Body Fluid Degradomics and Characterization of Basic N-Terminome

Research output: Chapter in Book/Report/Conference proceedingBook chapter – Annual report year: 2017Researchpeer-review

Without internal affiliation

  • Author: Sabino, F.

    Swiss Federal Institute of Technology Zurich

  • Author: Hermes, Olivia

    Swiss Federal Institute of Technology Zurich

  • Author: auf dem Keller, U.

    Swiss Federal Institute of Technology Zurich

View graph of relations

Rapid improvements in instrumentation and data analysis make mass spectrometry-based proteomics the method of choice for global characterization of proteomes and discovery of protein-based biomarkers. On the contrary to tissue biopsies, body fluids—e.g., blood, wound fluid, urine, and saliva—are noninvasive and easy to collect and process. However, they are very complex and present high dynamic ranges of protein concentrations, rendering direct shotgun proteomics analysis as inefficient for identification of low-abundance proteins in these specimens. Sample prefractionation, immunoaffinity depletion of highly abundant proteins, and enrichment of posttranslational modifications (PTM) are common strategies for proteome simplification of body fluids. Combinatorial peptide ligand libraries (CPLL) relatively deplete high-abundance proteins by binding equimolar amounts of protein species in the sample and provide an elegant species-independent alternative to immunoaffinity-based approaches. By cleaving target proteins, proteases catalyze an irreversible PTM, whereby uncontrolled proteolysis is associated with many diseases. Thus, proteolytic events represent powerful indicators for disease progression and their specific identification in body fluids holds great promises for establishment of novel biomarkers. Quantitative N-terminal enrichment strategies, such as terminal amine isotopic labeling of substrates (TAILS) detect protease-generated neo-N-termini with high specificity and increase coverage of low-abundance proteins by inherent proteome simplification. In this chapter, we describe a protocol that combines the CPLL technology with iTRAQ-based TAILS to systematically characterize the basic N-terminome of body fluid proteomes and its alterations in disease conditions that we have successfully applied to explore the wound fluid degradome at multiple time points after skin injury.

Original languageEnglish
Title of host publicationMethods in Enzymology
Volume585
PublisherElsevier
Publication date2017
Pages177-199
Chapter11
DOIs
Publication statusPublished - 2017
Externally publishedYes
SeriesMethods in Enzymology
Volume585
ISSN0076-6879
CitationsWeb of Science® Times Cited: No match on DOI

    Research areas

  • Body fluid, Combinatorial peptide ligand libraries, Degradome, iTRAQ, N-Terminome, TAILS

ID: 139435574