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.
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Corresponding Organization : Northwestern University
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Variable analysis
independent variables
- Settings used in Thermo Xcalibur 4.0 Qual Browser (Thermo Fisher Scientific, Inc.)
- Settings used in Unidec GUI version 3.2.0
- Settings used in TDValidator v1.0 (Proteinaceous)
- Signal-to-noise ratio (S/N)
- Deconvolution of MS1 spectra
- Assignment of recorded fragment ions to the primary sequence of analytes
- Not explicitly mentioned
- Positive controls: Not mentioned
- Negative controls: Not mentioned
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