Controversial Terms

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The information on this page was assembled between 2004 and 2006 during the discussion portion of the mass spectrometry terms project

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Collision Induced Dissociation vs. Collisionally Activated Dissociation

Should CAD be replaced in all cases by CID?

Collision-Induced Dissociation
Collisionally Activated Dissociation

In the literature

A search for occurrences (in 2005) of the two terms in the literature reveals a distinct preference.

Collision-induced dissociation (CID) and collisionally activated dissociation (CAD) refer to the process in which a collision between and ion and a neutral species results in the conversion of part of the translational energy into internal energy of the ion and subsequent fragmentation. The IUPAC document defines the two terms equivalently as does Price (JASMS, 2, 336, 1991). The ASMS Terms and Definitions document does not mention CAD. Sparkman defines CAD and CID equivalently, but notes his preference for CAD.

CID CAD.gif

A search of the literature for "collision induced dissociation" and "collisionally activated dissociation" suggests that the former term is preferred. In Figure 1, the number of occurrences of the above strings in journal articles is plotted as a function of the year of publication. The plot shows a clear preference for CID over CAD that increases after 1990. This trend can be seen clearly in Figure 2. The occurrence ratio is about 5 in the 80s and early 90s, then jumps to about 30 in the late 90s.

CID CAD ratio.gif

Based on this data, should the IUPAC document list collision induced dissociation/CID as the preferred term?

Google fight

Which is the more widely used term per Google: collision induced dissociation vs collisionally activated dissociation (CID usually wins).

Mass Resolution vs. Mass Resolving Power

How should Resolution and Resolving Power be defined?

Mass Resolution
Resolving Power (Mass)


Mass-to-Charge Ratio

Should the Thomson be used instead of m/z?

Should be m/z be replaced by m/q?

Atomic Mass Unit
Mass/charge Ratio
dalton
thomson


Parent/Daughter vs. Precursor/Product

Should Parent Ion/Daughter Ion be replaced with Precursor Ion/Product Ion? How about nth generation products?

Parent Ion
Daughter Ion
Precursor Ion
Product Ion

Statistics on Parent-Daughter vs. Precursor-Product

Here are some statistics (from 2005) on the Parent vs. Precursor and Daughter vs. Product debate.

A little more than a dozen years ago, it was suggested that the terms Parent Ion and Daughter Ion be replaced with Precursor Ion and Product Ion, respectively (see Glish, J. Am Soc. Mass Spectrom, 2, 349, 1991). The rationale is to avoid gender-specific terms to describe inanimate objects.

A check of the literature suggests that a shift in usage has in fact occurred. In the figure below, the occurrence of Daughter Ion is plotted as a function of year. The number of occurrences has dropped by about one-half since the early 90s. Quantifying the occurrences of Product Ion is difficult since the phrase yields results that are not related to mass spectrometry.

Daughter.gif

The plot below show the occurrences of precursor ion and parent ion. From this plot, it appears that the former term is now being used more frequently in place of the latter.

Parent precursor.gif

A plot of the ratio of occurrences seems to drive home this point.

Par prec ratio.gif

A remaining issue is the nomenclature for nth generation product ions. Glish suggests x generation product ions where x=n-1 for a MSn experiment.

Slashes and Hyphens

How should Slashes and Hyphens be used in combined techniques?

Slashes or hyphens for combined methods

There is a great deal of confusion on the use of slashes, hyphens, spaces, or no spaces to indicate the combination of techniques, particularly when acronyms and abbreviations are used. The Chicago Manual of Style tends to favor hyphens due to the ambiguity of the slash, which has connotations of "and/or" in many instances. The ACS Style Guide makes no specific recommendations but gives examples of slashes, hyphens, spaces and no spaces in examples. The American Institute of Physics Style Manual makes no specific recommendation but contains no examples of the slash usage. David Sparkman calls for separate connotations of the slash and hyphen with the former separating techniques and the latter instruments. Rapid Communications in Mass Spectrometry has called for a slash to separate combined methods and a hyphen to highlight a particular component such as the ionization method (Sparkman instead suggests a space to separate the ionization method). The Definitions of Terms Relating to Mass Spectrometry (IUPAC Recommendations 2013) suggests the use of the hyphen but indicates that the slash can also be used.

