Bioinformatics and mass spectrometry for microorganism identification: Proteome-wide post-translational modifications and database search algorithms for characterization of intact H-pylori

MALDI-TOF mass spectrometry has been coupled with Internet-based proteome d atabase search algorithms in an approach for direct microorganism identific ation. This approach is applied here to characterize intact H. pylori (stra in 26695) Gram-negative bacteria, the most ubiquitous human pathogen. A pro cedure for including a specific and common posttranslational modification, N-terminal Met cleavage, in the search algorithm is described. Accounting f or posttranslational modifications in putative protein biomarkers improves the identification reliability by at least an order of magnitude. The influ ence of other factors, such as number of detected biomarker peaks, proteome size, spectral calibration, and mass accuracy, on the microorganism identi fication success rate is illustrated as well.