Terminology Cheat Sheet


At the recent Targeted Proteomics Course at UW 2014, participants claimed that the many terms we have in mass spec proteomics with exactly the same meaning made the course much more difficult to follow.  They requested a glossary or cheat sheet that might help them translate between these various terms.  Here it is:

SRM - Selected Reaction Monitoring (sometime confused as Single Reaction Monitoring - no such thing).  Common synonym MRM (Multiple Reaction Monitoring).  Performed on triple-quadrupole instruments, where the instrument cycles through a pre-specified set of precursor m/z (Q1), product m/z (Q3) pairs called 'transitions', using the quadrupoles as filters (usually 0.5 to 1.0 m/z range).  Cycle time is determined by the sum of the dwell times of all transitions in the set.
MRM - Multiple Reaction Monitoring, a synonym for SRM created and trademarked by AB SCIEX, but extremely popular because of early popularity of AB Q TRAP instruments for performing this method.
scheduled-SRM = scheduled-MRM = dMRM = dynamic-MRM - In order to allow measuring a greater number of transitions in a run, transitions are specified with start and end times (or retention times and windows) to allow the instrument to measure each transition for only a fraction of the entire gradient.  Cycle time at any given time is determined by the sum of the dwell times of all transitions being measured at that time.
iSRM = intelligent-SRM = triggered-SRM = triggered-MRM = tMRM - In order to gain more confidence in the correct identification of a chromatogram peak in SRM without overly sacrificing quantitative throughput, the instrument measures a set of primary transitions, as in normal SRM/MRM until the intensity on those transitions exceeds some threshold.  When the threshold is exceeded, the instrument takes one or more measurements of a secondary set of transitions usually used only for peak identity confirmation, and not quantification. 

Targeted MS/MS = tMSMS = PRM = MRM-HR - Like SRM, but performed on a full-scan instrument (ion-trap or Q-TOF).  The instrument cycles through a pre-specified set of precursor m/z values, using quadrupole or ion trap isolation as a filter (usually 1.0 to 2.0 m/z range) and collects a full MS/MS fragment ion spectrum for each.  Cycle time is determined by the sum of the dwell/accumulation or scan times of all scans in the set.  Software is used to extract chromatograms from the resulting MS/MS spectra.  If the spectra are high-resolution, then extraction can be done using 50-100pm range, making it more selective than SRM.  Common synonyms PRM (Parallel Reaction Monitoring), MRM-HR (HR = High Resolution), pSRM (Pseudo Selected Reaction Monitoring).

MS1 [Full-Scan] Filtering - Chromatograms are extracted from the MS1 scans of normal DDA (Data Dependent Acquisition) data.  Because of the semi-random sampling approach, for MS/MS, of DDA, it is not possible to extract product ion chromatrams (time, intensity) with meaningful peaks for quantification.  Chromatogram-based quantification from DDA runs is limited to extracted ion chromatograms from the MS1 survey scans of such runs.  Common synonym Label Free Quant.

DIA = SWATH = HRM - Data Independent Acquisition is a technique where ranges of precursor m/z are isolated and subjected to fragmentation in a consistent pattern over cycles of time.  In this way a mass spectrometer can be set up to gather fragment ion spectra for large regions of precursor m/z space, independent of the actual precursor ions being fragmented, which may include fragments for multiple precrusors in any given scan.  Software can be used to extract product ion chromatograms from the acquired MS/MS spectra.  Cycle time is determined by the sum of the dwell/accumulation or scan times of all scans in the set.  (e.g. 20 ranges x 10 m/z = 200 m/z total range, 30 ranges x 20 m/z = 600 m/z total range)
SWATH - Popular synonym for DIA coined in Gillet, et al. MCP 2012, but also trademarked by AB SCIEX, originally specified as 32 x 25 m/z ranges covering 400 - 1200 m/z.
HRM - Hyper Reaction Monitoring, less common synonym for DIA/SWATH.
MSe - Type of DIA where ions are collected without prior filtering in alternating low- and high-energy scans (all precursors and fragments of all precursors respectively), coined and trademarked by Waters.  Common synonym All-Ions DIA.

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