Question: Why Is Mass Accuracy Of Mass Spectrometers Typically Expressed In Ppm?
gravatar for Bio_X2Y
7.8 years ago by
Bio_X2Y3.6k wrote:

At first glance, this might not look like a bioinformatics question. However, I suspect that an understanding of this area might influence my choice/usage of proteomic pipeline software (e.g. mass deviation thresholds are important parameters in peptide identification programs).

My first thought is that since mass (or rather m/z) is the thing being measured, accuracy should be measured in absolute units of m/z, i.e. thompsons (Th).

However, in practice, the relative unit ppm seems to be used instead. I find this confusing, since ppm will mean different things at different m/z values.

e.g. (taken from here)

  • 5 ppm @ m/z 300 = ±0.0015 Th
  • 5 ppm @ m/z 3000 = ±0.015 Th

When describing the latest-and-greatest new machines, the literature seems to stick with ppm, e.g. Parts per million mass accuracy on an Orbitrap mass spectometer via lock mass injection in a C-trap.

According to Gross in Mass spectrometry: a textbook:

As mass spectrometers tend to have similar absolute mass accuracies over a comparatively wide range, absolute mass accuracy represents a more meaningful way of stating mass accuracies than the more trendy use of ppm.

So, can someone perhaps shed light on why ppm seems to be preferred?

Even statistical treatments tend to use ppm where I would expect to see Th, e.g. see Fig. 1 from this paper from the Mann lab, which graphs the distribution of mass deviations in terms of ppm.

Thanks for your time.

UPDATE: I have cross-posted this question to the spctools-discuss google group, which is dedicated to proteomics questions.

mass-spec statistics • 12k views
ADD COMMENTlink modified 7.8 years ago by Craig30 • written 7.8 years ago by Bio_X2Y3.6k
gravatar for Craig
7.5 years ago by
Craig30 wrote:

I think scientists tend to like to work with numbers that range from low single digits to high triple digits. They often adjust the units they work with just to get numbers that fit into this range (I'm thinking mostly of spectroscopists, with crazy quantities like wavenumbers in units of cm[?]-1[?]). Parts per million is a straightforward way of doing this. However, I think Gross is correct in your textbook quote above, and in addition relative mass accuracies are less intuitive than absolute in my opinion. Milli mass units (mmu) would have been a better choice. A more cynical explanation is that "parts per million" sounds flashier in a journal article title...

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by Craig30
gravatar for Arjen Ten Have
7.8 years ago by
Mar del Plata Argentina
Arjen Ten Have340 wrote:

My guess (I do not work in mass spectrometry at all) is that it is because you re working with a gas, and concentrations of gas are expressed in ppm since a certain volume of gas always has the same amount of gaseous particles (=molecules + atoms), hence ppm or ppb etc.

ADD COMMENTlink written 7.8 years ago by Arjen Ten Have340
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