Peppy, up until now, only digested chromosomes inside of open reading frames. This is no more. There is now choice! In the properties file you can set if you want to digest the whole chromosome or only the ORFs. Read More

We were recently given by the Chen lab a set of spectra that were derived from the USP set of 50 proteins. We were told that there are probably a good amount of impurities in this set so some of the spectra will not correspond to peptides which can be found in the USP list. [...] Read More

I recently found that something exists called “MS-Fit”. I found this because had confused one of our lab members into thinking that it had something to do with MSMSFit. To avoid future confusion I am redubbing that scoring method “TandemFit”. The name works well in that it scores tandem mass spectrometry data, and it does [...] Read More

Just added a method and modified constructor to the Spectrum object which allows for normalization of the peaks intensities. It finds the maximum intensity for a given spectrum and then walks through each peak dividing the intensity by this found maximum intensity. This can be handy for SpectrumMatch as well as for comparing scores TandemFit [...] Read More

Peppy, the open-source proteogenomic mapping software has been benchmarked at processing over 600,000 spectra per day on a consumer-grade desktop… Read More