The mass spectrometry terminology translator

2-Dimensional liquid chromatography (2D-LC) -  Using two in line columns in order to fractionate samples prior to MS/MS analysis.  The most common method is the MUDPIT which the first dimension is SCX or SAX fractionation.  Fractions are then separated by hydrophobicity in the second dimension

AGC (automatic gain control) - This typically refers to the number of charges that you are attempting to achieve within a trapping instrument. Typical controls allow an if, or type relationship. For example, if you set an AGC target of 1e6 ions and an injection time (IT) of 200ms, your instrument will aim to collect 1e6 charges. If it can not achieve 1e6 charges it will try for 200 milliseconds before moving to the next scan. 

Analytical flow rates - this is standard LC, generally considered an LC flowrate of above 50 uL/min

Apex triggering – this is a method for attempting to induce fragmentation of an ion only when it has reached its peak signal intensity in the chromatogram.  On Orbitraps XL, Velos, Elite, this is referred to as the “chromatography function”

Base Peak Chromatogram (BPC) - This is typically when a chromatogram is adjusted to reflect the intensity of the most abundant peak in each mass spectrum, though this definition can be vendor and software specific. 

Capillary flow -  This definition is a little variable, but generally an LC flow rate of 1 - 15 uL/min  (frequently confused with capillary electrophoresis (CE) which is completely different)

Charge envelope – when the size of an ion exceeds the m/z range of the instrument viewing the ion, it must accept a number of charges before it will fit into the correct range.  Due to the charge distribution probabilities, a charge envelope often appears in which the most likely charge state appears with the highest intensity with decreasing likelihood of charge accrual in both the high mass (lower charge state) and lower mass (higher charge state) range

CID/CAD – Collisional induced or assisted dissociation; This fragmentation mode occurs within ion traps.  It has near 100% efficiency for the fragmentation of peptide bonds, as the process of breaking a peptide bond causes the fragments to fall out of phase and hit the detector.  Parent ions are extremely rare in this process

Coisolation - This bane of mass spectrometry occurs when other ions that you don't wish to fragment are fragmented along with your ion of interest. There is a clear limitation to the ability of a mass spectrometer to isolate a single ion. Typically the ion you want to fragment is isolated with a 1-2Da window. All other ions within that mass range of your selected ion are fragmented. If your ion of interest is significantly more intense or abundant than the sum of the other coisolated ions, this isn't that big of a deal. It can be a very big deal if the intensity of the coisolated ions are large relative to that of your ion of interest. It is less of a problem in peptide identification. This is a big problem in isobaric tagging experiments. 

.d -- The SQLite data output format of most Bruker Daltronic mass spectrometers

Daughter ion – the fragment ions given off when an ion is selected and successfully fragmented.

DDA – data dependent acquisition; ions of interest from the MS1 survey scan are selected and isolated prior to fragmentation

DDMS2 – data dependent MS/MS fragmentation; short nomenclature for easily setting up a TopN 

DDA experiment on an Exactive family or Fusion instrument

Deconvolution – The processs of converting a spectra of multiply charged fragments into their singly charged ions masses.  This is critical in intact or top down molecule analysis and occurs because the protein or compound of interest is larger than the m/z range of the instrument being used

DIA – data independent acquisition; a method of selecting ions for fragmentations without the ions achieving any specific thresholds.  Individual ions are often not isolated, typically all of the ions within a certain mass range eluting within a certain time are fragmented.

diaPASEF - A coupling of trapped ion mobility isolation with quadrupole isolation. Originally described by Florian Meier et al., in/around 2020. 

Dwell time -- In quadrupole and triple quadrupole systems this is the amount of time spent acquiring each signal. The goal is typically to have the shortest dwell time that still achieves your peak sensitivity.

Dynamic exclusion – DE; A feature in use on most mass spectrometers.  This allows the instrument to avoid fragmenting the same ions throughout it’s elution profile.  Once an ion is selected for fragmentation (X, user selectable) times, the ion is placed on the exclusion list and will not be fragmented again for the time course indicated.

