12 Glossary / Terminology

This chapter collects important terms used throughout the book, along with their definitions.

If you come across a term that is not yet defined here, please add it.

ESI (Electrospray Ionization): An ionization technique used to introduce peptides into a mass spectrometer, imparting one or more electrical charges to the peptide molecules. This produces charged precursor ions that can be separated and analyzed according to their mass-to-charge (m/z) ratios.
m/z (mass-to-charge ratio): The peptide property measured by a mass spectrometer’s mass analyzer.
MS1: The full mass spectrum recorded by the mass analyzer during the initial scan, which measures the m/z of precursor ions before fragmentation.
MS2 (MS/MS, tandem mass spectrometry): The fragmentation scan performed on selected precursor ions from the MS1 scan. This step is essential for determining the amino acid sequence of a peptide by generating characteristic fragment ions.
TOF (Time-of-Flight): A type of mass analyzer that determines the m/z of ions by measuring the time they take to travel through a field-free flight tube, with lighter (lower m/z) ions arriving at the detector faster than heavier ones. TOF analyzers are used in a variety of mass spectrometers, including the Bruker timsTOF.
PSM (Peptide-Spectrum Match): The result of comparing an experimental MS2 spectrum against a theoretical spectrum generated from a reference protein database during database searching. Each PSM is assigned a score reflecting the quality of the match, which is used to distinguish correct peptide identifications from incorrect ones.
CID (Collision-Induced Dissociation): A peptide fragmentation method, in which selected precursor ions collide with an inert gas, causing cleavage of the peptide backbone. The resulting fragment ions are commonly classified as b-ions and y-ions.
HCD (Higher-energy Collisional Dissociation): A refined form of CID in which ions are accelerated to higher collision energies.
DDA (Data-Dependent Acquisition): A mass spectrometry acquisition strategy in which the instrument selects precursor ions for fragmentation (MS2) in real time based on their intensity in the survey (MS1) scan, typically fragmenting the top N most abundant ions.
DIA (Data-Independent Acquisition): A mass spectrometry acquisition strategy in which all precursor ions within predefined, sequential mass-to-charge (m/z) windows are systematically fragmented, regardless of their intensity. This produces more comprehensive but also more complex MS2 spectra, which typically require spectral libraries and specialized software for interpretation.
SRM/MRM (Selected/Multiple Reaction Monitoring): A targeted mass spectrometry acquisition strategy performed on triple quadrupole instruments, in which a predefined set of precursor ion to fragment ion transitions is monitored throughout the run. SRM refers to monitoring a single transition, while MRM refers to monitoring multiple transitions in parallel.
PRM (Parallel Reaction Monitoring): A targeted mass spectrometry acquisition strategy, in which predefined precursor ions are isolated and fragmented, and all resulting fragment ions are recorded in a single high-resolution MS2 scan, rather than monitoring individual transitions as in SRM/MRM.
Bottom-up: An approach to proteomics analysis in which proteins are first digested into peptides, and then the resulting peptides are analyzed by mass spectrometry. This is the most common approach for identifying and quantifying proteins in complex mixtures.
Top-down: An approach to proteomics analysis in which intact proteins are directly analyzed by mass spectrometry, without prior digestion into peptides. This approach can provide information on protein isoforms and post-translational modifications, but is technically more challenging.
Middle-down: An approach to proteomics analysis in which proteins are partially digested into larger peptide fragments, which are then analyzed by mass spectrometry. This approach can provide a balance between the detailed information obtained from top-down analysis and the higher throughput of bottom-up analysis.