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

The performance of triple-stage quadrupole (TSQ), quadrupole ion trap (QIT) , and double focusing sector field (DFSF) mass spectrometers for the genera tion of fragment ions to obtain sequence information about oligonucleotides was compared. Upon electrospray ionization (ESI), the charge-state distrib ution of candidate precursor ions not only varied significantly with the ty pe of mass spectrometer, but also with the size and sequence of the investi gated oligonucleotides. While concentration limits of detection for an octa nucleotide were in the 100 pmol/L range on the QIT and in the 5-10 nmol/L r ange on the TSQ and DFSF instruments, those of a 24-mer were in the 2-13 nm ol/L range on all three instruments. Reproducibility of mass determination, an important prerequisite for reliable identification of fragment ions, wa s highest on the TSQ with 0.0037% relative standard deviation over three da ys. Finally, the tandem mass spectra of a dimethoxytritylated pentanucleoti de recorded on the three instruments were compared. Relatively simple spect ra dominated by complete series of fragment ions of the (a-B) and w type we re obtained on the QIT. Complete series of (a-B) and w ions were also obser ved 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-sour ce 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 s pectrometers were suitable for the generation of fragment ions, from which the complete nucleotide sequence of the pentanucleotide could be deduced. C opyright (C) 2001 John Wiley & Sons, Ltd.