Software Uncovers Sample Prep Protein Modifications

A new algorithm for analyzing protein mass spectrometry data has uncovered four types of previously undescribed protein modifications introduced during sample preparation (J. Proteome Res., DOI: 10.1021/pr800456q). The discovery could help prevent misassignments in protein identification due to confusion between the inadvertent modifications and cell-derived modifications. Yingming Zhao and colleagues of the University of Texas Southwestern Medical Center developed new software, called PTMap, to pinpoint sites at which proteins are modified after translation. The team used PTMap with HPLC/MS/MS to identify modifications occurring in the proteins bovine serum albumin and histone H₄ during storage, gel staining and destaining, and other types of protein preparations. The researchers detected esterification of aspartate and glutamate residues by glycerol and ethylation of those same residues. They also observed modifications to cysteine and lysine, although the specifics remain unclear. Zhao and coworkers suggest that esterification and ethylation might be prevented by avoiding acidic buffers rich in glycerol and ethanol during protein processing. They further advocate thorough assignment of all MS peaks to ensure accurate protein identification.