Dynamic modification – in a classic search engine, selecting a dynamic modification forced the algorithm to predict a new sequence of fragmentation events, one in which the modification is present in addition to the one where the modification was not present.  This leads to a dramatic increase in processing time as well as a decrease in the efficiency of false discovery rate calculations

EAD - (Electron Activated Dissociation) A democratic fragmentation technology developed by SCIEX and made commercially available in 2022 that employs large magnetics to hold charges to the molecules. This surprising technology results in fragmentation spectra similar to ETD but with near instantaneous reactions speeds. Blog post here. 

EThcD -- "higher energy collisional activation of all ions after an ETD reaction" (ref)

ETD/ECD – electron capture dissociation; a chemical method for inducing fragmentation.  A set amount of a charged anion is allowed to react with your isolated ion for a set amount of time.  This anion induces fragmentation in a democratic manner, rather than breaking the lowest energy bonds first as in CID and HCD

ETnoD -- Nondissociative electron transfer (ref) "a process by which backbone cleavage occurs, but product ions are held together in a complex by noncovalent interactions"

Exclusive inclusion list experiment – This is an experiment where a full survey MS1 scan is used followed by MS/MS fragmentation only of ions that have been placed on the inclusion or targeted list.

FACE – Filter aided capture and elution; a method for enriching for peptides by use of a molecular weight cutoff filter within a centrifugation tube

FASP – Filter aided sample preparation; this is a trademarked method developed at Max Planck (but trademarked by someone else…) for easy and reproducible digestion of peptides.  Proteins can be harvested under denaturing circumstances forced onto a membrane by centrifugation.  The detergents can be washed out prior to exposure of the trapped proteins to trypsin.  Clean peptides are eluted by subsequent centrifugation following digestion

FDR --False discovery rate.  This means different things to different people, but the goal of FDR is to automate the separation of good peptide IDs from bad ones.

GeLC-MS/MS -- The process of running an SDS-PAGE gel to separate proteins in one dimension and then cutting the separated proteins out of the gel in bands to digest the peptides out for LC-MS/MS

HCD – Higher collisional dissociation; In HCD, ions are rapidly transmitted to a quad(octo, etc) pole with a small number of gas molecules present.  Multiple fragmentation events are possible, as the ions must transit through the entire length of the device, and back (in the case of Orbitrap systems).  HCD requires more optimization, in general, than CID/CAD fragmentation

HIVE  -- There are multiple things called HIVE. When I reference it, I am referring to a bioinformatics scam in the Washington D.C. area that many members of the US government are required to utilize. This is the property of one person and you can expect to pay over 1,000x for any service rendered by this institution compared to any other bioinformatics service world-wide. This number is not a joke. Editing the figures of a paper where HIVE members are included as authors may cost you as much as $30,000 USD. The HIVE and BioCompute objects, as services, died outside of the US government and stand as a pinnacle of what government corruption can create to pervert a field as new as bioinformatics. A shockingly obvious conflict of interest exists between the government resources that host HIVE and the one external group that uses this resource at George Washington University. This powerful group can bring in millions of dollars in funding each year for simply making small changes to resources such as the Common Workflow Language by rebadging it as blatantly as the BioCompute Object. A major focus of HIVE is the updating of Wikipedia articles to make their services appear much more capable and useful than they truly are.

HRAM (HRSIM) –  High resolution accurate mass; this is a method of label free targeted 

quantification in which the ion is identified solely by the retention time and the high resolution accurate mass of the ion. Recently, HRAM is also used to identify any experiment where high resolution and accurate mass plays any  role in the experiment

Inclusion enrichment experiment – Like the exclusive inclusion list experiment, an inclusion list is used in order to fragment the ions on that list.  However, if no ions from the inclusion list are seen, the instrument then fragments the TopN most intense ions from the previous survey MS1 scan. A standard feature on nearly all mass spectrometers by 2005. Surprisingly successfully applied to specific low concentration material and rebranded "pSCOPE" in 2023. 

