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The Deca LCQ IT mass spectrometer was configured to optimize the duty cycle length with the quality of data acquired by alternating between a single full MS scan followed by three tandem MS scans on the three most intense precursor masses (as determined by Xcalibur mass spectrometer software in real time) from the full scan.
Data acquisition was carried out using the mass spectrometer software (Excalibur 2.0.7, Thermo Fisher, Palo Alto, CA, USA).
The molecular content of the mouse hippocampus extracts was determined via manual data analysis using the mass spectrometer software, DataAnalysis (Bruker Daltonics).
An MS survey scan was obtained for the m/z range 400-1800, and MS/MS spectra were acquired from the survey scan for the 10 most intense ions (as determined by Xcaliber mass spectrometer software in real time).
MS/MS spectra were acquired using data-dependent scan from the ten most-intense ions with charge states ≥ 2 in the survey scan (as determined by the Xcalibur mass spectrometer software in real time).
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The mass selective detector was operated in the electron impact mode (70 eV) with selected ion monitoring with a dwell time of 100 ms. The data were processed with proprietary mass spectrometer control software (HP G1701AA).
Furthermore, the field will benefit from improvements in peptide fragmentation enabled by HCD 79) and improved sensitivity and mass accuracy of mass spectrometers and software to deal in an automated fashion with the assignment of modification sites in peptides and quantification to detect changes in modification levels.
MALDI-TOF MS was performed using an AutoflexII mass spectrometer and FlexControl software (Bruker Daltonics), as previously described [13], [28].
For control and data evaluation of HPLC and mass spectrometer, the Analyst software (version 1.6.2; AB Sciex) was applied.
Although the MALDI-TOF MicroFlex LT mass spectrometer and associated software are expensive initially (approximately $200,000), the continuing consumable costs are inexpensive (less than $1 per isolate).
LIPOTYPE has designed a high throughput technology called Shotgun Lipidomics based on the Hamilton STARlet platform in combination with a mass spectrometer and LIPOTYPE' s proprietary software, LipotypeXplorer.
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