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Chromatographia

, Volume 82, Issue 1, pp 101–110 | Cite as

High-Resolution Nano-Liquid Chromatography with Tandem Mass Spectrometric Detection for the Bottom-Up Analysis of Complex Proteomic Samples

  • Magali Dams
  • José Luís Dores-Sousa
  • Robert-Jan Lamers
  • Achim Treumann
  • Sebastiaan EeltinkEmail author
Review
Part of the following topical collections:
  1. 50th Anniversary Commemorative Issue

Abstract

Liquid chromatography coupled with mass spectrometric detection is one of the major technologies used for protein sequencing, identification, and quantification. This review provides an introduction of the current state-of-the-art technology in peptide profiling using nano-liquid chromatography–mass spectrometry applied to large-scale protein or proteome analysis. In particular, different aspects of the bottom-up proteomics workflow are covered, including aspects of sample preparation such as protein digestion, nanoflow gradient reversed-phase chromatographic separation, LC–MS interfacing via electrospray ionization, tandem mass spectrometry of digests, protein identification via database searches, and finally peptide quantitation.

Keywords

Review Proteomics research Peptide mapping Peptide profiling Nano-LC 

Abbreviations

AC

Alternating current

CID

Collision-induced dissociation

DC

Direct current

DDA

Data-dependent acquisition

dp

Particle diameter

ESI

Electrospray ionization

FA

Formic acid

FAB

Fast atom bombardment

FDR

False discovery rate

HFBA

Heptafluorobutyric acid

HPLC

High-performance liquid chromatography

I.D.

Internal diameter

iTRAQ

Isobaric tag for relative and absolute quantitation

L

Column length

MALDI

Matrix-assisted laser desorption ionization

MRM

Multiple reaction monitoring

MSMS

Tandem mass spectrometry

m/z

Mass-to-charge ratio

N

Plate number

PSM

Peptide-spectrum match

QTOF

Quadrupole time-of-flight

RF

Radio frequency

RP-LC

Reversed-phase liquid chromatography

SILAC

Stable isotope labeling by amino acids in cell culture

SRM

Selected reaction monitoring

TFA

Trifluoroacetic acid

Th

Thomson

TMT

Tandem mass tag

Notes

Acknowledgements

This publication has been written as part of the Open Technology Programme with project number IWT.150467 (DEBOCS), which is financed by the Flemish Agency of Innovation and Entrepreneurship (VLAIO). JLDS and SE acknowledge the Research Foundation Flanders (FWO) for financial support (Grant nos. G 025916N and G033018N).

Compliance with Ethical Standards

Conflict of interest

All authors declare that they have no conflict of interest.

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Magali Dams
    • 1
  • José Luís Dores-Sousa
    • 1
  • Robert-Jan Lamers
    • 2
  • Achim Treumann
    • 3
  • Sebastiaan Eeltink
    • 1
    Email author
  1. 1.Department of Chemical EngineeringVrije Universiteit Brussel (VUB)BrusselsBelgium
  2. 2.Abundnz B.V.WoerdenThe Netherlands
  3. 3.Newcastle University, NUPPANewcastle upon TyneUK

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