Controversial Terms

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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."



Past definitions and discussion regarding m/z

The 2013 IUPAC recommendations retain the use of m/z as the x-axis of a mass spectrum which has been in place since the early 1970s (see ASMS 1974 and Beynon 1978). Note that m is taken as the mass in u (per Price 1991; McLafferty 1993) rather than mass number (per Todd 1991; Todd 1995).

2013 IUPAC Comment

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.

ASMS 1997 Terms and Definitions Poster

The ASMS 1997 definition is similar to the McLafferty 1993 definition.

Mass-to-charge ratio (m/z)
Daltons/electronic charge.
Note from a reader: on Thomson - the fluid dynamics people have already used that one; it is listed in the CRC Handbook and IUPAC documents. ASMS should be doing things in addition to or clarifying points mentioned (or not) in IUPAC. However, we should be cautious about doing anything that actually opposes or conflicts with IUPAC documents.

Gold Book

The IUPAC Gold Book uses the mass number definition of Todd 1991. The IUPAC Orange Book definition is simply "m/z ratio".

http://goldbook.iupac.org/M03752.html

The abbreviation m/z is used to denote the dimensionless quantity formed by dividing the mass number of an ion by its charge number. It has long been called the mass-to-charge ratio although m is not the ionic mass nor is z a multiple or the elementary (electronic) charge, e. The abbreviation m/e is, therefore, not recommended. Thus, for example, for the ion C7H72+, m/z equals 45.5..

Source: PAC, 1991, 63, 1541 (Recommendations for nomenclature and symbolism for mass spectroscopy (including an appendix of terms used in vacuum technology). (Recommendations 1991)) on page 1544

Todd 1995; Todd 1991

Todd uses the mass number definition of Beynon 1978.

m/z
This abbreviation is used to denote the dimensionless quantity formed by dividing the mass number of an ion by its charge number. It has long been called the mass-to-charge ratio although m is not the ionic mass nor is z a multiple of the elementary (electronic) charge, e. The abbreviation m/e is, therefore, not recommended. Thus, for example, for the ion C7H72+, m/z = 45.5.

. . .

The number of charges carried by an ion should be indicated by the symbol z. The ratio of the mass number of an ion to the number of charges carried (commonly referred to as the mass-to-charge ratio) should be written m1/z, m2/z, etc. m/e should not be used to indicate this ratio, e (italic) being reserved for the charge upon the electron and e (Roman) for the electron itself when it appears in an equation.

McLafferty 1993

McLafferty uses mass rather than mass number and notes the proposed thomson unit (see ASMS 1991).

m/z
The mass of the ion in daltons divided by its charge (usually unity), a Thomson; m/e has also been used.

Price 1991

Price 1991 definition uses mass rather than mass number usage.

m/z
An abbreviation used to denote the dimensionless quantity formed by dividing the mass of an ion by the number of charges carried by the ion. It has long been called the mass-to-charge ratio although m is not the ionic mass nor is z a multiple of the electronic charge, e-. The abbreviation m/e, therefore, is not recommended. Thus, for example, for the ion C7H72+, m/z = 45.5.

ASMS 1981

The 1981 ASMS meeting continues the mass number usage. ASMS Nomenclature Committee Workshops, Minneapolis, 1981 [13]

m/z
This abbreviation is used to denote the dimensionless quantity formed by dividing the mass number of an ion by the number of charges carried by the ion. It has long been called the mass-to-charge ratio although m is not the ionic mass nor is z a multiple of the electronic charge, e-. The abbreviation m/e is, therefore, not recommended. Thus, for example, for the ion C7H72+, m/z = 45.5.

Beynon 1978

Beynon 1978 is the first published recommendation for m/z as opposed to m/e.

An acronym, abbreviation or invented jargon should only be used after a full explanation of its meaning has been given in the text.

. . .

