	US 7,555,393 B2
	Evaluating the probability that MS/MS spectral data matches candidate sequence data
Rovshan Goumbatoglu Sadygov, San Jose, Calif. (US); and Andreas Huhmer, Mountain View, Calif. (US)
Assigned to Thermo Finnigan LLC, San Jose, Calif. (US)
Filed on Jun. 01, 2007, as Appl. No. 11/809,703.
Prior Publication US 2008/0300795 A1, Dec. 04, 2008
Int. Cl. G01N 33/48 (2006.01)

U.S. Cl. 702—19

20 Claims

1. A method for generating a compound probability that product ion spectral data matches a candidate sequence in a sequence database by random, the product ion spectral data having been generated by a non-ergodic process as implemented in a mass spectrometer instrument, comprising:

(a) generating a first product ion spectral data from one or more biological samples using the mass spectrometer instrument; wherein the steps following steps are preformed by a computer;

(b) preprocessing the first product ion spectral data;

(c) determining product ion abundance values and product ion mass-to-charge ratio values for each of a plurality of peaks from the pre-processed first product ion spectral data;

(d) utilizing the product ion abundance values to determine an intensity probability distribution, the intensity probability distribution representing a first probability that the product ion spectral data was generated at random;

(e) utilizing the mass-to-charge ratio values of the product ions to determine a fragment probability distribution, the fragment probability distribution representing a second probability that the product ion spectral data was generated at random;

(f) determining the compound probability based on the intensity probability distribution and the fragment probability distribution, the probability representing a probability that the generated product ion spectral data matches a candidate sequence in the sequence database at random; and

(g) displaying to a user, the candidate sequence which best matches the generated first product ion spectral data based on the determined compound probability.