Talk:Mass spectrum

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[edit] Disputed

According to the latest documents of IUPAC m/z is a dimensionless property and therefore not a mass-to-charge ratio as claimed in this article. Therefore, m/z hast to be replaced by the correct symbol m/Q. This is the symbol required by the IUPAC green book for the physical quantity mass-to-charge ratio.

Source: The IUPAC document clearly states [1]:

m/z – The three-character symbol m/z is used to denote the dimensionless quantity formed by dividing the mass of an ion by the unified atomic mass unit and also by its charge number (regardless of sign).
--Kehrli 15:31, 22 July 2006 (UTC)


See Talk:Mass-to-charge_ratio#Recommend_Merging_this_Entry_with_.22Mass_Spectrum.22 for argument in favor of merging mass-to-charge ratio with mass spectrum and against merging mass spectrum with mass spectrometry.

--Kmurray 02:56, 24 April 2006 (UTC)

I agree. This article should remain. It covers details that should not be in the main MS article and mass-to-charge ratio covers details that are redundant to this article. I'm fine with a physics mass-to-charge ratio that disambiguates to here for MS. It doesn't seem necessary and there reamins some MS specific details on the physics page but that is not our problem.

--Nick Y. 19:18, 24 April 2006 (UTC)

Kermit, Both suggested mergers are flawed. Mass-to-charge ratio is a very different concept than mass spectrum. Mass spectrum is used by mass spectrometrists only, whereas mass-to-charge ratio is used by tons of other people, too. Additionally, as long as the mass spec community sticks to the m/z misconception (which is not even compatible to the ISO norms), there is really no way the two things can be merged. Additionally, I have not seen any arguments in favor for merging in the reference you gave. Could you list them again, please? Mass spectrometry and Mass spectrum should also not be merged, but they should be better divided. Maybe they should be separated into mass spectrometer (instrumental aspects) and mass spectrum (chemical aspects), since mass spectrometry is too long already.

--Kehrli 05:01, 25 April 2006 (UTC)

Kermit, I have posted a suggestion for your IUPAC gold book entry here: Talk:Mass-to-charge_ratio#M.2FZ_suggestion_for_IUPAC. Please let me know what you think.

-- Kehrli 05:01, 25 April 2006 (UTC)

[edit] Detailed Merge Argument

Argument in favor of merging mass-to-charge ratio with mass spectrum:

1. In the mass-to-charge ratio article, the claim is made that mass-to-charge ratio is widely used, yet beyond the first sentence only mass spectrometry is discussed.

2. The history section covers only mass spectrometry, is incomplete and duplicates part of Mass_spectrometer#History (which is itself incomplete) and part of Mass_Spectrum#X-axis:_Mass-to-charge_ratio. The notation m/e was used up to the 1970s when it was replaced by m/z. The need to distinguish between mass and mass-to-charge only became important after the popularization of electrospray ionization and the routine observation of multiply charged ions (as Rockwood and Cooks point out[2]). If it were not for electrospray mass spectrometry, we would still be in a z=1 world and this article would not exist.

3. The definition of the Thomson unit is incorrect. Rockwood and Cooks define it as u/z, not as u/e, where z is the charge number. The units of Da and Th are identical, although the Th can be negative.

4. The ‘origin’ section duplicates part of Mass_spectrometry#Mass_analyzer.

Signal as a function of mass-to-charge ratio is a mass spectrum. The mass-to-charge ratio article is essentially an editorial that advocates a particular and not widely used notation for mass spectra. A balanced discussion of this issue belongs in the mass spectrum entry.

-- Kermit Murray -- Kmurray 17:14, 26 April 2006 (UTC)

Response de-threaded from argument and reproduced below.

[edit] Response to Detailed Merge Argument

Response to argument in favor of merging mass-to-charge ratio with mass spectrum:

Point 1. Response:

So what? It is evident that it is widely used, but it is just that no one of the other fields has written on the article yet.
Kehrli 17:31, 4 May 2006 (UTC)

Point 2. Response:

Is not true: the history section covers the detection of the electron which has nothing to do with mass spectrometry. The Lorentz formula and Newton formula are presented which are the basis of the optics of charged particles - not of mass spectrometry. Of course mass spec uses the optics of charged particles - but it is only one of many fields that does. If some mass spec people think they can book mass-to-charge ratio exclusively for themselves then this is pure arrogance. Those people should rather work on mass spec to comply with the international ISO standards.
Already Thomson and Aston in their very early papers noticed doubly and triply charged ions. It is completely wrong that multiple charged ions were only created with ESI. Nor did Cooks or Rockwood claim this. Already Thomson has left the z=1 world. It is time for all mass spectrometrists to do it too.
Besides: mass-to-charge ratio is also used for electrons. What is your z good for in this case? Thomson made his first measurements with electrons, and he calculated the mass-to-charge ratio of the electron long before he measured the first ions. In other words: mass spectrometers are not used exlcusively for ions, and z only works for ions.
Distinguishing between mass and mass-to-charge ratio has always been important, not only after the seventies. Mass spectrometers have ALWAYS measured mass/charge, never just mass. That is just a basic fact.
Kehrli 17:31, 4 May 2006 (UTC)

