Protonated molecular ion

Formation of reactive ions (CH," ) from methane (CH4) reagent gas and their reaction with sample molecules (M) to form protonated molecular ions [M + Hp. 

Lasers can be used in either pulsed or continuous mode to desorb material from a sample, which can then be examined as such or mixed or dissolved in a matrix. The desorbed (ablated) material contains few or sometimes even no ions, and a second ionization step is frequently needed to improve the yield of ions. The most common methods of providing the second ionization use MALDI to give protonated molecular ions or a plasma torch to give atomic ions for isotope ratio measurement. By adjusting the laser s focus and power, laser desorption can be used for either depth or surface profiling. 

A typical FAB mass spectrum of glycerol alone, showing a protonated molecular ion at m/z 93 accompanied by decreasing numbers of protonated cluster ions (m/z, 1 + nx92 n = 2, 3, 4,. ..). 

However, in both FI and FD, there are other neutral molecules on or close to the surface of the emitter and, in this region, ion/molecule reactions between an initial ion and a neutral (M(H)) can produce protonated molecular ions ([M + H]+), as seen in Equation 5.2. 

For this FAB experiment, a sample of the pentapeptidic enkephalin, Tyr.Gly.Gly.Phe.Leu., dissolved in glycerol was bombarded by xenon atoms. The resulting mass spectrum shows abundant protonated molecular ions at m/z 556. 

This last m/z value is easy to measure accurately, and, if its relationship to the true mass is known (n = 10), then the true mass can be measured very accurately. The multicharged ions have typical m/z values of <3000 Da, which means that conventional quadrupole or magnetic-sector analyzers can be used for mass measurement. Actually, the spectrum consists of a series of multicharged protonated molecular ions [M + nWY for each component present in the sample. Each ion in the series differs by plus and minus one charge from adjacent ions ([M + uH] + n -an integer series for example, 1, 2, 3,. .., etc.). Mathematical transformation of the spectrum produces a true molecular mass profile of the sample (Figure 40.5). 

A sample of the protein, horse heart myoglobin, was dissolved in acidified aqueous acetonitrile (1% formic acid in HjO/CHjCN, 1 1 v/v) at a concentration of 20 pmol/1. This sample was injected into a flow of the same solvent passing at 5 pl/min into the electrospray source to give the mass spectrum of protonated molecular ions [M + nH] shown in (a). The measured ra/z values are given in the table (b), along with the number of protons (charges n) associated with each. The mean relative molecular mass (RMM) is 16,951,09 0.3 Da. Finally, the transformed spectrum, corresponding to the true relative molecular mass, is shown in (c) the observed value is close to that calculated (16,951.4), an error of only 0.002%. 

If a substance (M) is under investigation, its molecules can collide with CH, with transfer of a proton (H ) to give [M + H]+, which can be called quasi-molecular or protonated molecular ions. 

Chemical ionization produces quasi-molecular or protonated molecular ions that do not fragment as readily as the molecular ions formed by electron ionization. Therefore, Cl spectra are normally simpler than El spectra in that they contain abundant quasi-molecular ions and few fragment ions. It is advantageous to run both Cl and El spectra on the same compound to obtain complementary information. 

The ablated vapors constitute an aerosol that can be examined using a secondary ionization source. Thus, passing the aerosol into a plasma torch provides an excellent means of ionization, and by such methods isotope patterns or ratios are readily measurable from otherwise intractable materials such as bone or ceramics. If the sample examined is dissolved as a solid solution in a matrix, the rapid expansion of the matrix, often an organic acid, covolatilizes the entrained sample. Proton transfer from the matrix occurs to give protonated molecular ions of the sample. Normally thermally unstable, polar biomolecules such as proteins give good yields of protonated ions. This is the basis of matrix-assisted laser desorption ionization (MALDI). 

The symbolism (M + H)+ can also be used to represent the protonated molecule. The widely used term protonated molecular ion to describe the MH+ ion is not recommended because it suggests an association product of a proton with a molecular ion. 

In many cases, a protonated molecular ion (M - - H)+ is the only ion observed in a thermospray spectrum but if ammonium acetate buffer is used, depending upon the relative proton affinities of the species present, an ammonium adduct (M - - NH4)+ may be the predominant ion. In addition, clusters may be formed with components of the mobile phase. Although the thermospray ionization process involves less energy than conventional Cl, and very little intense fragmentation is usually observed, the presence of ions due to the elimination of small molecules, e.g. water, methanol and ketene, is not unknown. These latter ions are usually of relatively low intensity when compared to the protonated or... 

