BREMEN, Germany—Most proteomic databases and software packages have difficulty identifying posttranslational modifications and researchers are often forced to identify aberrant peaks using time-consuming, laborious manual inspection. To address this challenge, scientists at Bruker Daltonik GmbH developed PTM-Explorer as an adjunct to more standard analysis packages. With colleagues at Protagen AG, they recently tested the software's ability to identify novel peaks in a study of αA-crystallin from mouse eye lens.

 

Using 2D-PAGE followed by LC-MS/MS, the researchers first scanned the spectra using standard search algorithms, such as Sonar, Thermo's Sequest, GeneBio's Phenyx or Matrix Science's Mascot. They then probed the remaining spectra with PTM-Explorer using criteria such as peptide modifications, cleavage rules, sequence tags, and sequence patterns. The scientists were able to show that previously unexplained spectra were the results of peptide phosphorylations or other modifications, and perhaps more importantly, they were able to identify modifications that had not been previously reported in the literature.