Mingze Bai

onsite: An Integrated Framework for Phosphosite Localization and False Localization Rate Estimation

The paper introduces onsite, a framework for estimating false localization rates in phosphoproteomics, showing pyLucXor achieves high accuracy and localization count.

quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experiments.

quantms-rescoring improves proteomics analysis by integrating multiple search engines and machine learning, increasing identified spectra and quantifying more phosphorylated peptides and modification sites.

ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata

ibaqpy computes iBAQ values for proteomics data using SDRF metadata, improving scalability and reproducibility in large-scale experiments.

Proteogenomics analysis of human tissues using pangenomes

The paper reanalyzes human tissue proteomics data using pangenome references to identify novel peptides and variants, demonstrating the effectiveness of proteogenomics approaches with pangenome data.

A comprehensive evaluation of consensus spectrum generation methods in proteomics

The paper evaluates consensus spectrum generation methods in proteomics, finding BEST and BIN to be the most reliable for peptide identification.

A proteomics sample metadata representation for multiomics integration, and big data analysis.

The paper introduces a standardized metadata format for proteomics datasets to improve reusability and integration across public repositories.

BioContainers Registry: searching for bioinformatics tools, packages and containers

The paper introduces the BioContainers Registry and API to improve the findability, accessibility, interoperability, and reusability of bioinformatics tools and containers.

Phoenix Enhancer: proteomics data mining using clustered spectra

Phoenix Enhancer improves proteomics data analysis by clustering spectra to identify potential mis-identifications and enhance peptide spectrum match confidence.