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

Zhang, Q.

doi:10.1101/2023.01.17.524387

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bioRxiv · 10.1101/2023.01.17.524387

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

Zhang, Q.

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Abstract

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 twenty 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.

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Zhang, Q.. 2023-01-19. ProteoM enables deep and precise identification of peptides in data-dependent acquisition proteomics. https://doi.org/10.1101/2023.01.17.524387

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