Peak picking, alignment and identification was performed based on R package metaMS70,71 with a retention time window match set to 0.5 min.
An appropriate retention time window for each analyte has been established in order to identify them in quality control sample (QC).
A 100-ms dwell time with a 3-ms pause time was used for the all MRM transitions in one single retention time window.
The MS/MS peak lists were extracted with RMassBank [8] using the ion mass and a retention time window of 0.4 min around the expected retention time and reported as absolute ion intensities.
The orthogonal information proved useful despite the large errors associated with the predictions (e.g. over 1 log unit or up to several minutes retention time window depending on the LC run length).
Dynamic MRM enables MRM acquisitions of compounds during a retention time window corresponding to the elution time of each compound, thus increasing the minimum dwell time (Liu et al. 2011).
As compared to the multiple reactions monitoring (MRM), dynamic MRM has an associated delta retention time window (Del RT) where it dynamically turns on and off without affecting the total cycle time.
The chromatograms showed noisy and non-reproducible drifting baselines or signals in the retention time window of perchlorate, which could not reliably be identified as the target peak even after standard addition experiments.
The main parameters were set as follows: retention time range 2 min to 55 min, mass range 100 to 1000, mass window 0.5, retention time window 1 min and signal-to-noise (S/N) ratio threshold 5. Variables that did not exist in 80% of participants in one group were filtered [15].
Compounds were detected using the following method parameters: S/N threshold set to 2, Intensity threshold set to 100 for both positive and negative, and a maximum number of 8000 compounds with a retention time window of 0.05 min. The.mgf files were uploaded to Mascot and searched against a T. turnerae database.
Delta retention time window was 4 or 5 min.