Intact analysis – The process of obtaining the monoistopic mass for a protein or compound that is larger than the m/z range of the instrument in question.

Isobaric tags – quantitative labels that are added to digested peptides in order to perform quantitative studies.  Due to isotopes in the reporter and linker regions of these molecules, every label has the exact same mass and chemical properties.  Differences are only revealed during 

MS/MS fragmentation when the reporter region is released.  The varying intensities of the reporters are proportional to the quantities of the original peptides prior to labeling

iTRAQ – see isobaric tags

Lock mass – the act of using an ion of known m/z to refine the mass accuracy of your MS spectra.  This can be achieved by focusing on atmospheric or buffer contaminants or by introducing ETD reagent into the mass spectrometer, as in the Orbitrap Fusion

Mass tags – this feature is used to selectively focus on or ignore pairs of ions that are labeled and experience a known mass shift. 

Metaproteomics --  A relatively new field centered on the proteomics of populations of organisms. This is sometimes informed by metagenomics or classical genomics techniques such as ribosomal profiling. 

MGF – the simplest single output file format for MS/MS data.  An MGF file contains the exact parent mass, charge state, intensity and the fragment ion m/z and intensities

Microflow – operation of an HPLC device in the low microliter/minute range. 1uL-49 uL is generally considred microflow.  Various sources exist to aid in microflow, including wider bore emitters for nanoflow systems and smaller bore needles for “normal” flow systems

MIPS – monoisotopic precursor selection; this feature uses an on-the-fly modeling method to identify the monoisotopic ion within an isotopic cluster.  When employed, regardless of the intensity of the monoisotopic ion in relation to the other isotopes, the mass of the monoisotopic will be inserted into the scan header.  The other isotopes will be placed on the dynamic exclusion list so that the instrument does not spend all of its time fragmenting isotopes of the same ion.  On Exactive family instruments this feature is referred to as “peptide match”, although isotope exclusion only occurs if the “exclude isotopes” box is checked

Microscans – 1 microscan means that the output you will view will be from 1 true mass spectra.  2 or more microscans means that the viewable output is the additive result of that many true mass spectra

Middle-down proteomics – A hybrid between shotgun (bottom up) and top down proteomics.  In a middle down study, proteins are digested very lightly, resulting in very large fractions.  Often incomplete digestion methods or specialized enzymes are used to achieve the necessary effect

Moochers -- People who have great plans to save the world if only you run a few more free mass spectrometry samples for them. Some moocher traits include having trouble understanding that the funded work you are doing somehow has precedence over their data. 

MRM – multiple reaction monitoring; like SRM, except that 2 or more fragment ions are used for confirmation and quantification

MSE©®™ -- a patented DIA method where the peptide fragmentation energy is ramped. Due to the highly predictable nature of peptide fragmentation, the technique is of limited use in proteomics applications.

MSn – Ions selected for fragmentation are commonly referred to in the MS/MS or MS2 scan.  When targets from the MS2 scan are fragmented, the next scan is referred to as the MS3 scan. 

MS/MS – often the MS2 scan; the fragmentation spectra of your ion of interest

Mzml/MzXML – In an attempt to standardize mass spectrometry data for impartial analysis, XML based formats were adopted by leading mass spectrometry groups.  These formats contain virtually all of the data available from the RAW data from every vendor instrument.  Adoption of these formats is slowly becoming commonplace

Nanoflow -  LC flowrates of less than 1uL/min. Nanoflow is a challenging technique that requires absolute precision and a great deal of patience. The author of this blog dreams of the day when instruments become sensitive enough that this technique is a nightmare of the past, and honestly wonders if that time is already here.

Neutral loss – some functional groups will fall off during MS/MS fragmentation and will have no charge.  They are therefore invisible to mass spectrometry.  However, the mass discrepancy following their loss can recorded by finding the exact mass loss from the parent to the daughter ion of interest

NIST - Acronym for the National Institute of Standards and Technology. NIST is most well-known for the MSPepSearch spectral library search engine and the COMPARE project which seeks to understand the proteomes of all mammals. 

