Style guide

From Mass Spectrometry Terms
Jump to: navigation, search

Templates

Direct link to templates

The text below is from templates that include text that is reproduced on multiple pages:

CAD and CID

QUOTED TEXT FROM IUPAC RECOMMENDATIONS 2013
The terms collision-induced dissociation (CID) and collisionally activated dissociation (CAD) are both recommended by IUPAC [1] 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.

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 [2][3]. 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.

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

Landé, 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

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 [4] and the similar definitions in the Orange Book [5]. 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 [6].

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 [7], 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.

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).

Nominal mass

Related definitions

Other definitions

Mallet and Down ISBN 0470027614
"The mass of a molecule or ion calculated using the integral masses of the most abundant isotopes of each element present"
Sparkman ISBN 0966081390
"The integer mass of the most abundant naturally occurring stable isotope of an element ... the nominal mass of an element is equal to the mass number of the most abundant stable isotope of an element"
de Hoffmann ISBN 0470033118
"The nominal mass is calculated using the mass of the predominant isotope of each element rounded to the nearest integer value that corresponds to the mass number ..."
Watson and Sparkman ISBN 0470516348
"The nominal mass of an element is the integer mass of its most abundant stable isotope ... the nominal mass of a molecule, radical, or ion is the sum of the nominal masses of all the atoms of its constituent elements." (common organic elements this is the lowest but not always)
Gross ISBN 3642423469
"the nominal mass of an element is defined as the integer mass of its most abundant naturally occurring stable isotope ... the nominal mass of an ion is the sum of the nominal masses of its constituent elements."

References

Resolution and resolving power controversy

QUOTED TEXT FROM IUPAC RECOMMENDATIONS 2013
The IUPAC definition of resolution in mass spectrometry expresses this value as m/Δm, where m is the mass of the ion of interest and Δm is the peak width (peak width definition) or the spacing between two equal intensity peaks with a valley between them no more than 10 % of their height (10 % valley definition) [8]. Resolving power in mass spectrometry is defined as the ability of an instrument or measurement procedure to distinguish between two peaks at m/z values differing by a small amount and expressed as the peak width in mass units [9]. Mass resolving power is defined separately as m/Δm in a manner similar to that given above for mass resolution [10]. These definitions of mass resolving power and resolving power in mass spectrometry are contradictory, the former is expressed as a dimensionless ratio and the latter as a mass. The definitions for resolution in mass spectrometry and resolving power in mass spectrometry come from Todd’s 1991 recommendations [11], and the definition for mass resolving power comes from Beynon’s 1978 recommendations [12]. Beynon’s work contains no definition for mass resolution.

Alternative definitions for resolution and resolving power in mass spectrometry have been proposed [13][14]. It has been suggested that resolution be given by Δm and resolving power by m/Δm; however, these definitions are not widely used.

The majority of the mass spectrometry community uses resolution as defined by IUPAC. The term resolving power is not widely used as a synonym for resolution. In this document, the IUPAC definition of resolution in mass spectrometry remains in place. The definition of resolving power has been adapted from the current IUPAC definition of mass resolving power.

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


Books defining resolution and/or resolving power

Books using “resolution is m/Δm”

Mass Spectrometry and its Applications to Organic Chemistry
J. H. Beynon, Elsevier, 1960
p. 51 "The terms 'resolution' and 'resolving power' have been used a great deal in the above discussion. It has been assumed that the doublet is 'resolved' when its constituent ion species are 'separated' and that the difficult of separation or 'resolving power' necessary to separate the adjacent mass peaks is given by M/ΔM."
Mass Spectrometry – Organic Chemical Applications
Klaus Biemann, McGraw-Hill, 1962
(p. 13) “the term ‘resolution’ is used in different ways … Throughout this book resolution will be considered as M/ΔM …”
Lasers and Mass Spectrometry
By David M. Lubman, Oxford University Press US, 1990, ISBN 0195059298
Interpretation of Mass Spectra
Fred W. McLafferty, Turecek, University Science Books, 1993, Language: English, ISBN 0935702253
Mass Spectrometry: Clinical and Biomedical Applications
By Dominic M. Desiderio, Springer, 1993, ISBN 0306442612
Practical Organic Mass Spectrometry: A Guide for Chemical and Biochemical Analysis
J. R. Chapman, Wiley_Default, 1995, ISBN 047195831X
Mass Spectrometry for Chemists and Biochemists
Robert Alexander Walker Johnstone, M. E. Rose, Cambridge University Press, 1996, ISBN 0521424976
Introduction to Mass Spectrometry
By J. Throck Watson, Lippincott-Raven, 1997, ISBN 0397516886
Ionization Methods in Organic Mass Spectrometry
By Alison E. Ashcroft, Royal Society of Chemistry (Great Britain), Royal Society of Chemistry, 1997, ISBN 0854045708
Accelerator Mass Spectrometry: Ultrasensitive Analysis for Global Science
Claudio Tuniz, John R. Bird, Gregory F. Herzog, David Fink, CRC Press, 1998, ISBN 0849345383
Mass Spectrometry in Biology & Medicine
By A. L. Burlingame, Steven A. Carr, Michael A. Baldwin, Humana Press, 1999, ISBN 0896037991
Mass Spectrometry and Genomic Analysis
J. Nicholas Housby, Springer, 2001, ISBN 0792371739
Mass Spectrometry Basics
Christopher G. Herbert, Robert Alexander Walker Johnstone, CRC Press, 2002, ISBN 0849313546
Liquid Chromatography Mass Spectrometry: An Introduction Robert E. Ardrey
Wiley, 2003, ISBN 0471498017
Mass Spectrometry: A Textbook
Jürgen H. Gross, Springer, 2004, ISBN 3540407391
Quadrupole Ion Trap Mass Spectrometry
By Raymond E. March, John F. Todd, Wiley-IEEE, 2005, ISBN 0471717975
The Expanding Role of Mass Spectrometry in Biotechnology
Gary Siuzdak, McC Pr, 2006, ISBN 0974245127
Quantitative Applications of Mass Spectrometry
Pietro Traldi, Franco Magno, Irma Lavagnini, Roberta Seraglia, Wiley, 2006, ISBN 0470025166
Assigning Structures to Ions in Mass Spectrometry
John L. Holmes, Christiane Aubry, Paul M. Mayer, CRC, 2006, ISBN 0849319501
Mass Spectrometry: Principles and Applications
Edmond de Hoffmann, Vincent Stroobant, Wiley-Interscience, 2007
ISBN 047003310X
Mass Spectrometry: Principles and Applications
Edmond de Hoffmann, Jean Charette, Vincent Stroobant, Wiley, 1996, ISBN 0471966975
p 287: "Resolution: the ratio of m/δm where m and m+δm are the mass numbers of the two ions that yield neighboring peaks with a valley depth of x% of the weakest peak's intensity."
Quantitative Proteomics by Mass Spectrometry (Methods in Molecular Biology)
Salvatore Sechi, Humana Press, 2007, ISBN 1588295710
Computational Methods for Mass Spectrometry Proteomics
Ingvar Eidhammer, Kristian Flikka, Lennart Martens, Svein-Ole Mikalsen, Wiley-Interscience, 2008, ISBN 0470512970