Point 3. Response:

Not true! On your own page [3] you cited: 1 Th = 1 u/atomic charge and not 1 Th = 1 u/atomic charge number. In the later case the thomson would be the same dimension as a dalton and there would be no need to introduce the thomson. Kehrli 17:31, 4 May 2006 (UTC)

Point 4. Response:

So what? Since mass spectrometers are instruments to measure the mass-to-charge ratio this is really no surprise. If you bother, you can delete it from the mass spec page and refer to the mass-to-charge ratio page, which is more fundamental. Kehrli 17:31, 4 May 2006 (UTC)
This is complete nonsense. A mass spectrum is a graph that relates two physical properties: mass-to-charge ratio and intensity. This means a mass spectrum is based on two quantities, one of them the mass-to-charge ratio. On the mass-to-charge ratio page there is of course no mentioning of intensity nor of mass spectra. Hence, there is also no advocacy of using notations for mass spectra. There is only mentioning of correct notation of mass-to-charge ratio according to ISO 31 rules. Some mass spectrometrists that are too stubborn to adapt to the internationally accepted rules may not like ISO 31, but that is their problem and they should not advocate their outdated and misconcepted use that was given up by the rest of the scientific community a long time ago. If you want to annoy the scientific community with your outdated m/z misconception then please do it on your own wikki page, but not here. Here we stick to the ISO 31 rules. Thanks. Kehrli 17:31, 4 May 2006 (UTC)


Signal as a function of mass-to-charge ratio is a mass spectrum. The mass-to-charge ratio article is essentially an editorial that advocates a particular and not widely used notation for mass spectra. A balanced discussion of this issue belongs in the mass spectrum entry.
This is not true at all. The mass-to-charge ratio article does not in any way advocate a particular and not widely used notation for mass spectra. It only explains the official notation for mass-to-charge ratio according to ISO 31. No mass spectra terms are advocated or even remotely discussed. Everything is just about mass-to-charge ratio. If some people in mass spectrometry use non-official terms that contradict the ISO 31 then this is their NPOV. It is that simple. Please stop vandalizing the mass-to-charge ratio page. Please stop enforcing your minority opinion on the larger scientific community, which has decided for ISO and against your m/z misconception. Thanks.
You say it: Signal as a function of mass-to-charge ratio is a mass spectrum. Mass spectra are about SIGNAL, not mass-to-charge ratio, which is only used because it is not possible to measure mass directly.

[edit] Totally Disputed Tag

What is in dispute? Please be specific so that I can provide proper sources. Thanks. Tag will remain for the time being as I will assume good faith. Remember wikipedia is about verifiability. I can backup every part of this article. I will not entertain truth here, only specific citations within the scientific literature. --Nick Y. 16:54, 24 July 2006 (UTC)

See on the very top of this page.

I can verify that m/z is refered to officially as a mass to charge ratio:

from [4]

"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."

This is an official IUPAC document clearly stating that m/z is refered to as a mass to charge ratio. I will wait a day before removing the tag just in case I didn't understand your request for verification. If you can not produce citations rebuting this the dispute is over and tag removed. Rantings and hypotheses will not be acceptable, specific citations are needed.

--Nick Y. 19:50, 26 July 2006 (UTC)

Nick, you are wrong for the following reasons:
  1. your article clearly says: " [m/z]... has long been called the mass-to-charge ratio although ..." which means m/z is no longer regarded as a mass-to-charge ratio.
  1. m/z cannot be a mass-to-charge ratio since it is dimensionless, and mass-to-charge ratio is per definition of dimension mass/charge

More citations

Websites:

  • [5] "For a given amplitude of the dc and rf voltages, only the ions of a given m/z (mass to charge) ratio will resonate, have a stable trajectory to pass the quadrupole and be detected. Other ions will be de-stabilized and hit the rods.
  • [6]"Matrix-Assisted Laser Desorption/Ionisation Time Of Flight (MALDI-TOF), Surface-Enhanced Laser Desorption/Ionization Time Of Flight (SELDI-TOF), and Liquid Chromatography (LC-MS/MS) are the main techniques. They separate gas phase ions according to their m/Z (mass to charge ratio) values producing huge volumes of data. MS output is represented, as a (large) sequence of value pairs, containing a measured intensity, which depends on the quantity of the detected biomolecules and a mass to charge ratio m/Z, which depends on the molecular mass of detected biomolecules. A MS experiment usually generates one or more datasets, said spectra, that contains a huge quantity of measurements (m/Z, intensity) said peaks."
  • [7]"m/z: Mass to charge ratio, synonymous with "m/e"."
  • [8]"The mass spectrometers operate at an optimal m/z (mass to charge ratio) range of 50-2000. Because electrospray ionization typically produces multiply charged ions, it is possible to analyze compounds of up to MW 150,000 Daltons"
  • [9]"M = m/z (mass-to-charge ratio)"

