DTA generation parameters were set for a MW range of 500 4000, threshold of 200, precursor mass of 2.0 Da, and a minimum ion count of 20.
with the following parameters: MW range 550 to 4000, group scan 1, minimum group count 1, minimum ion count 25, and an absolute threshold of 500.
The resulting MS/MS spectra (.raw files) were converted to.dta files using TurboSequest Bioworks version 3.1 (Thermo Fisher Scientific) (parameters = threshold cut-off 100, group scan default 100, minimum group count 1, minimum ion count 15, peptide tolerance 1.5).
Raw mass spectra were converted to DTA peak lists using BioWorks Browser 3.2 (ThermoFinnigan) with the following parameter settings: peptide mass range 300 5000 Da, threshold 10, precursor mass ±1.4 Da, group scan 1, minimum group count 1, minimum ion count 15.
The mass spectrometer was set as one full MS scan was followed by ten MS/MS scans on the ten most intense ions from the MS spectrum with the following Dynamic Exclusion™ settings: repeat count, 2, repeat duration, 0.5 min, exclusion duration, 1.5 min. All.dta files were created using Bioworks 3.1, with precursor mass tolerance of 1.4 Da, threshold of 100, and minimum ion count of 15.
Peak lists were generated using Extract-msn program in Bioworks package v3.1 (Thermo Electron) with the following parameters: minimum ion count threshold, 15; minimum intensity, 100.
Collision energy was set to 45, maximum inject time was 250 ms and maximum ion count was 1 × 10 counts.
Fragmentation conditions in the LTQ were 35% normalized collision energy, activation q of 0.25, 30 ms activation time, and minimum ion selection intensity of 500 counts.
The parameters used for MFE were minimum 500 counts, ion species H+, charge state maximum 1, compound ion count threshold 2 or more ions, and all other parameters were default settings.
Screen shots were taken of the distribution of tamoxifen precursor ion normalized on total ion count (TIC).
Data Dependant Analysis was utilized on the LTQ to perform MS/MS on all ions above an ion count of 1000.
