Hi, Mohammed -

As several others noted, the mass error is far to large for a high-resolution instrument.  The measured value should agree with the calculated value probably to at least the third decimal place; yours is off by about .3 daltons.  This is not good enough to publish.  (Are you sure the instrument was correctly calibrated?)  Also, to answer the question about purity assessment, unfortunately the answer is in the uploaded mass spectrum.  The signal you're looking for - it it's there at all - is buried in a very-low-abundance cluster.  If this is a MS spectrum (rather than a MS/MS spectrum), then the sample contains many other compounds of much higher abundance, i.e., the sample is not very pure.  In general, if you have to look too hard to find a signal you're looking for (that you hope is there), then the compound either isn't present or it's present at very low abundance (or perhaps doesn't respond well to the spray parameters).  You might try to get a purer sample, e.g., via preparative LC. For a pure sample, the data for the compound should dominate the mass spectrum.  Since you apparently know the structure of the compound you're after, can you get a standard that you can use for comparison?

Hope this helps.  Good luck!

This deviation is huge for most instruments. It is a relative error of about 1000 ppm. In principle with a TOF with internal calibration you could expect less than 5 ppm. What is actually your instrument (TOF, Orbitrap...) ?

The instrument used was a ToF. Could the error be a result of wrong calibration by the technician? Or is it that the compound is not very pure? 

Such a deviation suggests a wrong calibration - particularly if there is no signal at the expected m/z.

As to the purity - it is difficult to judge the purity of a sample basing on MS alone.

Thanks for your answer Maciej, so what is the acceptable deviation range in HRMS results, as I have found another peak which deviates from the calculated value by 0.03 units, is that fine?

This deviation is huge.  However, this is a phenomenon caused by high concentration. This happens in our lab daily.  The correct thing to do for such a sensitive and accurate instrument such as TOF is to make your sample very dilute. At that point, even if the concentration is not optimized, you can choose to use point mass rather than a mass average over a wide range. As you move to the shoulder of your MS peak, you have a better chance of getting a HRMS. It takes a bit of practice to get to the correct concentration range. Once measured properly, your HRMS should be within 5 ppm.

Thank you for your answer Guangtao, but is a deviation of 0.03 units acceptable? If I wanted to send it for publication would they refuse a mass difference of 0.03 units? 

0.03 (45 ppm) is still quite high. For instance JACS requires an error of less than 0.003 m/z unit for a molecule of less than 1000 u. I agree that you are most likely above the saturation limit of your detector. See the following article Rapid Commun. Mass Spectrom. 2008; 22: 1213–1222

Thank you so much Carlos, but I think that a deviation in m/z can be also caused by an overlapping of nearby peaks, this has been seen in the following paper " A rapid MALDI-TOF mass spectrometry workflow for Drosophila melanogaster differential neuropeptidomics ". Also I have  a strong feeling that the expected mass is in the spectrum but the technician did not include it in the list of masses, can you please check the spectrum and let me know your opinion.

The expected mass of the molecule itself is: 640.2956

I agree with Carlos. A deviation of 0.03 is a Still high for HRMS. I personally control the deviation within 0.001 m/z ratio. However, it is a legitimate analytical result for REGULAR MS (just not HRMS). In combination with other characterization such as NMR, it should be sufficient for structure elucidation.  With a proper sample run, you should be able to get the deviation under 0.003. 

Hi, Mohammed -

As several others noted, the mass error is far to large for a high-resolution instrument.  The measured value should agree with the calculated value probably to at least the third decimal place; yours is off by about .3 daltons.  This is not good enough to publish.  (Are you sure the instrument was correctly calibrated?)  Also, to answer the question about purity assessment, unfortunately the answer is in the uploaded mass spectrum.  The signal you're looking for - it it's there at all - is buried in a very-low-abundance cluster.  If this is a MS spectrum (rather than a MS/MS spectrum), then the sample contains many other compounds of much higher abundance, i.e., the sample is not very pure.  In general, if you have to look too hard to find a signal you're looking for (that you hope is there), then the compound either isn't present or it's present at very low abundance (or perhaps doesn't respond well to the spray parameters).  You might try to get a purer sample, e.g., via preparative LC. For a pure sample, the data for the compound should dominate the mass spectrum.  Since you apparently know the structure of the compound you're after, can you get a standard that you can use for comparison?

Hope this helps.  Good luck!

Hi, 

I don't think you will easily find Na cluster in an ESI infusion experiment. Adding this to what John and the other already said, I strongly believe that the spectrum you have does not contain the molecule you are looking for.

What concentration did you infuse? Is it a an infusion or a flow-through?

Purity: purity is normally assessed in two ways.

1) MALDI

2) LC (better if coupled with MS)

An infusion will hardly tell you anything about purity.

Hi Mohammed,

you should consider that a composition made up of C, H, O, and N (C0-100, H3-74, O0-4 and N0-4) at m/z 118 needs only an error not exceeding 34 ppm to be unambiguous; at m/z 750 requires precision better than 0.018 ppm to eliminate "all extraneous possibilities". In your case mass accuracy is 1051 ppm, so it is too high and it represents an ambiguous characterization (it should be lower than 4.5 ppm). You could improve your characterization by mass spectrometry performing a mass calibration, MSn (tandem mass spectrometry) experiments, RDB (double bond/ring equivalents) calculation, and isotopic cluster analysis.

I hope this could help you.