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J Biomol Tech. 2007 February; 18(1): 67.
PMCID: PMC2291976

P192-T On-Slide Chemical Modification as a Means to Improve Confidence in Protein Identifications Made by Peptide Mass Fingerprints


The identification of proteins from large protein databases such as NCBInr using peptide mass fingerprints (PMFs) obtained on a MALDI-TOF mass spectrometer continues to be a challenge. A strategy that can be used to improve confidence in these identifications is to carry out some form of chemical modification reaction known to be specific for selected residues after the original analysis has been completed. The identification made by the original PMF is confirmed only if the mass shifts predicted by the putative identification are observed on reanalysis. To be most useful it would be necessary to carry out the chemical modification “on slide” in such a way as to not compromise the quality of the reanalysis. This requires that the chemical modification reagents be volatile or, at least, easy to remove. Oxidation with perfomic acid is a commonly applied chemical modification that appears to meet these requirements. Here, we demonstrate the usefulness of on-slide peracid oxidation as a means to confirm PMF identifications.

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