The exact mass for the abundant isotope of C26H19F4N2O4Se+ is 579.044240 , calculated as a positive ion with the rest mass of an electron (0.000548 u) subtracted. If you calculate the abundant isotope for the neutral mass, the exact value is 579.044788 , which is close to your measured value. On a TOF, the most important thing is to use a reference mass list for calibration that is calculated the same way as the elemental composition calculation software. Just be consistent: if you are calculating elemental compositions as the positive-ion mass, the reference mass list for your calibration standard should use positive-ion masses. If you calculate compositions as neutrals, your reference masses should be neutral masses. This also applied for negative ions, where you add the electron mass.

The error in the measured mass will be exactly the same for positive ions or neutrals as long as you are consistent in your choice of reference masses, but please be aware that reviewers may prefer that you use ionic mass in reporting data. Charge correction to the measured mass is an option in my Mass Mountaineer software.

Note that if you are dealing with multiple charge ions, you will have to consider the number of electrons for a given charge state.

One more comment: if you are using a TOF or a magnetic sector electric field scan, the measured m/z will shift by +/- 0.000548 consistently with the choice of ionic or neutral masses for the calibration standard. This is NOT necessarily true for other mass analyzers. When I was working with FTICR (decades ago), using ionic masses for the reference standard made a significant difference in mass accuracy because the m/z axis wasn't exactly linear. (Trivial note: Fred McLafferty suggested the electron mass correction to me in 1986 or 1987 just before I left Nicolet). The same is true for peak matching on a magnetic sector: using the ionic mass for the reference standard is important for good accuracy.

I assume this is a ToF spectrum, right? Is it just this single peak that's deviating or is it like this for all peaks? If it's for all peaks, you may consider calibrating your spectrometer, e.g. with Agilent TuneMix. Otherwise a ToF is also affected by statistics; of course I can't diagnose your count numbers since I don't know what you get with other substances, but you if it's below a machine-specific threshold, it may be just a non-systematic deviation. After all, 0.001 u isn't exactly a lot.

Hi Jürgen,

thanks for your quick reply.

Your are right its a (ESI) TOF. The measured m/z value is 579.0448 (upper isotopic peak pattern), so the deviation from the calculated value is around 0.0006, which is below 2 ppm (error). Thats fine.

However, what is confusing me is the fact the calculted m/z value (579.0442, bottom table) is slightly differnt to the simulated monoisotopic peak (579.0441, lower isotopic peak pattern).

I always thought the "calculated m/z" corresponds to the monoisotopic mass (of the ion, divided by its charge) ... so it should be exactly the same value... no?

Oh, OK. Is it possible that it's just a rounding issue, so one number is mathematical rounding (1.5->2) and one is commercial rounding (1.5->1)? Maybe there was just one programmer doing one thing, one programmer doing the other, that's actually not the rarest phenomenon.

This was my first guess or maybe the program uses two different databases for the isotopic mass values... However, it does not make much sence from a programers poit of view. But as you say this happens from time to time I am happy with that explanation. Thanks.

"Not making sense from a programmer's point of view" is something you have to get used to with scientific instruments. Often enough those companies need to hire people who didn't study something IT-ish but rather guys like us since there are not enough IT graduates and that sometimes leads to weird software results.

haha... thats probably true. I`ll keep it in mind.

When you look at very exact masses of ions (in fact m/z), the electron mass, about 0.0005 u, is often forgotten, and ion masses are calculated as for molecules, using atomic masses, without correction for + or - charge and removing or adding the electron mass. Evidently this is negligible if you just compare m/z and are consistent in the calculation method. Also, the isotope masses are regularly revised, but the changes are very small, usually at the 10-10 level or less.

Good point about the electron masses. Let's combine that with my "two programmers" hypothesis and we don't even require to use different rounding procedures to come to different results.

You may try to compare the results with available programs or applets like this one

Article ChemCalc: A Building Block for Tomorrow's Chemical Infrastructure

The exact mass for the abundant isotope of C26H19F4N2O4Se+ is 579.044240 , calculated as a positive ion with the rest mass of an electron (0.000548 u) subtracted. If you calculate the abundant isotope for the neutral mass, the exact value is 579.044788 , which is close to your measured value. On a TOF, the most important thing is to use a reference mass list for calibration that is calculated the same way as the elemental composition calculation software. Just be consistent: if you are calculating elemental compositions as the positive-ion mass, the reference mass list for your calibration standard should use positive-ion masses. If you calculate compositions as neutrals, your reference masses should be neutral masses. This also applied for negative ions, where you add the electron mass.

The error in the measured mass will be exactly the same for positive ions or neutrals as long as you are consistent in your choice of reference masses, but please be aware that reviewers may prefer that you use ionic mass in reporting data. Charge correction to the measured mass is an option in my Mass Mountaineer software.

Note that if you are dealing with multiple charge ions, you will have to consider the number of electrons for a given charge state.

One more comment: if you are using a TOF or a magnetic sector electric field scan, the measured m/z will shift by +/- 0.000548 consistently with the choice of ionic or neutral masses for the calibration standard. This is NOT necessarily true for other mass analyzers. When I was working with FTICR (decades ago), using ionic masses for the reference standard made a significant difference in mass accuracy because the m/z axis wasn't exactly linear. (Trivial note: Fred McLafferty suggested the electron mass correction to me in 1986 or 1987 just before I left Nicolet). The same is true for peak matching on a magnetic sector: using the ionic mass for the reference standard is important for good accuracy.

In the Bruker software during the simulation you can add the required resolution, you might use too high. For molecular formula calculation the software may applies resolution value based on measurements. This is a critical factor, because resolution determines how many peaks (isotopologes) will be combined to get simulated values. Try to change the resolution in the isotope pattern software. With the use of 150000 (resolution), it is clearly seen that the m/z 579 peak is the combination of 4 isotopologues. m/z 579.0441 correspond to the monoisotopic one, the 579.0442 is the combination of many overlapping peaks.

To expand on Tibor's comment...

The calculated monoisotopic m/z for the positive ion is 579.0390777, but this is NOT the observed m/z because of the contributions of other isotopes to the measured peak at nominal m/z 579. Limiting the calculation to peaks within 0.001 u, here (below) are isotopic components at nominal m/z 579 that contribute to the observed m/z 579.044239.

Note that there are many more components of the isotope fine structure than this. I chose a tolerance 1 mmu to keep the list short. You will need a resolving power of at least 580,000 to see the isotopic fine structure to within 0.001, but the measured m/z of the abundant peak at nominal m/z 579 will be 579.044088 at a resolving power of 150,000 or higher.

m/z Rel. abundance

579.038926 0.0010

579.044069 100.0000

579.049098 0.3950

579.051574 1.8450

579.054801 0.0660

579.057561 0.0580

579.060270 0.0050