[Ingeniosuccinimide]

I took an MS spectrum of what I isolated from the reaction and then I compared it with one reported in the literature/generical database since it's a known compound.

The fragmentation pattern looks identical, and all the peaks are at same m/z ratio values as reported, but the relative intensities are different, some peaks having larger and some smaller intensity and viceversa when compared to reference spectrum.

Does that indicate something? Let's for simplification assume that the same fragmentation method, solvent and amount of compounds were used in both my and referent spectra.

One another question, unrelated to the upper: if I'm recording MS spectrum in EI mode and the peak of expected m/z for M or M⁺ (without any fragmentation) does not appear in the spectrum at all, but only the peaks with smaller m/z value are present, does that necessarily mean that I actually don't have my compound in the sample? Are there any rules or exceptions regarding the ionization method (I mentioned EI, but what if peaks corresponding to M or M⁺ are absent when using ESI)?

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On information from MS spectra

« on: Yesterday at 02:02:58 PM »

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I took an MS spectrum of what I isolated from the reaction and then I compared it with one reported in the literature/generical database since it's a known compound.

The fragmentation pattern looks identical, and all the peaks are at same m/z ratio values as reported, but the relative intensities are different, some peaks having larger and some smaller intensity and viceversa when compared to reference spectrum.

Does that indicate something? Let's for simplification assume that the same fragmentation method, solvent and amount of compounds were used in both my and referent spectra.

Unfortunately, it could mean everything or nothing !!

1.  Sample and ref. cmpd. could be isomers (positional, cis/trans etc).

2.  Could be the SAME cmpd. but recorded on different type (quadrupole vs. mag. sector vs. ion trap etc) of instrument.

One another question, unrelated to the upper: if I'm recording MS spectrum in EI mode and the peak of expected m/z for M or M+ (without any fragmentation) does not appear in the spectrum at all, but only the peaks with smaller m/z value are present, does that necessarily mean that I actually don't have my compound in the sample? Are there any rules or exceptions regarding the ionization method (I mentioned EI, but what if peaks corresponding to M or M+ are absent when using ESI)?

1. NOT necessarily, because about 20% of organic cmpds. do not give an [M+.] under EI.

2. Under ESI, [M+H]+ is generated, not [M+.].  Losses of small, neutral molecules (H2O, NH3, MeOH etc) from [M+H]+ may occur very readily, leaving only a low relative intensity signal at [M+H]+, and a high intensity [MH-H2O]+ signal.

[kriggy]

EI sometimes (most of the time?) doesnt give you molecular peak, however the splitting to fragments is very characteristic so you might be able to get unknown structure from EI-MS (unlike ESI-MS). There are also characteriestic ion peaks so you might be able to distinquis if the compound is aromatic or aliphatic etc..
If you use ESI there is usualy little to no fragmentation but there are adducts which have higher m/z. There is (M+H)⁺, (M+Na)⁺, (M+K)⁺ those are usualy always present since Na and K is present in solvent/used glass etc.. Then you have different adducts with solvent, mobile phase or buffer used (if you use HPLC-MS) like (M+NH₄)⁺ etc..

I suggest using another method to clarify - maybe NMR