Exploring extracellular matrix degradomes by TMT-TAILS N-terminomics

Elizabeta Madzharova, Fabio Sabino, Ulrich auf dem Keller*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

Abstract

Global characterization of protein N termini provides valuable information on proteome dynamics and diversity in health and disease. Driven by the progress in mass spectrometry-based proteomics, novel approaches for the dedicated investigation of protein N termini and protease substrates have been recently developed. Terminal amine isotopic labeling of substrates (TAILS) is a quantitative proteomics approach suitable for high-throughput and system-wide profiling of protein N termini in complex biological matrices. TAILS employs isotopic labeling of primary amines of intact proteins in combination with an amine-reactive high molecular weight polymer (HPG-ALD) for depletion of internal tryptic peptides and high enrichment of protein N termini by negative selection. Thereby, TAILS allows simultaneous identification of the natural N termini, protease-generated neo-N termini, and endogenously modified (e.g., acetylated) N termini. In this chapter, we provide a protocol for tandem mass tag (TMT)-TAILS analysis and further discuss specific considerations regarding N-terminome data interpretation using Proteome Discoverer™ software.

Original languageEnglish
Title of host publicationCollagen
EditorsIrit Sagi, Nikolaos A. Afratis
Number of pages12
PublisherHumana Press
Publication date2019
Pages115-126
Chapter8
ISBN (Print)978-1-4939-9094-8
ISBN (Electronic)978-1-4939-9095-5
DOIs
Publication statusPublished - 2019
SeriesMethods in Molecular Biology
Volume1944
ISSN1064-3745

Keywords

  • N-terminome
  • Proteolysis
  • Proteome Discoverer™
  • TAILS
  • TMT

Cite this

Madzharova, E., Sabino, F., & auf dem Keller, U. (2019). Exploring extracellular matrix degradomes by TMT-TAILS N-terminomics. In I. Sagi, & N. A. Afratis (Eds.), Collagen (pp. 115-126). Humana Press. Methods in Molecular Biology, Vol.. 1944 https://doi.org/10.1007/978-1-4939-9095-5_8
Madzharova, Elizabeta ; Sabino, Fabio ; auf dem Keller, Ulrich. / Exploring extracellular matrix degradomes by TMT-TAILS N-terminomics. Collagen. editor / Irit Sagi ; Nikolaos A. Afratis. Humana Press, 2019. pp. 115-126 (Methods in Molecular Biology, Vol. 1944).
@inbook{a2326a72888f43b5963d5806fb04916b,
title = "Exploring extracellular matrix degradomes by TMT-TAILS N-terminomics",
abstract = "Global characterization of protein N termini provides valuable information on proteome dynamics and diversity in health and disease. Driven by the progress in mass spectrometry-based proteomics, novel approaches for the dedicated investigation of protein N termini and protease substrates have been recently developed. Terminal amine isotopic labeling of substrates (TAILS) is a quantitative proteomics approach suitable for high-throughput and system-wide profiling of protein N termini in complex biological matrices. TAILS employs isotopic labeling of primary amines of intact proteins in combination with an amine-reactive high molecular weight polymer (HPG-ALD) for depletion of internal tryptic peptides and high enrichment of protein N termini by negative selection. Thereby, TAILS allows simultaneous identification of the natural N termini, protease-generated neo-N termini, and endogenously modified (e.g., acetylated) N termini. In this chapter, we provide a protocol for tandem mass tag (TMT)-TAILS analysis and further discuss specific considerations regarding N-terminome data interpretation using Proteome Discoverer™ software.",
keywords = "N-terminome, Proteolysis, Proteome Discoverer™, TAILS, TMT",
author = "Elizabeta Madzharova and Fabio Sabino and {auf dem Keller}, Ulrich",
year = "2019",
doi = "10.1007/978-1-4939-9095-5_8",
language = "English",
isbn = "978-1-4939-9094-8",
pages = "115--126",
editor = "Irit Sagi and Afratis, {Nikolaos A.}",
booktitle = "Collagen",
publisher = "Humana Press",
address = "United States",

}

Madzharova, E, Sabino, F & auf dem Keller, U 2019, Exploring extracellular matrix degradomes by TMT-TAILS N-terminomics. in I Sagi & NA Afratis (eds), Collagen. Humana Press, Methods in Molecular Biology, vol. 1944, pp. 115-126. https://doi.org/10.1007/978-1-4939-9095-5_8

Exploring extracellular matrix degradomes by TMT-TAILS N-terminomics. / Madzharova, Elizabeta; Sabino, Fabio; auf dem Keller, Ulrich.

Collagen. ed. / Irit Sagi; Nikolaos A. Afratis. Humana Press, 2019. p. 115-126 (Methods in Molecular Biology, Vol. 1944).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

TY - CHAP

T1 - Exploring extracellular matrix degradomes by TMT-TAILS N-terminomics

AU - Madzharova, Elizabeta

AU - Sabino, Fabio

AU - auf dem Keller, Ulrich

PY - 2019

Y1 - 2019

N2 - Global characterization of protein N termini provides valuable information on proteome dynamics and diversity in health and disease. Driven by the progress in mass spectrometry-based proteomics, novel approaches for the dedicated investigation of protein N termini and protease substrates have been recently developed. Terminal amine isotopic labeling of substrates (TAILS) is a quantitative proteomics approach suitable for high-throughput and system-wide profiling of protein N termini in complex biological matrices. TAILS employs isotopic labeling of primary amines of intact proteins in combination with an amine-reactive high molecular weight polymer (HPG-ALD) for depletion of internal tryptic peptides and high enrichment of protein N termini by negative selection. Thereby, TAILS allows simultaneous identification of the natural N termini, protease-generated neo-N termini, and endogenously modified (e.g., acetylated) N termini. In this chapter, we provide a protocol for tandem mass tag (TMT)-TAILS analysis and further discuss specific considerations regarding N-terminome data interpretation using Proteome Discoverer™ software.

AB - Global characterization of protein N termini provides valuable information on proteome dynamics and diversity in health and disease. Driven by the progress in mass spectrometry-based proteomics, novel approaches for the dedicated investigation of protein N termini and protease substrates have been recently developed. Terminal amine isotopic labeling of substrates (TAILS) is a quantitative proteomics approach suitable for high-throughput and system-wide profiling of protein N termini in complex biological matrices. TAILS employs isotopic labeling of primary amines of intact proteins in combination with an amine-reactive high molecular weight polymer (HPG-ALD) for depletion of internal tryptic peptides and high enrichment of protein N termini by negative selection. Thereby, TAILS allows simultaneous identification of the natural N termini, protease-generated neo-N termini, and endogenously modified (e.g., acetylated) N termini. In this chapter, we provide a protocol for tandem mass tag (TMT)-TAILS analysis and further discuss specific considerations regarding N-terminome data interpretation using Proteome Discoverer™ software.

KW - N-terminome

KW - Proteolysis

KW - Proteome Discoverer™

KW - TAILS

KW - TMT

U2 - 10.1007/978-1-4939-9095-5_8

DO - 10.1007/978-1-4939-9095-5_8

M3 - Book chapter

SN - 978-1-4939-9094-8

SP - 115

EP - 126

BT - Collagen

A2 - Sagi, Irit

A2 - Afratis, Nikolaos A.

PB - Humana Press

ER -

Madzharova E, Sabino F, auf dem Keller U. Exploring extracellular matrix degradomes by TMT-TAILS N-terminomics. In Sagi I, Afratis NA, editors, Collagen. Humana Press. 2019. p. 115-126. (Methods in Molecular Biology, Vol. 1944). https://doi.org/10.1007/978-1-4939-9095-5_8