In contrast, hyperparameters are only estimated once for the SIRIUS 3 method, and are not retrained for a new dataset; they are required for computing the prior probability of a FT. Mass accuracy parameters (sigma _{text{m}}, MA, m_{ MA }) and noise intensity parameters (x_{text{i}}, alpha _{text{i}}) can be determined individually for each dataset.
The search results were filtered with cross-correlation (Xcorr) via charge states (+1: 1.5, +2: 2.0, +4: 2.5, +4: 3.0), delta correlation (ΔCn > 0.1), molecular weight (m/z 500 Da m/z 2000 Da), and peptide mass accuracy (Δ1.5 Da) parameters.
In contrast, parameters for mass accuracy and peak intensities used for estimating the likelihood of a FT can be set individually for every analysis.
Protein identification was performed by searching for bacteria in the NCBI non-redundant database using the Mascot search engine (Matrix Science), using the following parameters: monoisotopic; mass accuracy, 0.1 Da; missed cleavages, 1.
Such parameters as mass accuracy, intensities of XIC, and retention times confirmed the locations of modification sites.
For databases searching parameters were mass accuracy thresholds of 0.5 (MS/MS) and 20 ppm (precursor), Trypsin/P+DP asprotease, maximum three missed cleavages, carbamidomethylation (C) as fixed modification and oxidation (M), phosphorylation (STY) and protein N-terminal acetylation as variable modifications.
FDRs for elemental composition search results of Orbitrap data can be estimated by the present method because the branching-ratio parameters for high mass accuracy data are available in Table S1.
The mass analyser depends on three key parameters: sensitivity, resolution, and mass accuracy.