Journals

  • Nature!"This shows the total ion chromatogram with recovery standard (SS) and internal standard (IS) peaks, and partial ion chromatograms for the metabolites 2-naphthoic acid (mass to charge ratio, m/z = 155); 5,6,7,8-tetrahydro-2-naphthoic acid (m/z = 131) and two isomers of decahydro-2-naphthoic acid (m/z = 164)."
  • BMC Bioinformatics"Mass spectrometry (MS) can then be used to separate the co-elutants according to mass-to-charge ratio (m/z). "
  • Protein Science"Abbreviations: CID, low-energy collision-induced fragmentation • Da/kDa, Dalton/(kilo)Dalton = atomic mass units • ESI, electrospray ionization • IMAC, immobilized metal affinity chromatography • 5-IU, 5-iodouracil • LRF, laboratory reference frame • MALDI, matrix-assisted laser desorption/ionization • m/z, mass-to-charge ratio • MS, mass spectrometry • MS/MS, tandem mass spectrometry • NTA, nitrilotriacetic acid • PAGE, polyacrylamide gel electrophoresis • SDS, sodium dodecyl sulfate • SSB, single-stranded DNA-binding protein • TOF, time-of-flight"

Many many more available.--Nick Y. 23:20, 27 July 2006 (UTC)

  • Nick, nobody is disbuting that m/z is widely used among the small group of mass spectrometrists. However, this still does not make m/z compatible with the international conventions established by the larger scientific community in ISO 31 and the IUPAC green book. Mass spectrometrists are not acting in an empty universum. There are established conventions and if (some) mass spectrometrist decide to go against those with their own inconsistent original research then they may do this, but please not so on Wikipedia. Here we publish what is the wider consesus and not the opinion of a small group of people.
  • There is no consensus even among mass spectrometrists on what m/z exactly is. It is used in many inconsistent ways: as physical quantity of mass, as a quantity of mass/charge, as a dimensionless quantity. Many don't use it at all and use m/q, m/e, Da, Th, instead. Your opinion is one of many.
  • nobody doubts that m/z for a long time has been a mass-to-charge ratio. But this has changed in the recent years when its meaning was changed and it was declared a dimensionless quantity. Please read your own source [10].
  • in all your references m/z is used the old way, as a quantity of dimension mass/charge and not as a dimensionless physical quantity which is what you defend. Therefore all these references speak against your arguments. (Thanks for your help, BTW) The frightning thing is that you don't even realize this inconsistency of yours.
  • you still did not respond to the following fact: m/z cannot be a mass-to-charge ratio since it is (now) dimensionless, and mass-to-charge ratio is per definition of dimension mass/charge. This is why m/z has to be changed into m/Q in this article. If you do not respond to this fact, I will go ahead and make the change.
Wikipedia is about verifiability not truth. The fact that everyone in the world does it the wrong way doesn't change anything. Nobody follows your suggestion otherwise you could provide a citation showing the use of "m/q (Th)" I have hundreds of citations showing that people refer to m/z as the mass to charge ratio, weather they are right or wrong does not matter. Your arguments are about truth not verifiability and therefore you are presenting this in teh wrogn place. Go write and article and get it published.--Nick Y. 18:34, 31 July 2006 (UTC)
Nick, you obviously have no idea about Wikipedia. This is not a platfor for spreading commonly made errors. It is about verifiability. If some small group of people make a mistake that is incompatible with the internatinal conventions established by the larger scientific community and is accepted in the ISO 31, then this mistake has nothing to do in Wikipedia. Please stop vandalizing this page with your PV. Read the UIPAC green book in order to learn the correct notation established by the wider scientific community.

[edit] Please remove tag

The one thing that you asked to be verified has been verified. m/z is refered to by ~ everyone who uses it as the mass to charge ratio. They might all be wrong but it is fully and completely verified. If you have another specific piece of information that needs to be verified please specify. Otherwise the tag should be removed.--Nick Y. 17:26, 4 August 2006 (UTC)

m/z used to be a mass-to-charge ratio, it no longer is. Read here: [11]
mass-to-charge ratio (in mass spectrometry), m/z
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.
Unfortunately, some authors have troubles to make this change. This, however, is no reason to have an outdated nomenclature on Wikipedia. You may mention that some people still use the wrong symbol m/z as a symbol for a mass-to-charge ratio, but in general you have to change the article to the modern terminology as given in the IUPAC green book. Until then the tag needs to stay. --Kehrli 19:51, 4 August 2006 (UTC)
I don't mean this in a rude way but perhaps you have a problem understanding english. "is used" is the present tense form of the verb "to use", perhaps you are confusing this with "used to be" which is a past tense form of the verb "to be". Some examples:
What is that remote control used for?
It is used to change the television channels on the TV.
Isn't there a MacDonalds on 52nd street?
There used to be a MacDonalds there but it is now a Burger King.