QUOTED TEXT FROM IUPAC RECOMMENDATIONS 2013
The hyphen, or alternatively the slash (forward stroke), can be used to indicate combined methods such as gas chromatography separation combined with mass spectrometry detection. Thus, the above combination can be written as gas chromatography-mass spectrometry or alternatively as gas chromatography/mass spectrometry. The corresponding abbreviations are GC-MS or GC/MS. The first use of a hyphen to indicate the combination of a separation method with mass spectrometry was in the early 1960s [1], and the use of a slash separator was in the 1970s [2]. The term hyphenated techniques was coined in 1980 [3]. Currently, hyphens and slashes are used interchangeably [4]. The journal Rapid Communications in Mass Spectrometry has in the past recommended that the combination of two analytical techniques be designated by a slash (Conventions adopted by RCM in Advice to Authors. Rapid Commun. Mass Spectrom. 17, Issue 1 (2003)). A recent Journal of Chromatography glossary also favors this usage [5]. IUPAC recommends that hyphens be used to describe variants of separation techniques, for example, gas-liquid chromatography and pyrolysis-gas chromatography [6]. The authors of this document are evenly split in their preference for hyphen or slash. For consistency with the prior recommendations, we use the hyphen for combined techniques but note that the slash can be used interchangeably.
From Definitions of Terms Relating to Mass Spectrometry (IUPAC Recommendations 2013); DOI: 10.1351/PAC-REC-06-04-06 © IUPAC 2013.

Other recommendations are given below.

Chicago Manual of Style

See http://www.chicagomanualofstyle.org/

The 16th edition of the Chicago Manual of Style indicates that slashes are most commonly used to indicate alternatives in the "and/or" formulation, for example "Hercules/Heracles."(CMOS 6.104) The CMOS also indicates that the slash is occasionally use to indicate "and" as in "Jekyll/Hyde." The "per" and "divided" by meanings are also noted.

The CMOS big table of hyphenation rules states that two nouns indicating two functions (the first noun doesn't modify the second) are hyphenated in both the noun and adjective forms.(CMOS 7.85)

American Chemical Society Style Guide

Chapter 10 of the ACS Style Guide[7] discusses editorial style including the use of hyphens and abbreviations.

Specific rules for combined methods are not given, but there are several examples in a list of abbreviations use space, no space, hyphen, en-dash, or slash. Surprisingly, neither GC-MS nor LC-MS are given in the list. Hyphen proponents will point to CE-MS, but slash advocates will point to CP/MAS.

Specific examples are: capillary electrophoresis mass spectrometry is abbreviated CE-MS, but cross-polarization/magic-angle spinning is abbreviated CP/MAS, but also CP-MAS, CP-MAS, CPMAS, and CP MAS are also indicated. Other examples are fast atom bombardment mass spectrometry (FABMS), Fourier transform ion cyclotron resonance (FTICR), Fourier transform infrared (FTIR, FT/IR, FT-IR, and FT IR), glow discharge mass spectrometry (GDMS), high-resolution mass spectrometry (HRMS), isotope dilution mass spectrometry (IDMS), isotopic ratio mass spectrometry (IRMS), laser desorption mass spectrometry (LDMS), matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS and MALDI-TOF MS), plasma desorption mass spectrometry (PDMS), pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS), time-of-flight mass spectrometry (TOFMS TOF MS), triple-quadrupole mass spectrometry (TQMS).

American Institute of Physics Style Manual

The AIP style manual uses the hyphen exclusively for combined terms.[8]

Mass Spectrometry Desk Reference

David Sparkman in his Mass Spectrometry Desk Reference recommends the use of the slash to indicate the combination of techniques and the hyphen to indicate the combination of instruments. Thus

Gas chromatography/mass spectrometry (GC/MS)
Gas chromatograph-mass spectrometer (GC-MS)

similarly

time-of-flight mass spectrometry (TOFMS)
time-of-flight mass spectrometer (TOF-MS)

Ionization methods are set apart by a space, for example

electron ionization time-of-flight mass spectrometry (EI TOFMS)

Rapid Communications in Mass Spectrometry

The journal Rapid Communications in Mass Spectrometry has in the past given instructions to authors on combined techniques. For example, from the July 12, 2009 RCM:

