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The optimized assay was capable of a minimum quantification limit of 10 cells/ml of E. coli in the spiked agricultural water samples.
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The minimum quantification limit of the procedure is ~0.2 ng of total mercury, corresponding to ~20 ppb in a typical 10 mg hair sample.
Final minimum detection level (lower limit of detection [LLOD]) and minimum quantification level (lower limit of quantification [LLOQ]) were calculated by taking the mean values across all plates.
For γH2AX, RPA, and RAD51 foci quantification, a minimum of 30 cells per experiment was scored blindly and error bars represent the SD between three experiments.
For label-free proteins quantification a minimum ratio counts of 2 was considered and the "LFQ intensities" which are the intensity values normalized across the entire dataset were used.
The resulting.dat file was used by the Quanti quantification algorithm [32] for label-free quantification with a minimum of three proteotypic peptides employed for calculation of abundance of each protein.
A minimum of two valid quantifications was required in either GA149-GFP or GFP quadruplicates.
Identifications were filtered at a 1% FDR at the peptide level, accepting a minimum peptide length of 7. Quantification required a minimum ratio count of 2. Requantification was enabled, and match between runs was allowed within a 5-min window.
We selected 10 mutant allele copies as a minimum number required for accurate quantification to minimize stochastic fluctuations in the variant representation.
Unique and razor peptides were considered for quantification with a minimum ratio count of 1. Retention times were recalibrated based on the built-in nonlinear time-rescaling algorithm.
AQUA peptides were serially diluted, and the AQUA peptide dilution with the closest intensity to the native peptide was used for quantification with a minimum of three independent measurements.
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