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. Author manuscript; available in PMC: 2014 Apr 9.

Published in final edited form as: J Proteomics. 2013 Feb 4;81:173–184. doi: 10.1016/j.jprot.2013.01.026

Managing Systematic Deviations in Mass Measurements Using the Sliding Dot Product. An ion trap mass spectrometer affords limited resolution in mass measurements. A slight deviation in mass measurement may misalign peptide fragments from the query and reference spectrum into different bin windows, which significantly affects the value of the dot product. A. As shown in the example spectrum for peptide ISVNDFIIK (Q8BMF4), without a mass adjustment, the DP value equaled 0.529; with adjustment, the DP value reached 0.684. B. With query spectra collected by a poorly-calibrated LTQ instrument, the sliding dot product workflow provided 15.7% (5.4% + 10.3%) additional spectral matches. C. With a well-calibrated instrument, this adjustment offered analytical benefits of 3.2% extra spectral matches.

Managing Systematic Deviations in Mass Measurements Using the Sliding Dot Product. An ion trap mass spectrometer affords limited resolution in mass measurements. A slight deviation in mass measurement may misalign peptide fragments from the query and reference spectrum into different bin windows, which significantly affects the value of the dot product. A. As shown in the example spectrum for peptide ISVNDFIIK (Q8BMF4), without a mass adjustment, the DP value equaled 0.529; with adjustment, the DP value reached 0.684. B. With query spectra collected by a poorly-calibrated LTQ instrument, the sliding dot product workflow provided 15.7% (5.4% + 10.3%) additional spectral matches. C. With a well-calibrated instrument, this adjustment offered analytical benefits of 3.2% extra spectral matches.