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Keywords {🔍}

article, google, scholar, cas, protein, proteomics, digestion, proteome, trypsin, res, analysis, quantitative, kinetics, labeling, research, cheng, liu, zou, proteins, mass, wang, chem, pan, privacy, cookies, content, trypsincatalyzed, isotope, dimethyl, cleavage, sites, anal, data, publish, search, analytical, mao, peptides, stable, residues, access, peptide, spectrometry, nat, missed, biol, springer, china, site, information,

Topics {✒️}

mass spectrometry–based proteomics month download article/chapter isotope dimethyl labeling trypsin-catalyzed protein digestion tandem mass spectrometry s-2-aminoethyl-l-cysteinamide proteome-wide protein quantification tryptic peptide hydrolysis national chromatographic research tandem digestion approach relative protein abundance isobaric terminal labeling fangjie liu & jing liu privacy choices/manage cookies isobaric chemical labeling bioanalytical chemistry aims protein digestion priority label-free methods trypsin-catalyzed cleavage trypsin-catalyzed hydrolysis gel tryptic digestion full article pdf trypsin digestion kinetics specific digestion artifacts quantitative proteomics reveals bovine trypsin exemplified quantitative proteomics workflow n-terminal pyroglutamylation european economic area α-benzoyl derivatives amino acid composition fully automated system ltq orbitrap velos quantifying human proteins electronic supplementary material protein abundance missed proteolytic cleavages conditions privacy policy label-free cleavage sites surrounded protein digestion proteome analysis database missed cleavage sites sequence logo generator mingliang ye applied quantitative proteomics accepting optional cookies neighboring charged residues cleavage site types check access

Questions {❓}

• Rodriguez J, Gupta N, Smith RD, Pevzner PA (2007) Does trypsin cut before proline?

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         description:Trypsin is the popular protease to digest proteins into peptides in shotgun proteomics, but few studies have attempted to systematically investigate the kinetics of trypsin-catalyzed protein digestion in proteome samples. In this study, we applied quantitative proteomics via triplex stable isotope dimethyl labeling to investigate the kinetics of trypsin-catalyzed cleavage. It was found that trypsin cleaves the C-terminal to lysine (K) and arginine (R) residues with higher rates for R. And the cleavage sites surrounded by neutral residues could be quickly cut, while those with neighboring charged residues (D/E/K/R) or proline residue (P) could be slowly cut. In a proteome sample, a huge number of proteins with different physical chemical properties coexists. If any type of protein could be preferably digested, then limited digestion could be applied to reduce the sample complexity. However, we found that protein abundance and other physicochemical properties, such as molecular weight (Mw), grand average of hydropathicity (GRAVY), aliphatic index, and isoelectric point (pI) have no notable correlation with digestion priority of proteins.
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      headline:Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion
      description:Trypsin is the popular protease to digest proteins into peptides in shotgun proteomics, but few studies have attempted to systematically investigate the kinetics of trypsin-catalyzed protein digestion in proteome samples. In this study, we applied quantitative proteomics via triplex stable isotope dimethyl labeling to investigate the kinetics of trypsin-catalyzed cleavage. It was found that trypsin cleaves the C-terminal to lysine (K) and arginine (R) residues with higher rates for R. And the cleavage sites surrounded by neutral residues could be quickly cut, while those with neighboring charged residues (D/E/K/R) or proline residue (P) could be slowly cut. In a proteome sample, a huge number of proteins with different physical chemical properties coexists. If any type of protein could be preferably digested, then limited digestion could be applied to reduce the sample complexity. However, we found that protein abundance and other physicochemical properties, such as molecular weight (Mw), grand average of hydropathicity (GRAVY), aliphatic index, and isoelectric point (pI) have no notable correlation with digestion priority of proteins.
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