ArticleJournal of proteome research2013
Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in 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 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed, 86 citations in OpenAlex.
- Synergistic Arg-C Ultra and Lys-C Digestion for Quantitative Proteomics.bioRxiv : the preprint server for biology · 2025Article
- Fluorescent Switch-on Detection of Cadmium(II) Using Salicylaldehyde-Decorated Gold Nanoclusters.Journal of fluorescence · 2025Article
- Clean and Complete Protein Digestion with an Autolysis Resistant Trypsin for Peptide Mapping.Journal of proteome research · 2024Article
- A Framework for Quality Control in Quantitative Proteomics.Journal of proteome research · 2024Article
- A framework for quality control in quantitative proteomics.bioRxiv : the preprint server for biology · 2024Article
- Quenching Trypsin Is Unnecessary in Filter-Based Bottom-Up Proteomics.Journal of the American Society for Mass Spectrometry · 2024Article
- Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells.Journal of proteomics · 2024Review
- Assessing the Role of Trypsin in Quantitative Plasma and Single-Cell Proteomics toward Clinical Application.Analytical chemistry · 2023Article
- Toward an Integrated Machine Learning Model of a Proteomics Experiment.Journal of proteome research · 2023Review
- Cell Proteomic Footprinting: Advances in the Quality of Cellular and Cell-Derived Cancer Vaccines.Pharmaceutics · 2023Review
- Review on Extraction, Modification, and Synthesis of Natural Peptides and Their Beneficial Effects on Skin.Molecules (Basel, Switzerland) · 2023Review
- Mass spectrometry-based tear proteomics for noninvasive biomarker discovery.Mass spectrometry reviews · 2022Review
- Mass Spectrometry, Structural Analysis, and Anti-Inflammatory Properties of Photo-Cross-Linked Human Albumin Hydrogels.ACS applied bio materials · 2022Article
- X-ray free-electron laser studies reveal correlated motion during isopenicillinScience advances · 2021Article
- Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation.Nature protocols · 2021Review
- Boosting Detection of Low-Abundance Proteins in Thermal Proteome Profiling Experiments by Addition of an Isobaric Trigger Channel to TMT Multiplexes.Analytical chemistry · 2021Article
- SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry.Journal of proteome research · 2021Article
- Improving production of Streptomyces griseus trypsin for enzymatic processing of insulin precursor.Microbial cell factories · 2020Article
- Exploring the Use of a Modified High-Temperature, Short-Time Continuous Heat Exchanger with Extended Holding Time (HTST-EHT) for Thermal Inactivation of Trypsin Following Selective Enzymatic Hydrolysis of the β-Lactoglobulin Fraction in Whey Protein Isolate.Foods (Basel, Switzerland) · 2019Article
- Comparison of Protein Hydrolysis Catalyzed by Bovine, Porcine, and Human Trypsins.Journal of agricultural and food chemistry · 2018Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
Trypsin is an endoprotease commonly used for sample preparation in proteomics experiments. Importantly, protein digestion is dependent on multiple factors, including the trypsin origin and digestion conditions. In-depth characterization of trypsin activity could lead to improved reliability of peptide detection and quantitation in both targeted and discovery proteomics studies. To this end, we assembled a data analysis pipeline and suite of visualization tools for quality control and comprehensive characterization of preanalytical variability in proteomics experiments. Using these tools, we evaluated six available proteomics-grade trypsins and their digestion of a single purified protein, human serum albumin (HSA). HSA was aliquoted and then digested for 2 or 18 h for each trypsin, and the resulting digests were desalted and analyzed in triplicate by reversed-phase liquid chromatography-tandem mass spectrometry. Peptides were identified and quantified using the NIST MSQC pipeline and a comprehensive HSA mass spectral library. We performed a statistical analysis of peptide abundances from different digests and further visualized the data using the principal component analysis and quantitative protein "sequence maps". While the performance of individual trypsins across repeat digests was reproducible, significant differences were observed depending on the origin of the trypsin (i.e., bovine vs porcine). Bovine trypsins produced a higher number of peptides containing missed cleavages, whereas porcine trypsins produced more semitryptic peptides. In addition, many cleavage sites showed variable digestion kinetics patterns, evident from the comparison of peptide abundances in 2 h vs 18 h digests. Overall, this work illustrates effects of an often neglected source of variability in proteomics experiments: the origin of the trypsin.
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