FAQ AMS Glossary

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This is a glossary of terms and acronyms typically used by the AMS community. It is a work in progress - so is by no means complete or comprehensive. Please continue to add and edit!

Current Curator: and Jose-Luis Jimenez (Colorado)

Hardware and Data Acquisition

  • ACSM: Aerosol Chemical Speciation Monitor. A smaller and cheaper version of the AMS using a small quadrupole, designed for monitoring purposes. Does not have size-resolved capabilities. Details: Users' Meeting, Publication
  • ADQ: Data acquisition card for fast mass spectra acquisition (new model). Details here
  • AMS: Aerosol Mass Spectrometer. In our community it always means the Aerodyne AMS, but a few other groups have named other instruments "AMS", which are unrelated to the Aerodyne AMS. The review paper on the AMS is here
  • AP240: Data acquisition card for fast mass spectra acquisition (old model). Details here
  • BFSP: Brute-Force Single Particle Mode of the ToF-AMS DAQ. Used to acquire single-particle signals for IE calibration (and sometimes other purposes).
  • bitwise: The page of the ToF-AMS DAQ software that allows setting the baseline and threshold of the AP240. Details here
  • CRiTTR: Piece of software to run the pulsers and move the chopper independently of the AMS Data Acquisition software (DAQ)
  • ePToF Mode: Efficient PToF. New method/module for PToF mode (see PToF below) where chopper is based on a multiplexed particle beam chopper system with 50% particle throughput (compared to ~2%), providing significantly improved signal-to-noise. Description here
  • FMS mode: Fast MS mode (see below for MS mode) where rather than spending similar time in open and closed (standard MS mode), open data is acquired continuously up to 10 Hz and periodically a relatively short period of closed data is acquired. Used for fast sampling (e.g. aircraft, eddy covariance fluxes). Details here
  • HDF: Hierarchical Data Format, a high-performance random access data file format, developed by NCSA with NASA funding for satellite applications. The ToF-AMS data is now always saved in HDF5. Details here.
  • Light Scattering: see LS-AMS below.
  • LS-AMS: AMS with an internal adaptor used to measure particle size and presence optically inside the AMS (>200 nm). First described by Cross et al. (AS&T, 2007)
  • L-ToF-AMS or L-AMS: Long High-Resolution Time-of-Flight Aerosol Mass Spectrometer, which has higher resolution and signal than W-mode, available but not yet published as of Dec. 2016.
  • MAB-AMS: Metastable Atom Bombardment AMS. An adaptation of the AMS which uses soft ionization for analysis of organic aerosols with lower fragmentation. Details here
  • Mini-AMS: a smaller version of the AMS. A key difference is that the ACSM does not measure size (does not have PToF mode), while the mini-AMS does.
  • MS mode: mass spectrum data acquisition mode in which the chopper is used to alternatively open and block the particle beam. Description here
  • PToF Mode: Particle Time-of-Flight data acquisition mode in which the chopper slit opening provides an initial time for the acquisition of size-resolved data. Description here
  • SP-AMS: Soot Particle AMS. New instrument developed which combines the SP2 (Single Particle Soot Photometer) particle vaporization and the AMS ionization and mass spectrometry. Details: Users' Meeting, publication
  • ToF-ACSM: Time-of-Flight Aerosol Chemical Speciation Monitor. Similar to the ACSM (see above), except it uses a time-of-flight detector, similar to that used on the C-ToF-AMS Details here.

