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I want to ask not difference about the principle or applicability to GC and LC, but the peak behavior of spectra. EI is hard ionization method, so there occurs many fragments, sometimes losing molecular ion. In contrast, ESI is soft ionization method, so there are a few fragments. But this can be disadvantage because of lack of molecular information. To complement this, ESI-MS/MS proceeds more fragmentation. Then what is the difference of EI-MS and ESI-MS/MS? Both methods have fragmentation. If my sample is available in both GC and LC, then can I get similar peaks and information in GC-EI-MS and LC-ESI-MS/MS?

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2 Answers 2

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Assuming the present question relates to the characterization of a commercial sample 2,3,5-tribromothiophene here, with results used to monitor the progress of a chemical synthesis of simple small molecules (no forensics, no proteins, no polymers, etc.), then EI-MS might suffice (especially if combined with IR, 1H and 13C-NMR spectroscopy) and ESI-MS/MS be an overkill.

  • GC-MS is a hyphenation. This means, at first you separate compounds by gas chromatography. Then these fractions are ionized, shatter into fragments which eventually are separated along the ratio of mass/charge by mass spectroscopy.

  • In LC-MS (equally a hyphenation), liquid chromatography performs the separation of the compounds. Because the mechanism of LC differs from the one of GC, you are not able to equate retention times by GC with those of the same compounds of LC. Because of the large excess of solvent molecules in LC in comparison of your analyte molecules, the chemistry of ionization in the mass spectrometer equally differs from the one by GC.

  • Contrasting to spectroscopic methods like NMR, the shape of the spectra obtained by mass spectrometry, the relative intensity of the individual peaks experimentally recorded may differ quite a lot from one experiment to an other. Among the influential parameters are the method of ionization like CI (chemical ionization) with a gas, or EI electron ionization where electrons hit your molecules. The parameters of the ionization interfere, e.g., an EI with an accelerator potential of $\pu{20 eV}$ is softer (with less fragmentation) than the standard $\pu{70 eV}$; however with the possibility that some molecules are less well ionized at all and subsequently less well seen because of lesser fragmentation.

    The conditions of fragmentation in a GC-MS equally differ from those for a LC-MS. In the case of the later, ionization and fragmentations of your analyte molecules interfere much more with the ionization and fragmentations of the carrier molecules (the excess of solvent compared to your analyte running the LC).

  • As nicely described @M.Farooq's answer, the combination of MS-MS primarily targets larger molecules where by sheer structural complexity of the molecule's structure (e.g., proteins, polymers) one identifies fragments of first generation by characterization of their subsequently formed fragments. This is an example of tandem mass spectroscopy.

    For the synthesis of small organic molecules, the detailed elucidation of these fragmentation pathways in the mass spectrometer however often are not relevant. Your time and energy typically are better invested in the characterization of your compounds along the compound characterization checklist by your group or / and the targeted journal (example J. Org. Chem., yet you may use it anyway as a guide). In many cases, this includes recording

    a) a low resolution MS with characteristic peaks assigned ($\ce{M+}$, adducts, important isotopic peaks (e.g., halogen pattern); a few important assigned fragmentations (e.g., $\ce{- H2O}$, decarboxylation, tropylium cation) or pattern (e.g., McLafferty)

    and b) one high-resolution HRMS for the newly prepared compound

    altogether with a self-consistent set of other (spectroscopic) data (UV, IR, NMR, melting point, combustion analysis, etc.).

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  • $\begingroup$ Actually my desired product has molecular weight about 500 Da and supposed to be nonvolatile, so I excluded option using GC-MS. When I searched for analytical MS instruments available in my university, there were GC-MS (EI type), MALDI-TOF, and LC-MS/MS (ESI/APCI multimode). In the description of MALDI-TOF, it was written that it is used for samples with relatively high molecular mass. So I finally chose LC-MS/MS and also requested for starting materials to compare with product sample data. I wanted to see data with single MS, but there wasn't except MALDI-TOF. $\endgroup$
    – Krang Lee
    Aug 7, 2021 at 19:22
  • $\begingroup$ @KrangLee, Earlier you said it was not an LC MS experiment but direct infusion. Get more information from the analyzer about what he did exactly. You have half information and you are writing even less info in your query. Earlier you stated your M must be around 320 and now you state it around 500. People cannot predict beforehand. $\endgroup$
    – AChem
    Aug 7, 2021 at 20:02
  • $\begingroup$ @M.Farooq In summary, 2,3,5-tribromothiophene (previous question, MW=320) is one of the starting materials and purchased, and requested MS as standard. And my product sample is supposed to have molecular weight around 500 (didn't mention in the previous question). Sorry for confusion. I'll be back with more information tomorrow. $\endgroup$
    – Krang Lee
    Aug 8, 2021 at 4:36
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There is no comparison of EI-MS as ESI-MS or ESI-MS/MS. They work on different principles, serve different classes of molecules, but the end goal is to identify a given molecule. Just like an airplane vs. helicopter, both serve to carry a person from one place to another, but their lifting capacities are different. EI is used for small molecules (< 400 amu) which can be conveniently vaporized into gas phase and as you noticed it is a hard ionization technique (causes a lot of fragmentation).

ESI was not meant for heavy fragmentation, it was meant to make elephants fly, as the inventor said. You do not want a lot of fragments of a big molecule. Imagine the messy spectrum with hundreds of peaks. ESI was designed for large and huge molecules, where GC fails badly. Nowadays electrospray is routinely used for small molecules too. Since the purpose of both is to identify molecules, ESI-MS does cause fragmentation despite the name soft ionization, but some time the spectra is still too complex or inconclusive. Then you try the tandem approach. You take a certain ion(s) from the first MS, take it to another one, cause fragmentation by various means, and use that mass spectrum for final confirmation of the unknown.

Connecting with your previous query, the mysterious m/z 382 could be chosen and made to break into pieces in tandem. This would help to identify the adduct or the impurity in your analyte. BTW, as your sample contains bromine, you must see bromine isotopic peak near m/z 382 in the expected ratio.

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  • $\begingroup$ When analyzing reaction mixture using LC-MS/MS, if mobile phase condition doesn't work well, there can be bad separation so that there are two or more compounds in one peak in chromatogram. Then in tendam MS, do we pick the most desired product-looking or informative peak in the first MS and continue fragmentation of this peak in the second MS? So in the final data are we looking the MS data for only one ion? $\endgroup$
    – Krang Lee
    Aug 7, 2021 at 18:52
  • $\begingroup$ Ah, you answered certain ion'(s)'. Then Do I have to ask what or how many peaks did the analyzer select, to interpret each final peaks? $\endgroup$
    – Krang Lee
    Aug 7, 2021 at 19:00
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    $\begingroup$ Your first comment is a separate question. You have to get the exact information from the analyzer. Before that it is useless to think about it. $\endgroup$
    – AChem
    Aug 7, 2021 at 19:57
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    $\begingroup$ Ask your analyzer what experiment did he do? First was it LC-MS/MS? Then what ions were chosen in the second MS? $\endgroup$
    – AChem
    Aug 7, 2021 at 20:03

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