Mzion enables deep and precise identification of peptides in data-dependent acquisition proteomics
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...
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| Published in | Scientific reports Vol. 13; no. 1; pp. 7056 - 9 |
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| Main Author | |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
29.04.2023
Nature Publishing Group Nature Portfolio |
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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 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. |
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| AbstractList | 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. 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.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. 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 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. |
| ArticleNumber | 7056 |
| Author | Zhang, Qiang |
| Author_xml | – sequence: 1 givenname: Qiang surname: Zhang fullname: Zhang, Qiang email: zhang.qiang@WUSTL.EDU organization: Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/37120666$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1021/pr101065j 10.1021/acs.jproteome.0c00186 10.1021/ac00096a002 10.1038/nmeth.3255 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 10.1002/rcm.1196 10.1007/s00216-012-6203-4 10.1074/mcp.M110.003822 10.1074/mcp.M110.003830 10.1186/1471-2105-13-S16-S1 10.1021/pr5003017 10.1074/mcp.O113.030189 10.1038/nmeth.4256 10.1038/nmeth1113 10.1038/s41587-021-00968-7 10.1016/1044-0305(94)80016-2 10.1074/mcp.M900317-MCP200 10.1038/ncomms6277 10.1002/pmic.200300744 10.1038/nbt1240 10.1016/j.jprot.2010.08.009 10.1016/j.cell.2021.07.016 10.15252/msb.20178126 10.1038/nbt.3287 10.1016/j.jprot.2012.12.007 10.1038/s41467-019-13866-z 10.1021/pr301024c 10.1074/mcp.R111.009522 10.1002/pmic.201200439 10.1038/s41596-018-0006-9 10.1007/978-1-4939-6747-6_23 10.1073/pnas.0405549101 10.1021/pr101196n 10.1038/nbt.4236 10.1007/978-1-60761-444-9_5 |
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| SubjectTerms | 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 |
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| Title | Mzion enables deep and precise identification of peptides in data-dependent acquisition proteomics |
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