Books that use “resolution is Δm”

Mass Spectrometry Desk Reference
David Sparkman, Global View, 2006, ISBN 0966081390
"Incorrect: resolution – when defined in the same way as resolving power. Resolution is the inverse of resolving power and expressed as ΔM at M."
Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation
J. Throck Watson, O. David Sparkman, Wiley, 2007, Language: English, ISBN 0470516348
Fundamentals of Contemporary Mass Spectrometry
Chhabil Dass, 2007, ISBN 0471682292
p. 68: "[mass resolution] is the inverse of resolving power (RP), given as RP=m/Δm"
Proteomics in Practice: A Guide to Successful Experimental Design
Reiner Westermeier, Tom Naven, Hans-Rudolf Höpker, Wiley, 2008, ISBN 3527319417

Other IUPAC definitions of resolution

Gold Book

GOLD BOOK DEFINITION

IUPAC. Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”). Compiled by A. D. McNaught and A.Wilkinson. Blackwell Scientific Publications, Oxford (1997).

Style guide

http://goldbook.iupac.org/R05319.html

resolution (in optical spectroscopy)

Wavenumber, wavelength or frequency difference of two still distinguishable lines in a spectrum.

Source: Green Book, 2nd ed., p. 31


IUPAC Gold Book
Index of Gold Book Terms


Gold Book

GOLD BOOK DEFINITION

IUPAC. Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”). Compiled by A. D. McNaught and A.Wilkinson. Blackwell Scientific Publications, Oxford (1997).

Style guide
http://goldbook.iupac.org/P04465.html

peak resolution, Rs (in chromatography)

The separation of two peaks in terms of their average peak width at base (t R2 > t R1):

R s = t R2 ? t R1 w b1 + w b2 2 = 2 ( t R2 ? t R1 ) w b1 + w b2

In the case of two adjacent peaks it may be assumed that w b1 ? w b2, and thus, the width of the second peak may be substituted for the average value:

R s = t R2 ? t R1 w b2

Source: PAC, 1993, 65, 819 (Nomenclature for chromatography (IUPAC Recommendations 1993)) on page 847

Orange Book, p. 108

IUPAC Gold Book
Index of Gold Book Terms


Gold Book

GOLD BOOK DEFINITION

IUPAC. Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”). Compiled by A. D. McNaught and A.Wilkinson. Blackwell Scientific Publications, Oxford (1997).

Style guide

resolution (in gas chromatography)

http://goldbook.iupac.org/R05317.html

A characteristic of the separation of two adjacent peaks. It may be expressed according to the equation:

RAB = 2(|dR(B)-dR(A)|)/(|wB+ wA|)

where RAB is the resolution, dR (A) and dR (B) are the retention distances (time or volume) of each eluted component A and B, and wA and wB are the respective widths of each peak at its base.

PAC, 1990, 62, 2167 (Glossary of atmospheric chemistry terms (Recommendations 1990)) on page 2211

IUPAC Gold Book
Index of Gold Book Terms


Gold Book

GOLD BOOK DEFINITION

IUPAC. Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”). Compiled by A. D. McNaught and A.Wilkinson. Blackwell Scientific Publications, Oxford (1997).

Style guide
http://goldbook.iupac.org/E02113.html

energy resolution (in radiochemistry)

A measurement, at given energy, of the smallest difference between the energies of two particles or photons capable of being distinguished by a radiation spectrometer.

Source: PAC, 1994, 66, 2513 (Nomenclature for radioanalytical chemistry (IUPAC Recommendations 1994)) on page 2519

IUPAC Gold Book
Index of Gold Book Terms

IUPAC reaction monitoring terms

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).

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 [15], and the use of a slash separator was in the 1970s [16]. The term “hyphenated techniques” was coined in 1980 [17]. Currently, hyphens and slashes are used interchangeably [18]. 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 [19]. IUPAC recommends that hyphens be used to describe variants of separation techniques, for example, gas-liquid chromatography and pyrolysis-gas chromatography [20]. 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[21] 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.[22]

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."

Old pages

Categories