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Scientific article
English

The application of 2-D dual nanoscale liquid chromatography and triple quadrupole-linear ion trap system for the identification of proteins

Contributors

Tschäppät, Viviane; Varesio, Emmanuel; Signor, Luca; Hopfgartner, Gerard

Published in

Journal of separation science, vol. 28, no. 14, p. 1704-1711

Publication date

2005

Abstract

2-D nanoscale LC combined with a triple quadrupole-linear ion trap mass spectrometer was applied to the analysis of a complex peptide mixture. A 2-D dual nanoscale LC-MS/MS system was compared to a conventional one. Peptides were separated with a strong cation exchange (SCX) microcolumn in the first dimension and two C18 nanocolumns were used as second dimension. MS experiments were performed using information-dependent data acquisition, where two precursor ions were selected from an enhanced MS (EMS) or an enhanced multicharged ion (EMC) as survey scan. The major benefit of EMC instead of EMS was a two-fold reduction of the data file and a 15% increase of characterized proteins. The advantage of the 2-D dual nanoscale LC-MS/MS system versus the conventional 2-D nanoscale LC-MS/MS system was reflected in the significant increase of peptides which were successfully identified within the same time frame. The first factor contributing to this increase was that the mass spectrometer was collecting twice the number of relevant MS/MS data. The second factor is the use of twice the number of SCX salt fractions in the first dimension, allowing a better sample fractionation, thereby reducing the number of peptides transferred to the second chromatographic dimension per salt fraction.

Keywords

  • Animals
  • Caenorhabditis elegans
  • Caenorhabditis elegans Proteins/chemistry/isolation & purification
  • Chromatography, High Pressure Liquid/methods
  • Nanotechnology/methods
  • Peptide Fragments/chemistry/isolation & purification
  • Proteins/chemistry/isolation & purification

UNIGE affiliation entities

Citation (ISO format)

TSCHÄPPÄT, Viviane et al. The application of 2-D dual nanoscale liquid chromatography and triple quadrupole-linear ion trap system for the identification of proteins. In: Journal of separation science, 2005, vol. 28, n° 14, p. 1704–1711. doi: 10.1002/jssc.200500149

Main files (1)

Article (Accepted version)

Identifiers

Journal ISSN

1615-9306
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Technical informations

Creation

20/07/2009 14:47:00

First validation

20/07/2009 14:47:00

Update

14/03/2023 15:10:20

Status update

14/03/2023 15:10:20

Last indexation

29/10/2024 11:52:30
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