Mzion enables deep and precise identification of peptides in data-dependent acquisition proteomics

• Published in: Scientific reports Vol. 13; no. 1; pp. 7056 - 9
• Main Author: Zhang, Qiang
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29.04.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/114/2784; Databases, Protein; Datasets; Humanities and Social Sciences; multidisciplinary; Peptides; Phosphopeptides; Proteins; Proteins - analysis; Proteomics; Science; Science (multidisciplinary); Search Engine; Search engines; Software
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-34323-4

Sensitive and reliable identification of proteins and peptides pertains the basis of proteomics. We introduce Mzion, a new database search tool for data-dependent acquisition (DDA) proteomics. Our tool utilizes an intensity tally strategy and achieves generally a higher performance in terms of depth and precision across 20 datasets, ranging from large-scale to single-cell proteomics. Compared to several other search engines, Mzion matches on average 20% more peptide spectra at tryptic enzymatic specificity and 80% more at no enzymatic specificity from six large-scale, global datasets. Mzion also identifies more phosphopeptide spectra that can be explained by fewer proteins, demonstrated by six large-scale, local datasets corresponding to the global data. Our findings highlight the potential of Mzion for improving proteomic analysis and advancing our understanding of protein biology.