Processing oligonucleotides using Bio Tool Kit software

For research use only. Not for use in diagnostic procedures.

Answer

The Bio Tool Kit software was designed to analyze protein and peptide workflows, including manual sequencing and peptide mapping. It can also deconvolute oligonucleotides in negative mode. The example below shows an oligonucleotide with resolved Isotopes for molecular weight determination.


The upper panel shows the raw oligonucleotide spectrum and its multiple charge states. An expanded view of the peak for m/z 761.63 reveals multiple isotopes for the oligonucleotide. The lower panel shows a reconstructed spectrum of the oligonucleotide with its salt adducts.

To process oligonucleotide data in Bio Tool Kit software, open the raw spectrum by selecting the Reconstruct Protein option in the Bio Tool Kit menu in PeakView™ or SCIEX OS software. A Reconstruction Options screen appears, where users enter the parameters for deconvolution or reconstruction.



Here are the steps to process oligonucleotide data in Bio Tool Kit:

1. Select the Use limited input m/z range checkbox and indicate the start and stop values to limit the input mass range to reduce noise contribution.
2. Use online calculator tools to determine the theoretical oligonucleotide mass; then estimate an output mass range and set the expected start and stop mass range. The step mass can be set to 0.05 Da.
3. Set the isotope resolution based on the quality of the QTOF instrument data.
4. Set the Charge agent to H+. Obtaining the correct reconstructed mass for an oligonucleotide in negative mode requires H+ to be entered as the charge agent, not the negative electron option.

The Bio Tool Kit MicroApp, an add-on feature within PeakView and SCIEX OS software, requires activation with a separate license file. Read more here about how to license this software.