The Xtract algorithm uses a fitting scheme similar to the THRASH algorithm to deconvolve and de-isotope isotopically resolved mass spectra of proteins, peptides, and oligonucleotides.

The following figure shows an isotopically resolved mass spectrum:

Figure Isotopically resolved mass spectrum
Isotopically resolved mass spectrum

The Xtract algorithm does the following:

  1. Examines a cluster of isotopically resolved peaks and uses the peak spacing of a cluster to determine an initial estimate of the mass of the relevant component.
  2. Fits an averagine distribution to the observed peak profile in that cluster to determine the monoisotopic mass that best reproduces that profile.
  3. Combines results for all observed charge states for each mass component to produce a single mass value for that component.

The resulting spectrum shows only the monoisotopic masses for the components that the algorithm identified.

When used properly, the Xtract algorithm reduces spectral noise and provides a high-intensity mass spectrum of monoisotopic peaks. You can use the monoisotopic mass list or the extracted spectra (not the original MS/MS spectra) as the input to various search engines for further analysis.

NOTE

Refer to the following article for more information on the technique Xtract uses to determine monoisotopic masses:

Senko, M.W., Beu, S.C. and McLafferty, F.W. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrometry 1995,6, 226–233.

You can specify the Xtract algorithm parameters for an Intact Mass Analysis experiment on the Parameters > Component Detection page of the processing method editing wizard. See Component Detection parameters and Xtract deconvolution parameters.