To demonstrate:
You said: "m/z used to be a mass-to-charge ratio..."
and then quoted "The abbreviation m/z is used to denote the.."
I really don't mean to be rude; however this really does seem to be a point of confusion for you. What any native english speakers interpretation of the text you quote would be ~'it currently is used for this purpose, today' and not 'it used to be the mass to charge ratio'. Again 'It is used' is present tense, 'It used to be' is past tense. Your confusion may have been furthered by all of the caveats to the present tense statement however those cavets are clearly ment to explain the history and qualify it's current usage, which we both know is awkward and inconsistent. However, this statement is a clear endorsement to continue use of m/z while summarily dismissing it's shortcomings and quirks. "It has long been called" is an appeal to historical usage to justify its current usage in this form and does not imply that it no long is. Yes, it is a poorly worded and confusing statement that relies on mastery of the english language. However you can not change a present tense verb into a past tense verb to fit your (our) opinion. Again I am assuming good faith however it seems to me that the head of the IUPAC commitee explained this to you recently.
--Nick Y. 00:02, 5 August 2006 (UTC)

--

Nick, this is a nice try but there are other arguments that show that m/z is no longer considered a mass-to-charge ratio:
1) m/z now has the wrong dimension (this is the most important argument, but it needs some knowledge of metrology to understand, read the IUPAC green book).
2) in the latest draft of the same IUPAC document the term mass-to-charge ratio is deleted. This clearly states that m/z is no longer a mass-to-charge ratio. [12]:
m/z – The three-character symbol m/z is used to denote the dimensionless quantity formed by dividing the mass of an ion by the unified atomic mass unit and also by its charge number (regardless of sign).
3) Kermit Murray, who (unfortunately) is head of the work group in charge of establishing MS terms (which obviously is far beyond his expertice) himself writes [13]:
Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge-ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge.
Ok, Nick, here are three IUPAC sources that prove that you are wrong. Now, please, stop your vandalizm. --Kehrli 09:14, 5 August 2006 (UTC)
Now to your grammar lesson:
  1. I know that m/z is (at this time) used to to denote the dimensionless quantity formed by dividing the mass number of an ion by its charge number. Exactly for this reason I am against using m/z for mass-to-charge ratio, because m/z would then be used for two very different quantities.
  2. "It has long been called" is an appeal to the historical name of m/z in order to differentiate from its current usage for mass number per charge number.
  3. Kermit understands it exactly the same way as I do. (Which, looking at his expertice in metrology, is not necessarily a very strong argument, I must admit.
--Kehrli 10:36, 5 August 2006 (UTC)

Kehrli: Leave Wikipedia and find another place to push your personal opinion! Add a sentence or >>one short<< paragraph to the article about it with a link to the green book and then stop vandalizing mass spectrometry related erticles. Do not think that Nick Y. is the only one watching these pages, we others just got sick of arguing with you. Cacycle 20:12, 5 August 2006 (UTC)

Cacycle, I do not push my personal opinion. I strictly keep to the IUPAC green book. Read it before you critisize my edits. --Kehrli 20:46, 7 August 2006 (UTC)
I agree with both Cacycle and Nick Y. that Kehrli is completely going over the top with pushing the usage of the proper, ISO approved definition for mass-to-charge ratio, not only on this page but on related mass spectrometry pages. Three times on this talk page he has referred to the scientific community who is "inappropriately" using m/z as a "small group of people". I am quite confident that the mass spectrometry community using m/z is by no means small. As mentioned at Talk:Mass Spectrometry, m/z is commonly used in mass spectrometry, except when dealing with physics where m/q is sometimes used. Alchemistmatt 06:50, 26 August 2006 (UTC)
Alchemistmatt, you seem to think that the whole MS community is using m/z. This is not true. Some people use m/z, some m/e, some m/q, some m/Q, some Da, some Da/e, some amu/e, some Th, and there are even more versions. The question is: what should be used on wikipedia? Wikipedia is not Google, this means that it is not the majority opinion that counts. Wikipedia should give a fair consideration to the international standards established in the ISO 31 document. This does not mean that it should ignore m/z. But it is fair to mention that m/z is not compatible with the rules established by the wider scientific community. --Kehrli 15:13, 2 September 2006 (UTC)
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