The only exceptions, relating to mass spectroscopy, should be the following few commonly accepted initials that may be used freely and without amplification:

. . .

m/z meaning mass-to-charge ratio

. . .

The number of charges carried by an ion should be indicated by the symbol z. The ratio of the mass number of an ion to the number of charges carried (commonly referred to as the mass-to-charge ratio) should be written m1/z, m2/z, etc. m/e should not be used to indicate this ratio, e being reserved for the charge upon the electron and e- for the electron itself when it appears in an equation.

ASMS 1974

The 1974 ASMS meeting marks the m/e to m/z changeover.

Progress Report from ATSM Committee E-14 Subcommittee 10, presented at the Twenty-Second Annual Conference on Mass Spectrometry and Allied Topics, Philadelphia, Pennsylvania, May 19-24, 1974. pp. 545-561 [14]

. . .

Mass, mass-to-charge ratio, m/e, etc.

The major problem here, which has troubled many workers, lies in the symbol "m/e." As one of our group has stated the matter, in most of chemistry and physics, "m" means the mass in grams and "e" is the charge on the electron (or the electron itself when it is part of an equation). The use of 'M' for molecular mass in atomic mass units and that of "z" for the number of charges on an ion are established and unambiguous in physics and chcmistry(1,2). Thus, "M/z" would appear to be the preferred notation.

A minor problem centers about the term used to denote this same quantity. Not too many years back, the established term was "specific mass"(3), which perhaps merits revival. Such revival would not be in accord with the lUPAC recommended usage of the word "specific," preceding the name of an extensive physical quantity, to mean "divided by mass"(4). On the other hand, it would not be the only exception to this recommendation. For example, "specific ionization" is a well established term denoting the number of ion pairs produced per unit of distance along the track of an ionizing particle(5,6).

Incidentally, the lUPAC-recommended symbol for atomic mass units is "u" rather than "amu"(4).


1.1. Since m/e is such a well-established term, I think it should not be abandoned, especially since the meaning of m and e in this context is clear, After all, m has quite a number of meanings. M/z would apply only to M+ what about the other "m/e" values?


1.II. M/z is acceptable.


1.III. Very good. I agree that specific mass might well be an acceptable method of expressing mass to charge ratio.


1.IV. "z" would appear to be preferable to e as the number of charges on the ion but if M is used for the mass of any ion (as is done in the A.V.S. Standard)(7) it will conflict with the definition of M for the molecular ion. One could, of course, call the molecular ion P (molecular parent ion or primary ionised species) but the use of M is well established. If M is the molecular ion we must use m/z for the mass to charge ratio of ions other than M and ignore the fact that m is usually mass in grams. I do not like referring to an ion of mass m but can see no way out of it other than using M*, M[bar] or some other horrible device for the molecular ion. M is already used for the apparent mass of a metastable ion and M signifies an average). Mass units should be in line with IUPAC using "u", i.e. the loss of 28 u.


1.V. In order to say what we mean and have general scientific understanding, I favor "M/z" for mass-to-charge ratio and "µ" for atomic mass unit.


1.VII. 'M/z' indeed appears to be the preferred notation. It would not lead to great difficulties for those familiar with the symbol m/e. For atomic mass units 'u' is also preferable. To denote M/z, the term "specific mass", although not recommended by the IUPAC, is still better than "mass over charge" or "mass-charge ratio".


1.IX.

I whole-heartedly approve of the notation M/Z for mass-to-charge ratio. However, with respect to the term "specific mass", I cannot show any enthusiasm. I feel that the additional length of the term "mass-to-charge ratio" is worthwhile inasmuch as there is now a distinct difference between it and mass. The most important thing in this regard is for journals and referees to insist on mass-to-charge ratio for mass spectral scales and mass for whenever they mean mass. The term "specific mass" will probably be subjected to the same sloppy writing habits as its predecessor, but will not have any of the advantages in clarity.


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 [15][16]. 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 [17] 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.