Collision-induced fragmentation was performed using the ion-trap device of the ES-MS instrument.
Upon collision-activated dissociation (CAD) of precursor ions, MS/MS spectra were acquired using the ion trap as the analyser.
Based on the efficient fragment ion analysis using an ion trap instrument, informative fragment spectra of sodium adducts can be obtained with minute amounts of material, allowing insights into defects of glycoconjugates degradation, and investigation of metabolic and catabolic pathways.
Component proteins were extracted using novel methods for preserved tissues, separated, subjected to tryptic digestion and LC-MS MS 2 LC-MS MS 2sing analysisrap mass spectrometer, and identified with reference to databases.
Extracted and dried peptides were subjected to liquid chromatography tandem mass spectrometry (LC MS/MS) analysis using a linear ion trap-orbitrap hybrid mass spectrometer (LTQ-orbitrap, Thermo-Electron, San Jose, CA) set up as described previously (Haas et al, 2006; Roskens et al, 2010).
The 2-AB-labeled glycans were identified by MS and MS by use of the ion-trap mass spectrometer.
The mass spectrometer is a hybrid ion-trap time-of-flight (TOF) instrument in which the ion-trap is used in radio frequency-only mode, with DC-pulse ejection, to provide decoupling of the different timescales required for CEC separation and TOF mass analysis.
The captured glycoproteins were then probed with four different fluorescently labeled lectins in a sandwich array format, followed by characterization in situ by on-plate digestion and direct analysis using MALDI-QIT (quadrupole ion trap -TOF-MS.
The ion-trap was set to detect positively charged ions using a spray voltage of 2.5 kV and an automated data-dependent MS/MS analysis performed on the five most abundant ion species from each MS full scan before another MS full scan was performed.
Mass values extracted from this survey spectrum are used to generate an instrument control script for subsequent acquisition of MSn data using the LTQ ion trap, an instrument optimized for very high sensitivity fragmentation analysis.
