ArticleJournal of proteome research2013
In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics.
Article in Journal of proteome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 57 citations in OpenAlex.
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- Detecting aspartate isomerization and backbone cleavage after aspartate in intact proteins by NMR spectroscopy.Journal of biomolecular NMR · 2021Article
- Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant.Molecular & cellular proteomics : MCP · 2020Article
- Nonspecific cleavages arising from reconstitution of trypsin under mildly acidic conditions.PloS one · 2020Article
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- Applying an Internal Standard to Improve the Repeatability of In-electrospray H/D Exchange of Carbohydrate-Metal Adducts.Journal of the American Society for Mass Spectrometry · 2019Article
- Proteomics Analysis Reveals That Caspase-Like and Metacaspase-Like Activities Are Dispensable for Activation of Proteases Involved in Early Response to Biotic Stress inInternational journal of molecular sciences · 2018Article
- Optimization of Electrospray Ionization Source Parameters for Lipidomics To Reduce Misannotation of In-Source Fragments as Precursor Ions.Analytical chemistry · 2018Article
- Extending a Tandem Mass Spectral Library to Include MSJournal of the American Society for Mass Spectrometry · 2017Article
- Peptide Markers for Rapid Detection of KPC Carbapenemase by LC-MS/MS.Scientific reports · 2017Article
- Computational Metabolomics: A Framework for the Million Metabolome.Chemical research in toxicology · 2016Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Partially tryptic peptides are often identified in shotgun proteomics using trypsin as the proteolytic enzyme; however, their sources have been controversial. Herein, we investigate the impact of in-source fragmentation on shotgun proteomics profiling of three biological samples: a standard protein mixture, a mouse brain tissue homogenate, and mouse plasma. Because the in-source fragments of peptide ions have the same LC elution time as their parental peptides, partially tryptic peptide ions from in-source fragmentation can be distinguished from other partially tryptic peptides based on their elution time differences from those computationally predicted data. The percentage of partially tryptic peptide identifications resulting from in-source fragmentation in a standard protein digest was observed to be ∼60%. In more complex mouse brain or plasma samples, in-source fragmentation contributed to a lesser degree of 1-3% of all identified peptides due to the limited dynamic range of LC-MS/MS measurements. The other major source of partially tryptic peptides in complex biological samples is presumably proteolytic cleavage by endogenous proteases in the samples. Our work also provides a method to identify such proteolytic-derived partially tryptic peptides due to endogenous proteases in the samples by removing in-source fragmentation artifacts from the identified peptides.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.