Analysis Software and Results

  • APES: Analytical Procedure for Elemental Separation. An Igor tool for performing an elemental analysis (i.e. O/C ratio). In Pika 1.07 most of this code was merged with the pika code, but a version of APES remain as a stand-alone Igor code. Details here
  • Background: In general this term should be avoided or qualified, as it can be ambiguous. (Background ambient measurement conditions? Background instrumental signal? etc.) The use of 'Closed mass spectra' is encouraged where appropriate.
  • Baseline (in Squirrel): In a mass spectra, the 'region between the peaks' for an open, closed or difference mass spectra. Not to be confused with the PToF baseline or the AP240 baseline.
  • Batch Table (in Squirrel): A table of waves which defines species. This includes the names given to species, a frag wave associated with a species, a collection efficiency value, and other items.
  • Closed: The mass spectrum taken with the chopper in the 'blocked' position, and typically considered instrument background and gas-phase contribution to AMS signal
  • CD-CE: Composition-Dependent Collection Efficiency. Algorithm to correct concentrations for sub-unity collection efficiency using measured AMS composition. Details here.
  • Diff: The Difference Spectrum; difference in chopper-open mass spectrum and chopper-closed mass spectrum; typically considered the mass spectrum due to particles and gases entering the AMS. See also 'semi-refractory'.
  • dva: see vacuum aerodynamic diameter
  • Elemental Analysis or EA: the technique to determine the elemental composition of a mixed organic aerosol based on HR-TOF-AMS signals. This is currently implemented in the APES software. Introduced by Aiken et al. (Anal. Chem., 2007), (ES&T, 2008), and Canagaratna et al. (ACP, 2015). Typically only the oxygen-to-carbon (O/C) and hydrogen-to-carbon (H/C) ratios are reported due to their much higher accuracy than others (e.g., N/C, S/C). They are always reported as MOLAR ratios. On the other hand, OA/OC (or in older literature OM/OC) is always reported as a mass ratio. Sometimes the carbon oxidation state (OSc) is used and approximated as 2 O/C – H/C.
  • fx: the fraction of the total organic signal that is observed at m/z = x. E.g. f44 is the fraction of the total OA signal at m/z 44. Sometimes also written as 44/Org or 44/OA. Commonly reported fx's (and tracer association) include: f44 (more-oxidized OOA, organic acids), f43 (less-oxidized OOA, non-acid oxygenated functional groups), f57 (HOA), f60 (biomass burning POA), and f82 (IEPOX-SOA).
  • frag wave: a text wave in the AMS software describing a linear combination of sticks. The display of all frag waves is called a frag table. The syntax for describing the linear combination uses a comma for addition. There is often one frag wave which uniquely identifies a species, such as nitrate.
  • fragments: a vaporized molecule is ionized in the AMS to a series of ions, which are then detected by either a quadrupole or time-of-flight mass spectrometer; the resulting ions are referred to as 'fragments'
  • HR: High Resolution (as opposed to UMR, typically referring to either the High-Resolution Time-of-Flight Aerosol Mass Spectrometer, or to the data derived from that instrument). See HR-ToF-AMS above.
  • Igor or Igor Pro: a commercial data analysis software package developed by Wavemetrics, Inc., in Oregon, US. All the standard AMS data analysis software is written in Igor. Details here.
  • ipf: Igor Procedure File. See Igor above.
  • itx: Igor Text File. See Igor above.
  • Non-refractory (NR) species: chemical components of aerosol that are volatilized in the AMS, and are observed in the "Difference spectrum". This requires evaporation in a time scale shorter than chopper open/closed movement, whish is typically 3-5 seconds. Examples include the usual AMS species: sulfate, nitrate, ammonium, chloride, and organic (OA). Note that these species can also have some semi-refractory signal, although this is typically a small fraction (5-10% of the NR signal under typical operating conditions).
  • raw spectra: the non-integrated spectra. It is often displayed in units of signal (bits or average ion counts) on the y axis and ns (ion time of flight, typically in ns units) or mass to charge (m/z) on the x axis. Displays of raw spectra show the 'hills and valleys' - integrated and baseline regions.
  • Refractory (R) species: chemical components of aerosol that are not volatile enough to vaporize in the AMS on a time scale of several hours, and thus are never observed by the instrument. Examples include black carbon and most chemical forms or mineral dust (see SP2-AMS).
  • Semi-refractory (SR) species: chemical components of aerosol that are relatively less volatile, and only slowly vaporize in the AMS. Functionally, they are observed in both the the Closed and Open signals (time-scale for vaporization is much longer than the time scale of open/closed chopper movement). Examples include some chemical forms of Pb (lead) and possibly NaCl. Some details here.
  • SPARROW: Single PARicle Retrieval Of Waves. The Igor analysis tool for AMS light scattering data. Details here.
  • SQUIRREL: SeQUential Igor data RetRiEvaL. The Igor analysis tool for non-Quad AMS data. Details here.
  • Open: Mass spectra acquired when the chopper is in the 'open' position - both air and aerosols are entering and being detected
  • stick: An integrated value. It is called a stick because integrated mass spectra are often displayed as vertical lines from zero, and in Igor this display option is described as 'sticks to zero'. Users will typically encounter 3 different sets of 'sticks'. The 'DAQ sticks' are integrated values found by the DAQ and saved in the hdf DAQ files yymmdd_rrrrrrr_m.hdf. There can be 'MS (regular) sticks', 'PToF sticks', 'open sticks', 'closed sticks', 'diff sticks' (calculated from fitting/integrating open minus closed raw spectra), 'open minus closed sticks' (calculated open sticks minus closed sticks), UMR (unit mass resolution) sticks, HR (high resolution) sticks.
  • PIKA: Peak Integration by Peak Analysis. This is a somewhat contorted acronym, but this name really indicates "High Resolution Analysis" or HR analysis where individual peaks (e.g., C3H6 and C2H2O at ~ m/z 42). Details here
  • UMR: Unit Mass Resolution (as opposed to HR: ie, signal observed at m/z 28 is UMR, whereas HR data typically shows two peaks, one from N2+ and another from CO+)
  • Vacuum Aerodynamic Diameter (dva): the diameter measured by the AMS and other instruments operating in the free-molecular regime. This includes all instruments using Liu-type aerodynamic lenses. Not to be confused with other diameters such as geometric diameter, mobility diameter, optical diameter, etc. Details in DeCarlo et al., AS&T 2004.


