11. Fragment Based MS/MS Quantification

  1. Ingvar Eidhammer,
  2. Harald Barsnes,
  3. Geir Egil Eide and
  4. Lennart Martens

Published Online: 10 JAN 2013

DOI: 10.1002/9781118494042.ch11

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry

How to Cite

Eidhammer, I., Barsnes, H., Eide, G. E. and Martens, L. (2013) Fragment Based MS/MS Quantification, in Computational and Statistical Methods for Protein Quantification by Mass Spectrometry, John Wiley & Sons Ltd, Oxford, UK. doi: 10.1002/9781118494042.ch11

Publication History

  1. Published Online: 10 JAN 2013
  2. Published Print: 4 JAN 2013

ISBN Information

Print ISBN: 9781119964001

Online ISBN: 9781118494042

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Keywords:

  • fragment based MS/MS quantification;
  • isobaric peptide termini labeling (IPTL);
  • peptide variant quantification;
  • protein quantification

Summary

In fragment based MS/MS quantification the peptides are labeled at each terminus, and the labels stay connected to the fragments after fragmentation. The recognition of corresponding fragments thus resembles the recognition of peptide variants in labeled MS spectra. The fragment ions themselves are then used for quantification. Isobaric peptide termini labeling (IPTL) is one fragment-based labeling technique that can be used to compare two samples. Fragment based quantification implies that the quantification is performed using the same peaks as the identification. General search programs (such as Mascot) can be used for spectrum identification. In contrast to reporter based quantification, where peptide variant quantification is determined by a single peak for each version, the fragment based quantification is derived from a number of fragment intensities. From the peptide ratios the protein ratios can be calculated.

Controlled Vocabulary Terms

Computational statistics; Inferential statistics