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The 'traffic light' assay also demonstrated a high degree of analyte detection when testing spiked milk samples (92 101%) and accuracy (quantitation error <8% of the mean).
To determine the quantitation error of phosphopeptides, DNP-regulated protein expression changes were used to determine the median H/L ratio.
The increased accuracy in the BSAS method was attributed to the decrease in quantitation error over the traditional approach, seen in the standard curves generated.
Differences in sample read counts are more likely due to pipetting or quantitation error when the sequencing libraries are initially combined prior to the enrichment process.
Although the coincident measurement of a pair of annihilation photons by a ring of detectors surrounding the patient is disturbed by random and scattered (Fig. 2) coincidences as well as by events lost due to tissue attenuation, the related errors can be corrected sufficiently so that the final quantitation error is in the range of a few per cent.
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To avoid possible interference from naturally occurring endogenous acids and quantitation errors 3- 4-chlorophenyl) propionic acid was chosen as an internal standard.
Fewer than 4% of the data points were found to have peak matching and quantitation errors of >10%, see legend to Table 1).
The generation of peak list, SILAC- and extracted ion current-based quantitation, calculated posterior error probability, and false discovery rate based on search engine results, peptide to protein group assembly, and data filtration and presentation was carried out using MaxQuant.
Major points: 1) There is a general concern throughout the manuscript that interpretations about relative potencies (and half-max ligand concentrations) are made without quantitation or (therefore) error bars – and it is not stated how many repeats of each analysis were done.
The standard curves generated from the Sanger/ESME method have variations ranging from 5% to over 20% error in quantitation, while the BSAS method produced variation consistently less than 5% error.
There are a few important problems, though, most notably the tendency to draw quantitative conclusions about relative potencies from dose-response curves that are not saturated, and from data presented without proper quantitation or assessment of error (see point 1).
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