The Rapid Communications in Mass Spectrometry author guidelines state

"A single analytical technique, or a type of instrument, is abbreviated without hyphens. Thus, TOFMS, FTICRMS."
"A hyphen is used when highlighting a particular component or feature of an instrument or technique. Thus, MALDI-TOFMS, ESI-MS/MS. When 2 or more different analytical techniques are coupled in tandem, this is represented by a solidus placed between the abbreviations for the techniques. Thus we write Py/GC/EI-MS, CZE/TOFMS."


m/z issues

QUOTED TEXT FROM IUPAC RECOMMENDATIONS 2013
The labeling of the x-axis of a mass spectrum engendered the most discussion during the creation of this document; however, in spite of a general desire for a better way to label the x-axis of mass spectra, there was no broad consensus for any of the proposed changes. Therefore, this document continues the use of the definitions of the Gold Book [9] and the similar definitions in the Orange Book [10]. The Gold Book recommendation is for the use of m/z as an abbreviation for mass-to-charge ratio, a dimension- less quantity obtained by dividing the mass number of an ion by its charge number [11].

The thomson unit, defined as the quotient of mass in units of u and the number of charges (z), was proposed nearly two decades ago [12], but has not been widely adopted and is therefore not recommended. Labeling the x-axis of a mass spectrum with any unit of mass such as dalton (Da), atomic mass unit (amu), or unified atomic mass unit (u) is strongly discouraged due to the confusion that would result when reporting spectra of multiply charged ions. The quantity plotted on the x-axis of a mass spectrum is a function of both the mass and charge of the ion. Furthermore, the use of amu in place of u is strongly discouraged in all cases; it has been used to denote atomic masses measured relative to the mass of a single atom of 16O, or to the isotope-averaged mass of an oxygen atom, or to the mass of a single atom of 12C

From Definitions of Terms Relating to Mass Spectrometry (IUPAC Recommendations 2013); DOI: 10.1351/PAC-REC-06-04-06 © IUPAC 2013.


The 39th ASMS Conference on Mass Spectrometry and Allied Topics [ 1991 / pp 1770-1771 ]

Nomenclature for Mass-to-Charge Ratio

A Workshop Sponsored by the Measurements and Standards Committee

The Measurements and Standards Committee sponsored a workshop on nomenclature for mass-to-charge ratio. After a welcome by Michael Bowers, Alan Rockwood gave a short presentation. This was followed by an open discussion. At the end of the workshop, participants returned an informal survey which has been forwarded to the Measurements and Standards Committee for further consideration.

It was proposed that mass spectrometrists adopt a unit for mass-to-charge ratio to be called a thomson (in honor of J. J. Thomson) or some other suitable name. The 12C+ ion would have a mass-to-charge ratio of 11.9994514198 thomsons and the 12C- ion would have a mass-to-charge ratio of 12.0005485802 thomsons. Thus, the thomson would have a value of 1.0364272 x 108 kilograms/coulomb with the polarity of the ion included in the scale. A proposed abbreviation for the thomson was also discussed, and it was pointed out that the originally suggested abbreviation, Th, conflicts with the abbreviation of thorium so something like Tn might be a better choice.

Supporters of the nomenclature proposal generally felt that present nomenclature has encouraged (or at least failed to discourage) imprecise usage, particularly the use of terms related to mass when mass-to-charge ratio is meant. In part this may be attributed to the lack of a convenient name for a unit of mass-to-charge ratio. Imprecise usage may lead to faulty communication or worse, particularly when one is dealing with multiply charged ions. In the past this imprecision has not been a great problem because multiply charged ions were relatively uncommon, but with the advent of techniques capable of producing tens or even hundreds of charges on an individual ion the distinction between mass and mass-to-charge ratio must be more strictly maintained. For example, according to one anecdote given at the workshop, the confusion between charge and charge-to-mass had led to false conclusions about the upper molecular weight limit of a particular analyzer when used with electrospray ion sources. It was argued that defining and naming the thomson as an explicit unit of mass-to-charge ratio would help enforce a strict distinction between mass and mass to charge ratio and lead to clearer and more concise communication. A second reason for supporting the proposal is that given the central role of mass-to-charge ratio in the field of mass spectrometry as the quantity actually measured in mass spectrometers, it makes sense that the unit for this quantity be given a convenient name.

