Scan‐Centric, Frequency‐Based Method for Characterizing Peaks from Direct Injection Fourier Transform Mass Spectrometry Experiments

We present a novel, scan‐centric method for characterizing peaks from direct injection multi‐scan Fourier transform mass spectra of complex samples that utilizes frequency values derived directly from the spacing of raw m/z points in spectral scans. Our peak characterization method utilizes intensity‐independent noise removal and normalization of scan‐level data to pro-vide a much better fit of relative intensity to natural abundance probabilities for low abundance isotopologues that are not present in all of the acquired scans. Moreover, our method calculates both peak‐ and scan‐specific statistics incorporated within a series of quality control steps that are de-signed to robustly derive peak centers, intensities, and intensity ratios with their scan‐level vari-ances. These cross‐scan characterized peaks are suitable for use in our previously published peak assignment methodology, Small Molecule Isotope Resolved Formula Enumeration (SMIRFE).