Figure 2.

Diagrammatic summary of LIT- and Orbitrap-based mass spectrometers for proteomics. All but the IR fragmentation (orange box) is commercially available either as a single mass spectrometer or a combination of some essential components. Peptides are electrosprayed direclty from a LC separation into the heated inlet source where desolvated peptide ions are focused by a stacked ring ion guide (S-lens), then focused, filtered (typically 300–2000 m/z), and transferred by the square quadrupole and octapole to the dual LIT. Peptide ions are collected, isolated, and fragmented by CID in the high pressure cell. Isolated precursor and fragment ions are passed to the low pressure trap for detection. This sequence of events is currently considered a state-of-the-art LIT experiment primarily for protein identification and label-free protein quantification. For higher resolution and mass accuracy detection, precursor or fragment ions can be passed to the Orbitrap mass analyzer via the second quadrupole and C-trap. Beam-type collision can be performed in the HCD collision cell instead of the ion trap for detection with Orbitrap. The Orbitrap detects ion currents of peptide ions that process around an orbital electrode. A Fourier transform is used to convert the frequency-based ion current to a m/z value. Either of these fragmentation schemes with Orbitrap detection are considered state-of-the-art for high mass accuracy peptide analysis and are most often used for protein and post-translational modification identification and quantification with isotopic labeling. Alternative fragmentation methods of ETD, IRMPD, or the combination IR-ETD can be used in conjunction with either the LIT or Orbitrap mass analyzers. The simplest configuration most recently demonstrated is a Q-Orbitrap with HCD detection which consists of only the S-lens, quadrupole mass filter, C-trap, Orbitrap, and HCD collision cell. This configuration and experiment design is quite similar to the QToF illustrated in Figure 3.