For LC-MS/MS method development, I performed infusion of my compounds and recorder product ion scan with, obviously, the mass of the molecular ion in the Q1. I usually see a few fragment ions, of which I choose the one with the highest intensity. But now, I see a lot fragment ions (>>20) that do not differ so much in intensity. I choose a few that I sum in the method for quantification. I am trying to propose possible fragment ion structures and I am struggling. So Actually I have two questions 1) what does it mean when there are so many fragment ions? and 2) where can I find more information to learn how to propose possible fragment ions in LC-MS/MS (electrospray ionisation).
I feel your cone voltage and source temperature are very high causing in-source fragmentation. optimise your instrument parameters for the molecule such that lesser fragments are seen.
Fragmentation Pattern of a molecule depends on its character, ie whether it is protein/peptide/lipid/small molecule. For proteins and peptides the fragmentation pattern is in abc or xyz form and for small molecules usually pubchem has a list of common fragments possible. you can check the same.
Sanovar Bhargava . The parameters you suggest to adjust are source parametes. I record a product ion spectrum. That means that, if there are fragments in the source, these fragments are filtered out because you select the molecular ion in the Q1. The fragments that are observed are produced in the collision cell. I think only the collision energy (which is not very high) and the gas settings (standard units) affect fragmentation there.
I am analyzing small molecule drugs
Mr. Asali,
Your questions assume that there is a lack of basic knowledge of mass spectrometry, covering from analytical instrumentation to systematic fragmentation rules depending on the type of analytes.
You could concentrate on the following two references [1,2].
[1] https://www.amazon.de/Mass-Spectrometry-Textbook-J%C3%BCrgen-Gross/dp/3540407391;
[2] https://www.amazon.de/-/en/Gerhard-Spiteller/dp/B0000BTDT6.
Particularly, talking about systematic textbook(s) devoted to fragmentation reactions of chemical compounds, there is a lack of new literature sources, owing to the fact that reference [2] dates from 1966.
So, you could learn the latter issue from research publications or review-articles; if any, for your concrete compound, respectively, class of analytes.
Very frequently, however, the publications lack of such detail, so that you could collaborate with expert in the field explicitely, in order to gain adequate and reliable information about mass spectrometry.
You should bear in mind that the method is exact quantitative and 3D structural approach.
Thus, effort devoted to establish fruitful collaboration with expert in the field of mass spectrometry is justifiable and very import for your work in any field of the chemistry, and not only.
Despite, experts developing mass spectrometry cannot be found so easy. The largest number of them are chiefly in USA.
Owing to your affiliation, I should mention, that in EU, generally, the largest part of experts are already retirees, and, in parallel, the management of Higher Education suffers from serious problems, so that, if you would like to learn in-depth mass spectrometry, then you should concentrate on your self-education or to carry out MSci or PhD degree in USA or both of these.
For RG readers,
The following answer I have received from Mr. Asali as a result of my comment on his questions:
...''Hi, You have answered my question. I would like to say a few things personally to you. First of all, your English is very bad. Second, I wouldn't say I have poor knowledge about my field, which I have been working in for 10 years now. Third, your whole answer to my question is very negative and focused on what is bad in this field. Try to be a bit more positive and try to actually help people ans answer their question instead of being negative. We should all help each other. Lastly, I work in a lab with people having over 30 years of experience and they also were not sure. They all had suggestions and possible explanations but not one knew the answer. That is why I asked it on here. So, if you are telling me I lack basic knowledge with 10 years experience of which 4 years as a PhD, then you are also telling my supervisors and great colleagues with great experience in this field that they lack in basic knowledge. So thank you very much....''
My comments on his reply are following ones:
There is not important how long as period of time you ''stay'' at an Institution (University, Research Institute, Authority, et cetera,) there is most important which achievements you have public available to the Society, because of the scientific contributions serve the interests in the Society, Economy and the Culture, respectively.
Public available means: publications, textbooks, patents, textbooks, monographs, et cetera.
Thus, you can work even 50 years at your Institution (a lot of institutions pay for social contacts and play a role of social service,) this does not mean that you are expert. Let I do not show you who is who in the scientific community, Mr Asali, because of you shall have problems to obtain even visa for visitor within the framework of EU.
...Let the people judge.
Yours sincerely,
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