The process of ion formation is extremely soft usually no fragmentation occurs. Mass spectra in ESI+ mode are dominated by pseudo-molecular ions (M+, [M + H] + or [M + Na]+) and cluster ions formed by the addition of one or more solvent molecules. For samples with molecular masses up to ca. 1000 Da (as in case of polymer additives), the ions produced from ESI are similar to those formed by other soft ionisation techniques, namely a protonated molecular ion (MH+) in the positive ionisation mode for basic compounds such... 

In the latter case the dopant is ionised, interacts with the solvent and, subsequently, solvent clusters interact with the analyte. Molecular and protonated molecular ions are observed, indicating that ionisation can occur via proton (toluene) and electron transfer (acetone). 

An algorithm has been developed to search databases for suites of protein masses automatically (Pineda et al.).65 In this case data from only one axis is being used, m/z values for the protonated molecular ions. Relative intensities are not used in the analysis. The algorithm also assesses the probability of accidental matches and false identifications. Significance testing allows a value to be assigned to each microorganism identification. 

To gain insight into the structure of these biomarkers, ESI MS/MS analyses were carried out by selecting the protonated molecular ions of the compounds of interest in the first quadmpole of the mass spectrometer. This cation was then collided with argon at a chosen energy in the second quadmpole and analysed in the third quadmpole (Gamier... 

In addition to these numerous results, two other points are discussed by the authors fatty acid speciation and oil identification. These two aspects are developed in another publication written by the same authors [Keune et al. 2005]. The fatty acid speciation is based on the positive ion ToF-SIMS analysis and aims to prove if the fatty acids detected exist as free fatty acids, ester bound fatty acids or metal soaps. On account of the study of different standards, it is shown that when free fatty acids are present, the protonated molecular ion and its acylium ([M-OH]+) ion are detected. In cases of ester-bound fatty acid only the... 

MS condition — An API 4000 equipped with a Turbo Ionspray from Applied Biosystems was used as the mass detector and [M + NH4]+ was chosen as the precursor ion for multiple reaction monitoring (MRM) due to the lack of protonated molecular ions. A transition of m/z 434.4 — 273.2 was chosen for paricalcitol and m/z 450.5 —> 379.2 was selected for the structure analog internal standard. 

Protonated Molecule An ion formed by interaction of a molecule with a proton, and represented by the symbol [M+H]+. The term protonated molecular ion is deprecated this would correspond to a species carrying two charges. The terms pseudo-molecular ion and quasi-molecular ion are deprecated a specific term such as protonated molecule, or a chemical description such as [M+Na]+, [M-HJ, etc., should be used [1],... 

A little recognized systematic error in the calculation of accurate masses of, for example, small radical cation molecular ions (as in electron ionization (El)) or protonated molecular ions (as seen in the soft ionization methods) is the fact that the electron has a small, but finite mass. The accurate masses of radical cations, in which a valence electron has been removed, of anions that have been created by capture of an electron, and of protonated species produced by soft ionization processes, should take into consideration this small mass difference [19]. For example, there is a small difference between the relative atomic mass of a neutral hydrogen atom and a proton. The accepted accurate mass of 1H° is 1.007825 Da. The accurate mass of 1H+ is 1.007276 Da. To be completely correct, expected accurate masses of protonated molecular ions, [M+H]+, produced by electrospray should be calculated using the mass of one H+, rather than all of neutral hydrogen atoms. Mamer and Lesimple do acknowledge, however, that, for large molecules, the error is of little consequence. 

Fig. 2.1.2. Mass chromatograms in the SIM mode using protonated molecular ions of LAS trifluoroethyl esters, (a) LAS standard mixture and (b) LAS found in a sediment. Peak labels indicate the position of the benzene sulfonate moiety on the linear alkyl chain. Reproduced with permission from Ref. [18]. 1997 by American Chemical...

At low extraction voltages, the in-source CID process is greatly inhibited and the spectra display intense signals for the protonated molecular ions. By raising the extraction voltage, in-source CID spectra were obtained. Neutral losses of the carboxylated ethoxy chain and... 

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