straightforward as multiple peptides might contribute to a single site, multiple phosphorylation sites can occur on the same peptides, and protein isoforms complicate site specification. Currently only limited support is available from a commercial software package via a platform-specific solution with a rather simple site quantification method. Here, we present sitereport, a software tool implemented in an extendable Python package called msproteomics to report phosphosites and phosphopeptides from a DIA-MS phosphoproteomics experiment with a proven quantification method called MaxLFQ. We demonstrate the use of sitereport for downstream data analysis at site level, allowing benchmarking different DIA-MS processing software tools. AVAILABILITY AND IMPLEMENTATION sitereport is available as a command line tool in the Python package msproteomics, released under the Apache License 2.0 and available from the Python Package Index (PyPI) at https//pypi.org/project/msproteomics and GitHub at https//github.com/tvpham/msproteomics.
Texte intégral:
1
Collection:
01-internacional
Base de données:
MEDLINE
Sujet principal:
Phosphoprotéines
/
Logiciel
/
Protéomique
Langue:
En
Journal:
Bioinformatics
Sujet du journal:
INFORMATICA MEDICA
Année:
2024
Type de document:
Article
Pays d'affiliation:
Pays-Bas
Pays de publication:
Royaume-Uni