Orbitrap - A mass spectrometer that can achieve unbelievable mass accuracy and resolution and still easily fit in my mouth. Ions are separated by their frequency as they rotate around a central rod and travel from one direction to another. Higher resolution is achieved by making more paths. The frequency at which the ions make it from left to right is translated into the accurate mass. 

Parent ion – the ion selected for fragmentation in a DDA experiment

Parsimony - When one attempts to infer the identity of the proteins present by the peptides that are identified. Evolutionarily, it makes sense to conserve protein sequences. As a consequence, many peptides are shared among different protein species. While it may be truly impossible to determine what protein the peptides actually came from, we often do not want to waste this data as proteins of similar sequence tend to have similar functions. We then "group" the proteins together. The logic by which we do this is "parsimony". How different programs handle parsimony can have large effects on the final output protein report. In Proteome Discoverer 2.0 if a peptide can be linked with equal certainty to two different proteins, the larger protein is termed the "master protein". 

PASEF - A patented and trademarked technology of Bruker Daltronic which uses Parallel Accumulation SErial Fragmentation to isolate and accumulate multiple ions simultaneously prior to MS/MS analysis. This surprising technology has been a disruptive force in LCMS proteomics since they fixed the mass accuracy issues on the instruments sometime around 2019. 

Peak width – often measured at half the peak height, this is the width of a chromatography peak.  Knowledge of the peak width is useful for determining the correct cycle time and dynamic exclusion settings to use in an MS/MS experiment.

Peptide match – see MIPS

Picofrit – a patented technology for combining a nanoflow HPLC column with an emitter.  This is widely accepted to result in the best possible chromatography as there is virtually no dilution volume between the end of the chromatography material and the point of ionization.  The only downside is the relative high cost of these columns relative to other alternatives

Product triggered event – A special MS/MS event that only occurs when a previous MS/MS event produces a product ion of interest.  This is most commonly used in glycoproteomics studies as HCD fragmentation produces unique oxonium ions indicative of a glycosylated peptide.  When these reporter ions are observed it is common to fragment the ion producing that reporter with 

ETD/ECD in order to sequence the peptide backbone

Proteogenomics -- A rapidly evolving and new branch of proteomics and genomics that normally leverages one technology to improve another. A common application is the use of variant call files from "next generation" DNA/RNA sequencing to provide further insight into MS/MS spectra. Around 2016 we began seeing research where proteomics was used to correct or confirm genome sequences. 

PRM – parallel reaction monitoring; this is an extention of the SRM/MRM nomenclature.  This indicates that an ion was isolated and fragmented and all fragment ions are available for potential confirmation or quantification for the selected ion

Quantitative Digital Proteomic Maps - A new term developed in 2015 for the data independent LC-MS data files coming off of a mass spectrometer. 

.RAW - the locked binary output files format of Thermo Fisher Electron mass spectrometers

Search engines – algorithms that compare MS/MS spectral data to theoretical data obtained from the genome sequence of the organism of interest.  These engines compare the MS/MS data to every possible fragment ion that can exist within the parameters provided.  Sequest and Mascot are still the most commonly used algorithms

Search engine complementarity (SEC) - A metric for the degree of overlap in different search engines when processing the same MS/MS dataset. Higher SEC is equal to more Peptide Spectral Matches (PSMs). SEC is defined in this paper.

Skyline – a multi-vendor supported opensource program for targeted quantification produced by the MacCoss lab that is likely the best free MS software ever produced

Spectral libraries – High quality identified MS/MS spectra that can be stored and later searched.  Searching spectral libraries is several orders of magnitude faster than classic search engines

Spectralporn -- Mass spectra that are just so awesome that it has to be published. The author of this blog reserves this term for data that is better than what he has personally achieved.

