Decryptor: System for  identification of alterations using mass spectrometry of proteome

Introduction

Methods used for identification of reference peptides from MS/MS spectra are not directly transferrable to identification of altered peptides. In general, many theoretical peptides agree with the mass spectrometric measurement to the same or similar degree. As a consequence, it is not desirable to select candidate peptide interpretation purely on its agreement with measurement. In case of altered peptides, there often exist other equally plausible interpretations which are, however, more likely (e.g. peptides with PTM instead of alteration). Therefore, it is desirable to rule out these situations to enhance the specificity of the identification method.

Materials/methods

Decryptor exploits additional (non-MS/MS) structure in mass spectrometric data to further reduce the set of peptides agreeing with the measurement to similar degree. Given precise chromatographic conditions, theoretical retention time is predicted and compared with observed retention time. Additionally, the difference between theoretical isotopic distribution and observed peaks in precursor spectrum is evaluated. Finally, the system tries to reject altered peptide interpretations by searching for more likely interpretation.

Results and conclusions

The system was recently evaluated on the proteome of colorectal cancer cell line HCT-116 measured on Orbitrap Elite instrument (3 technical replicates, 20 fractions each). Decryptor was able to identify 22 unique non-SNPs and 99 unique SNPs. Identified altered peptides correspond, in general, to alterations in highly expressed genes. In summary, the system enables the use of mass spectrometry for identification of limited number of highly expressed alterations.