Thermo xcalibur 4.0 qual browser

Spectra were manually inspected and analyzed using Thermo Xcalibur 4.0 Qual Browser (Thermo Fisher Scientific, Inc.) and assembled into a figure for publication using Adobe Illustrator CC 2015.3. Table S3 contains spectral parameter averages and ranges derived for the indicated base peak(s), as well as values for resolution, baseline intensity, and noise intensity. SNR was calculated by subtracting the baseline intensity (B) from the signal intensity (NL) and the noise (N) intensity, and dividing: SNR = (NL-B) / (N-B). The mass spectra data files (.RAW) of the protein standards measured on the QE-EMR are publicly available online at https://massive.ucsd.edu under Accession Number MSV000083343. Fragmentation data were analyzed using ProSight Lite [30 (link)] with a 25 ppm error cutoff for identified fragments.

Spectra were analyzed manually using Thermo Xcalibur 4.0 Qual Browser (Thermo Fisher Scientific, Inc.). S/N, taking the highest charge states of a protein distribution in consideration, was calculated as follows: S/N = (NL-B) / (N-B), where NL is the signal intensity, B is the baseline intensity, and N is the noise intensity. Deconvolution of MS¹ spectra was performed using Unidec GUI version 3.2.0 [47 (link)] and detailed parameter settings can be found in Table S7. TDValidator v1.0 (Proteinaceous) [48 (link)] (max ppm tolerance: 10 ppm; sub ppm tolerance: 5 ppm; cluster tolerance: 0.35; charge range: 1 to at or below that of the analyte; minimum score: 0.5–0.73; S/N cutoff: 1–5; Distribution Generator: BRAIN; minimum size: 2) was used to assign recorded fragment ions to the primary sequence of analytes. Annotated fragments were manually validated thereafter.