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Does trypsin cut before proline?

Jesse Rodriguez1, Nitin Gupta, Richard D Smith

  • 1Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.

Journal of Proteome Research
|December 11, 2007
PubMed
Summary
This summary is machine-generated.

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The established "Keil rule" for trypsin cleavage before proline in mass spectrometry is inaccurate. Re-analysis of 14.5 million tandem spectra reveals frequent trypsin cleavages before proline, necessitating updated peptide identification algorithms.

Area of Science:

  • Proteomics
  • Enzymology
  • Bioinformatics

Background:

  • Trypsin is a key enzyme for protein digestion in mass spectrometry.
  • Current peptide identification algorithms rely on strict trypsin specificity rules, including the
  • Keil rule
  • which excludes cleavage before proline.

Purpose of the Study:

  • To re-evaluate trypsin specificity rules using a large-scale dataset.
  • To investigate the frequency of trypsin cleavage before proline.
  • To propose modifications to peptide identification algorithms.

Main Methods:

  • Analysis of 14.5 million tandem mass spectrometry spectra.
  • Statistical examination of observed tryptic cleavage sites.
  • Hypothesis testing for observed cleavages before proline.

Related Experiment Videos

Main Results:

  • A significant number of trypsin cleavages before proline were identified, contradicting the established
  • Keil rule
  • .

Conclusions:

  • The
  • Keil rule
  • for trypsin specificity is outdated and requires revision.
  • Peptide identification algorithms should be updated to include cleavages before proline.
  • The methodology can be applied to reassess specificity rules for other proteases.