Data Analysis

CPP data can be analyzed with standard proteomics software packages such as PaSER*, Proteome Discoverer** and others. Conformational changes are directly reflected by changes of the MS1 ratio of the two labels and can be quantified with software such as Skyline or Census (available on GitHub). 

No access to suitable software or no time to analyze the data ? We are happy to help with custom solutions. Contact us to discuss your data analysis needs.

peptide identification with ProLuCID

Identified Spectrum of a labeled peptide. Spectra were searched with ProLuCID and filtered with DTASelect 2.0.

A. Analysis of conformational changes for a single lysine site in a target protein upon treatment with different drugs.  B. Conformational changes of the proteome upon mild heat shock, which leads to unfolding of proteins (from Bamberger, Pankow et al., JPR, 2021).

* PaSER is a database search platform by Bruker.

** Proteome Discoverer is a protein informatics platform trademarked and owned by Thermo Fisher Scientific.