Factors determining the performance of triple quadrupole, quadrupole ion trap and sector field mass spectrometers in electrospray ionization tandem mass spectrometry of oligonucleotides. 1. Comparison of performance characteristics

Abstract

The performance of triple-stage quadrupole (TSQ), quadrupole ion trap (QIT), and double focusing sector field (DFSF) mass spectrometers for the generation of fragment ions to obtain sequence information about oligonucleotides was compared. Upon electrospray ionization (ESI), the charge-state distribution of candidate precursor ions not only varied significantly with the type of mass spectrometer, but also with the size and sequence of the investigated oligonucleotides. While concentration limits of detection for an octanucleotide were in the 100 pmol/L range on the QIT and in the 5-10 nmol/L range on the TSQ and DFSF instruments, those of a 24-mer were in the 2-13 nmol/L range on all three instruments. Reproducibility of mass determination, an important prerequisite for reliable identification of fragment ions, was highest on the TSQ with 0.0037% relative standard deviation over three days. Finally, the tandem mass spectra of a dimethoxytritylated pentanucleotide recorded on the three instruments were compared. Relatively simple spectra dominated by complete series of fragment ions of the (a-B) and w type were obtained on the QIT. Complete series of (a-B) and w ions were also observed on the TSQ. However, additional fragments belonging to the b, c, d, x and z series were found in the spectrum. In the spectrum recorded after in-source fragmentation in the DFSF, only fragments corresponding to the loss of a nucleobase and a complete series of w ions were observed. All three mass spectrometers were suitable for the generation of fragment ions, from which the complete nucleotide sequence of the pentanucleotide could be deduced.

Rapid ESI–MS method for examining the thermal decomposition of pharmaceuticals

“…In some instances, higher mass fragments (i.e., dimeric species) were observed and they were included in the quantitative ratio calculations. As can be seen from these data, the temperature of the inlet capillary had a significant effect on the ESI–MS spectra, consistent with changes in the spectra observed for other compounds12,13 and similar interface designs14–16 (i.e., irrespective of absolute changes in the total ion yield, the relative degree of fragmentation increases with increasing inlet temperature).…”

Structural study of spirolide marine toxins by mass spectrometry

“…Mass spectrometry is also an essential analytical tool for the structural elucidation of minor compounds and has been successfully used in this manner [18,19]. Triple-quadrupole mass spectrometers are rugged instruments giving reliable MS-MS data [20,21], and are often used for the detection of unknown compounds. The arrival of electrospray quadrupole ion-trap (Paul trap) instruments afforded the ability to carry out multiple stages of tandem mass spectrometry (MS n ) [22].…”

Metabolite profiling in rat urine by liquid chromatography/electrospray ion trap mass spectrometry. Application to the study of heavy metal toxicity

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