The First-in First-out (FIFO) mode of data acquisition was used for data collection with an ADC resolution of 4096 over a 10 ns measurement period.
This mode of data acquisition has led to enormous overlap in the identification of highly abundant proteins in subsequent LC-MS injections.
The alternate scanning mode of data acquisition during LC MS analysis allows a comprehensive inventory of all precursor ions with their corresponding time-resolved product ions.
As a consequence, adjustments to the type of sample preparation and mode of data acquisition were made to allow additional spectroscopic measurements via Raman microscopy [ 18], and the analysis of archival tissue blocks.
The notation used XXX/YYY (LTQ/LTQ or FT/FT or LTQ/FT or FT/LTQ) refers to the mode of data acquisition for MS and MS/MS spectra.
The undersampling limitations of the data-dependent 'shotgun' mode of data acquisition that was utilized did not allow for unequivocal conclusions about the absence of specific N-glycosites in a sample [ 20], a question that would best be answered with targeted analyses.
The LTQ Orbitrap XL mass spectrometer was run in data-dependent acquisition mode using Xcalibur 2.2 software (Thermo Scientific) using the positive ion mode for data acquisition.
Acquisition and analysis of mass spectrometry data was done essentially as described in (Hekmat et al. 2010; Rosengren et al. 2012), using a MALDI-TOF 4700 Proteomics Analyzer (Applied Biosystems, Framingham, CA) in positive reflector mode for data acquisition.
However, since the FDG uptake and subsequent SUV measurements are influenced by many factors such as tumour size, blood glucose level, time interval and mode of PET data acquisition as well as PET image reconstruction and analysis, the use of SUV measurements is not yet in widespread clinical practice.
In addition, the use of profile mode in data acquisition seems to be valuable because of the higher probability of correct peptide identification.