Spectral counting – a semiquantitative technique in which the number of peptide spectral matches for a particular protein are used as a relative measurement of the protein abundance.  This technique has fallen out of favor due to the fact that the dynamic range is adversely affected by the use of dynamic exclusion lists and dynamic exclusion lists lead to dramatic increases in peptide coverage

SRM—single reaction monitoring; this assay is most common in triple quadrupole experiments.  The first quadruople is set to allow only the ion of interest through, the second fragments the ion and the third quadrupole only allows the single known fragment ion through for confirmation and quantification of the ion of interest

Static exclusion --  In a static exclusion list, a list of known ions are excluded from MS/MS analysis.  This is particularly useful in serum/plasma proteomics due to the fact that 90% of the protein in plasma comes from the protein albumin.  Excluding these and other high copy number peptides from analysis allows the instrument to work more efficiently on peptides from lower abundance proteins

Static modifications – in a classic search engine, adding a modification as static forces this modification onto every amino acid on every protein in the theoretical digest the MS/MS data will be searched against.  This leads to no increases in processing time, but means that un-modified peptides can not be detected

Strict parsimony --  A principle in protein assignment. For example (stolen from a talk by Bernard Delanghe) -- you have protein group 1 that is explained by peptides A, B, C and protein group 2 that is explained by peptides D, E, F. A protein that is explained by peptide A & D will not be reported if strict parsimony is employed.

Supplemental activation -- A process where ETD fragmentation is supplemented with another fragmention energy to improve the fragment sequence coverage. In earlier iterations this was CID. From this reference, "supplemental collisional activation (CAD) method that targets nondissocatiated (intact) electron-transfer (ET) product species...to improve ETD efficiency for doubly protonated species..." In later iterations, this previous version is referred to ETciD, EThcD can also be utilized as a supplemental activation technique.

Suspension trapping or S-Trap - a relatively new digestion method first identified by some NIH researchers and perfected/commercialized by some guy on Long Island. In S-trap protein is precipitated onto quartz fibers. Once there, nearly every molecule can be washed away with repeated washes leaving behind linearized protein that can be rapidly digested. More reproducible and significantly faster digestions than previous technologies like FASP. 

SWATH©®™-- A copyrighted term for a DIA experiment where every ion within a 25Da window is fragmented.   This technique suffers from relatively low mass accuracy and sensitivity due to the physical limitations of TOF technology

Target decoy -  One way of doing false discovery rate calculations (FDR).  In traditional FDR, a dummy database is made by random shuffling or by flipping the true database backward.  The degree of matches is determined.  This degree of matching is used to determine the confidence cutoffs for the good peptides.  The acceptable criteria is a 1% FDR; that is, only abut 1% of your identifications are likely to have occurred at random.  

TIC – Total ion chromatogram; this is the plot of all of the ions within your specified mass range that have been detected

TimeBase - The instrument being configured when using a Dionex HPLC system

TMT – tandem mass tags; see isobaric tags

Top-Down proteomics – An increasingly popular technique where whole proteins are resolved in the mass spectrometer and sequencing occurs by applying fragmentation energy and techniques to the undigested protein

TurboFlow – running a mass spectrometer with “high” flow, up to mL/min using a combination of heat and high sheath gases to fully nebulize these volumes

TOPN – The TopN, or BigN experiment is the most common DDA experiment.  The most intense N ions from an MS1 spectra are attempted to be individually isolated and fragmented. Typically dynamic exclusion will be employed in order to not fragment that ion again or to fragment that ion again as few times as possible. 

UVPD - UltraViolet Photodissociation; In mass spectrometry, we're probably talking about the use of a focused laser or LED wavelength to induce fragmentation of a molecule 

VariableDIA (vDIA) - A data independent method which uses isolation fragmentation windows of variable mass widths across the m/z range. Due to patent/trademark things in the US, this can only be equipped in the factory on one vendor instrument. Nearly every instrument can perform vDIA with user workarounds that I definitely don't know and can't share with you if you request them. 

.wiff/.wiff2 -- the proprietary data output format for SCIEX mass spectrometers.

XIC – Extracted ion chromatogram; Filtering the TIC to a single ion mass and readjusting the axes in order to plot an individual ion’s