PNNL

Abstract

Identification of peptides through analysis of peptide ion fragmentation mass spectra is key to proteomic/peptidomic studies. Advanced mass spectrometry has enabled measurement of peptide fragments with ~ppm mass error levels; however, mass accuracy has not been widely utilized in broad aspects of peptide identification. In this work we describe how peptide high-precision fragments measured with Fourier transform mass spectrometry can provide a powerful discriminative capability to distinguish true peptide ‘hits’ from possible incorrect peptides. For identification of peptides having multiple termini and carrying multiple charges, we show that the simple utilization of high-precision mass fragments information results in improved peptide analysis coverage and consistency, with coverage of >95% peptides identified totally from different spectral scoring and peptide statistic probability methods developed for moderate accuracy mass spectral peptide identification.