Opponents of the proposal countered that m/z is already a very clear, well defined and convenient terminology. It was also pointed out that the "thomson" is not self defining, that like the hertz, the units are not explicitly conveyed by the name. This could confuse some readers, particularly the uninitiated. (Whether m/z is a self defining unit was not discussed, but at least it has become understandable through wide and long usage). It was also pointed out that imprecision is not inherent in present nomenclature and that by a combination of present nomenclature and careful language one can write and speak without ambiguity, although at times some extra wordiness might be required.

Both sides presented good reasons for their respective positions, and this seems to have been reflected in the vote. Forty-seven response forms were returned with 57% in favor of the proposal, 34% opposed, and 9% uncommitted. (Not counted in the balloting were letters of support from two editors, and the moderator (ALR) clearly advocated the proposal but didn't vote.) Regardless of the positions on the proposal itself, there was widespread agreement that imprecise communication is sometimes a problem and that mass spectrometrists should be encouraged to avoid incorrect or ambiguous usage.

A surprising part of the workshop was a widespread disagreement on the correct dimensionality of m/z. Three opinions were expressed. The view of the workshop leader going into the workshop was that m/z represents mass-to-charge ratio so the proper dimensionality would be mass divided by charge. This would be the correct dimensionality to use In the equations of motion for a charged particle in a mass spectrometer and it would be analogous to the usage in tables of fundamental constants in which (for example) the charge-to-mass ratio of the proton (e/mp) is given as 9.5788309 x 107 coulombs per kilogram. This is also closely related to the terminology of "grams per equivalent" and "equivalent weight" from electrochemistry. A second more popular view was that m is a mass but z Is a pure number (being charge number, not charge), so m/z would have dimensionality of mass. A third view held that both m and z are dimensioniess so m/z is a dimensionless number. The official definition of m/zis that it is a dimensioniess number that is proportional to the charge-to-mass ratio. In this respect it somewhat resembles other dimensionless numbers such as reduced parameters from thermodynamics (e.g., reduced temperatures) and dimensioniess groups from engineering (e.g., Reynolds numbers). Calling m/z the mass-to-charge ratio is a bit of convenient linguistic shorthand that Is not strictly correct. (A subtle difference between the thomson and m/z then would be that the thomson has the dimensionality of mass/charge while m/z is dimensionless, although in magnitude the two are identical.) This widespread disagreement on the correct meaning of such a widely used symbol as m/z indicates a possible need (or opportunity) for an effort in education or self education. The nomenclature summary that will soon appear in J. Amer. Soc. Mass Spec, is a significant effort in this direction, and it should be read by all mass spectrometrists.

In one of the lighter moments of the workshop, it was pointed out that a natural form to plot electrospray mass spectra would be intensity versus charge-to-mass ratio (rather than the mass-to.charge ratio) resulting in almost evenly spaced peaks. The unit of charge-to-mass ratio could be called a nosmoht which is thomson spelled backwards. (This is analogous to the unit of inverse resistance, the mho, which is ohm spelled backwards.) However, support for the nosmoht appeared to be minimal.

Submitted by:

Alan L. Rockwood Battelle, Pacific Northwest Laboratory

Reference: R. G. Cooks and A. L. Rockwood, Rapid Commun. Mass Spectrom., 5, 93 (1991).http://dx.doi.org/10.1002/rcm.1290050210


Multiple reaction monitoring is not deprecated

Please note that the term multiple reaction monitoring is not deprecated in the IUPAC "Standard definitions of terms relating to mass spectrometry" Pure Appl. Chem., 2013, 85, 1515. There is no small amount of confusion regarding this fact due in part to the seven years that elapsed between the posting of the unreviewed 2006 draft of the document (still linked as "provisional recommendations" on the IUPAC website) and the publication of the peer reviewed document in 2013. Comments from reviewers during the peer review process led to a revision of the definition to what is now indicated on the multiple reaction monitoring page of this wiki. In several publications between 2006 and 2012, the draft definition was cited (e.g. http://dx.doi.org/10.1038/msb.2008.61, http://dx.doi.org/10.1002/pmic.200800577, http://dx.doi.org/10.1039/c0mb00159g, http://dx.doi.org/10.1002/pmic.201200042), inadvertently leading to further confusion. Again, please note that the IUPAC recommendation for multiple reaction monitoring is the one indicated in http://dx.doi.org/10.1351/PAC-REC-06-04-06.

