title: Nonparametric mass calibration using hundreds of internal calibrants.
abstract: In situations where many molecular ions (>100) can be identified to the level of their elemental composition, such as in proteomics, metabolomics, and glycomics, a final mass calibration is possible for every sample without reliance on any analytical description of instrument behavior. This is achieved by applying a nonparametric calibration curve determined from the difference in observed, centroided m/z values of the known, internal calibrant molecular ions versus that calculated from their elemental compositions, over the m/z range. In examples here, proteomic data are examined for two sets of samples of complex mixtures composed of tryptic peptides from human and mouse blood proteins using high-resolution time-of-flight mass spectra from on-line liquid chromatography-mass spectrometry experiments. Resultant, postcalibration median absolute value mass errors and root-mean-square errors for peptides between 300 and 1100 m/z for many samples ranged from 3.1 to 4.4 and 5.2 to 6.9 ppm, respectively. The method may be applied to other types of mass spectrometers.
authors.affiliation: PPD, Inc., 1505 O'Brien Drive, Menlo Park, California 94025, USA. Christopher.Becker@menlo.ppdi.com
authors.forename: Christopher H
authors.initials: CH
authors.lastname: Becker
authors.forename: Praveen
authors.initials: P
authors.lastname: Kumar
authors.forename: Ted
authors.initials: T
authors.lastname: Jones
authors.forename: Hua
authors.initials: H
authors.lastname: Lin