Straightforward N-glycopeptide analysis combining fast ion trap data acquisition with new ProteinScape functionalities

Application Note

Expression Proteomics

LCMS-66

Ion Trap

2012

amaZon speed, ProteinScape 3.0, GlycoQuest

Kristina Neue, Andrea Kiehne, Markus Meyer, Marcus Macht, Ulrike Schweiger-Hufnagel, Anja Resemann Bruker Daltonik GmbH

LCMS-66, #284649

Abstract

The current approach demonstrates the performance
of the amaZon speed ETD system for the analysis of
N-glycosylated peptides. The instrument combines new
hardware and software features such as faster precursor
isolation and reduced fragmentation time to deliver a
significantly faster MS/MS duty cycle compared to the
previous platform, providing high quality MS/MS spectra,
even from heterogeneous co-eluting glycopeptides.

Data processing was performed using ProteinScape 3.0,
a sophisticated bioinformatics platform. The workflow
comprised classification of N-glycopeptide MS/MS spectra
from the LC-MS/MS data set, automatic determination
of peptide masses, and glycan database search using the
search engine GlycoQuest. This led to the identification of
a total of 22 different glycan structures for the glycopeptide
EEQFNSTFR from MOPC-21 in one LC-MS/MS run.

Related Products

amaZon speed series
ProteinScape
Glycans / Glycopeptides

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