  • Types of OA:
    • OA: organic aerosol. Also referred to as OM (organic mass) in older literature. Some authors also refer to this as POM, for particulate organic mass. OA is different from OC (organic carbon) which only refers to the mass of the carbon atoms (OA refers to the entirety of the organic aerosol mass).
    • HOA: Hydrocarbon-like Organic Aerosol
    • BBOA: Biomass Burning Organic Aerosol
    • COA: Cooking Organic Aerosol
    • POA: Primary Organic Aerosol, that emitted into the atmosphere in the particle phase. PMF factors do not directly represent POA directly, but the POA concentration can be estimated with some assumptions (e.g. summing all the primary-type factors).
    • SOA: Secondary Organic Aerosol, that formed within the atmosphere via in situ chemistry.
    • OOA: Oxygenated Organic Aerosol, sometimes used as an approximate surrogate for SOA.
    • OOA-1: the more oxidized fraction of OOA. Frequently referred to as LV-OOA or MO-OOA.
    • OOA-2: the less oxidized fraction of OOA. Frequently referred to as SV-OOA or LO-OOA.
    • LV-OOA: Low volatility OOA. Details here
    • SV-OOA: Semi-Volatile OOA. Details here
    • MO-OOA: More-oxygenated OOA. Used when a correlation between O/C and volatility is not observed.
    • LO-OOA: Less-oxygenated OOA
    • IEPOX-SOA: SOA formed from the isoprene epoxydiol uptake pathway. See e.g. Hu et al. ACP 2015 and references therein for details.
  • Other terms:
    • bootstrapping: a statistical method used with PMF to estimate uncertainty of PMF solutions by solving a many resampled versions of the original dataset (see bootstrapping at Wikipedia)
    • FPEAK: a "knob" in PMF that can be used to explore the some rotations of the solution space. (more on the PMF-AMS wiki)
    • ME-2: Multilinear Engine (ME-2 solver). PMF where source profiles and time series inputs can be constrained.
    • PET: PMF Evaluation Tool. An interface for examining the results of many PMF analyses.
    • PMF: Positive Matrix Factorization. A least-squares, bilinear factorization that is constrained to give only positive values in the factor matrices. (more on the PMF-AMS wiki)
    • Q or Q value: Q is the objective function that PMF minimizes to find its solution. It is the sum of the squared residual at each datapoint, divided by the squared error estimate for that datapoint (i.e. Q = sum over matrix (residual/error)^2)
    • seeds: the seed value used to generate random values used at the start of a PMF run. It's possible that different different solutions may result from different seeds. (more on the PMF-AMS wiki)
    • SoFi: Source Finder tool for running and evalulating ME-2. Details here.