Summary of reaction monitoring definitions

Term Acronym Definition Diagram Reference
Selected ion monitoring SIM Operation of a mass spectrometer in which the abundances of ions of one or more specific m/z values are recorded rather than the entire mass spectrum.      . Gold Book
Selected reaction monitoring SRM Data acquired from one or more specific product ions corresponding to m/z selected precursor ions recorded via two or more stages of mass spectrometry.
Note 1: Selected reaction monitoring in multiple-stage mass spectrometry is known as consecutive reaction monitoring.
Note 2: Selected reaction monitoring applied to multiple product ions from one or more precursor ions is known as multiple reaction monitoring.
SRM.jpg
de Hoffmann. J. Mass Spectrom. 31, 129 (1996).
Consecutive reaction monitoring CRM Multiple-stage mass spectrometry experiment with three or more stages of m/z separation in which products of sequential fragmentation or bimolecular reactions are selected for detection.
CRM.jpg
Tomer, Guenat, Deterding. Anal. Chem. 60, 2232 (1988).
Multiple reaction monitoring MRM Application of selected reaction monitoring to multiple product ions from one or more precursor ions.
Note: This term should not be confused with consecutive reaction monitoring, which involves the serial application of three or more stages of selected reaction monitoring.
MRM-Single.jpg
Roepstorff, Fohlman. Biomed. Mass Spectrom. 11, 601 (1984).

Mass defect

Mass defect in mass spectrometry and nuclear physics

Mass defect (mass spectrometry)
The difference between the exact mass and the nearest integer mass
Mass defect (physics)
The difference between the mass of a composite particle and the sum of the masses of its parts

Links

Land, A. Neutrons in the Nucleus. I. Phys. Rev. 43, 620-623 (1933).
http://dx.doi.org/10.1103/PhysRev.43.620
Carlson (1960); High Resolution Mass Spectrometry. Interpretation of Spectra of Petroleum Fractions
http://dx.doi.org/10.1021/ac60167a032
Kendrick (1963); A Mass Scale Based on CH2= 14.0000 for High Resolution Mass Spectrometry of Organic Compounds.
http://dx.doi.org/10.1021/ac60206a048
Hughey (2001); Kendrick Mass Defect Spectrum:? A Compact Visual Analysis for Ultrahigh-Resolution Broadband Mass Spectra
http://dx.doi.org/10.1021/ac010560w
Zhang (2003); A software filter to remove interference ions from drug metabolites in accurate mass liquid chromatography/mass spectrometric analyses
http://dx.doi.org/10.1002/jms.521
Hall, M.P., Ashrafi, S., Obegi, I., Petesch, R., Peterson, J.N., Schneider, L.V. Mass defect tags for biomolecular mass spectrometry. J. Mass Spectrom. 38, 809-816 (2003).
http://dx.doi.org/10.1002/jms.493
Zhang (2009); Mass defect filter technique and its applications to drug metabolite identification by high-resolution mass spectrometry
http://dx.doi.org/10.1002/jms.1610
Sleno (2012); The use of mass defect in modern mass spectrometry
http://dx.doi.org/10.1002/jms.2953
Pourshahian (2017); Mass Defect from Nuclear Physics to Mass Spectral Analysis
http://dx.doi.org/10.1007/s13361-017-1741-9

Daughter ion and related terms

QUOTED TEXT FROM IUPAC RECOMMENDATIONS 2013
The anthropomorphic terms for ions involved in fragmentation reactions, for example, daughter ion, have fallen into disuse after strong sentiments against the use of the term were voiced two decades ago [13][14]. The term product ion is recommended in place of daughter ion and precursor ion in place of parent ion. The use of nth-generation product ion is recommended in place of granddaughter ion and similar terms.
From Definitions of Terms Relating to Mass Spectrometry (IUPAC Recommendations 2013); DOI: 10.1351/PAC-REC-06-04-06 © IUPAC 2013.


QUOTED TEXT FROM IUPAC RECOMMENDATIONS 2013
The terms collision-induced dissociation (CID) and collisionally activated dissociation (CAD) are both recommended by IUPAC [15] and are used interchangeably in recent literature. They are listed as synonyms in this document.
From Definitions of Terms Relating to Mass Spectrometry (IUPAC Recommendations 2013); DOI: 10.1351/PAC-REC-06-04-06 © IUPAC 2013.