Extended Data Fig. 3: DI-SPA scouting experiments for untargeted peptide identification.
From: Quantitative shotgun proteome analysis by direct infusion
a, Fixed and varied parameters for each of the parameter scouting experiments in Fig. 2a–c. Values highlighted in yellow were varied with the other values in that row fixed. b, Schematic of scouting experiment with actual data. Peptides were directly infused into the mass spectrometer over the duration of a scouting experiment. The first selection is performed by FAIMS according to compensation voltage (CV). FAIMS CV is fixed at a value between −30 volts and −80 volts while cycling through the second selection by m/z with the first quadrupole isolation window. is stepped across the m/z range of interest (400–1,000 here) to isolate specific subfractions of the peptide population. The FAIMS and quadrupole-selected peptides are fragmented by HCD, and finally the fragment ions are detected in the orbitrap to produce a tandem mass spectra. No precursor ion scans (MS1) are collected. MS/MS spectra from DI-SPA are identified by spectral library search.
