Progenesis ClearSpec – reduce the spectral complexity of high resolution MS/MS spectra

clearspec-iconIt’s always exciting to write a blog post announcing a new product and this one is something different. We have developed a simple application, called Progenesis ClearSpec, which fulfils a critical task for protein characterisation by deisotoping and charge deconvoluting thousands of high-resolution MS/MS spectra in seconds.

Until recently this stand-alone application was only available as a custom program for the Aebersold group within the Institute of Molecular Systems Biology at ETH Zürich. They kindly provided us with a quote to share how it has helped them.

“To reduce the spectral complexity of high resolution MS/MS spectra, we were looking for a tool that fulfils the task of deisotoping and deconvolution of high resolution MS/MS spectra from Orbitap instruments. Different available tools were tested; however visualization and function in Progenesis convinced us.”
ETH Zürich, IMSB, Aebersold group

What is Progenesis ClearSpec and how does it work?

After a recent survey of our Progenesis LC-MS customers we found a lot of interest in making this functionality available to everyone as a simple program.  So we have developed Progenesis ClearSpec to support some of the different applications our customers told us it would be useful for, including:

  • Increasing reliability and accuracy of peptide and protein database searches
  • Characterising the structure of proteins to resolve their biological function e.g. cross-linking studies
  • Analysing MS/MS spectra from very low amounts of samples
  • Analysis of intact proteins by LC-MS/MS
  • Building high quality spectral libraries



Figure 1: (top) MS/MS spectra of a triply charged parent ion with m/z 465.2511 (bottom) same MS/MS spectra deisotoped, charge deconvoluted and fragment ion count limited to the top 20 most intense peaks.

From talking to Progenesis users with a need for deisotoping and charge deconvolution of MS/MS spectra we have been able to include many features requested, such as:

  1. Support for loading data files from all major MS instruments
  2. Export .MGF, .DTA and .csv file formats for common database searching including Mascot, SEQUEST and PEAKS
  3. Accurate assignment of parent ion mass and charge using MS1 isotope distribution data
  4. Deconvolute high charge state fragments

You can see more details on our website including an overview of the simple workflow.

Try Progenesis ClearSpec today

You can try it on your own data, in less than 15minutes in most cases, so you can quickly see where it can help in your own protein and peptide characterisation workflows. Or you can contact us and we can arrange an on-line demonstration with some example files.

As it’s a new product we have decided to make some special offers available to existing Progenesis customers as well as anyone new to our software. Get in touch and we can share details of these offers with you.