The QCorr algorithm compares a tandem mass spectrum to a reversed copy of the same spectrum using a cross correlation (Analytical Chemsitry, 2006, 78, 1921-1929). In this manner, the correlation score typically maximizes when complementary fragment ions (i.e., b and y, c and z etc..) overlap. Because complementary ions are formed from the cleavage of the same amide bond, their summation (assuming a +1 charge state for both ions) is equal to the molecular weight of the precursor ion + two protons. By calculating the offset between complementary ion pairs, it is therefore, possible to determine the molecular weight of the precursor peptide.
The speed of the program is dependent on the number of peaks used in the cross correlation and the number of shifts, but for typical settings (i.e., isolation window = 3, number of peaks less than 500), the program processes ~20-50 spectra/s on a single cpu machine. Therefore, it is feasible to use this approach on the front end of database searches where the number of potential spectra can be quite large (i.e., 500,000 spectra).
The program can now be licensed for use at your university, institute, or company. Academic and nonprofit use is free of charge. To start the licensing process, fill out this form.