Progenesis PG600 is a software solution that enables researchers to detect potential peptide biomarkers from complex biological samples analysed using either MALDI-TOF or SELDI-TOF mass spectrometry.
Peak Detection and Alignment
- Automatic peak detection of raw spectral data
- Choice of powerful peak detection methods:
- ‘Isotope Masking’, which highlights the mono-isotopic peaks for high-resolution spectra
- ’Generic Detection’ which picks peaks from lower-resolution spectra (such as SELDI data)
- Noise and background removed before detection using wavelet analysis or powerful filters (Savitzky-Golay filter combined with Top-Hat morphology)
- Automatic peak alignment across all spectra with customisable m/z window
- Iterative peak detection creates complete table of comparative intensities across all spectra with the ‘Isotope Mask’ detection method – i.e. no missing values
- Optional normalisation of peaks using Total Ion Current (TIC) of each spectra
- View and export peak measurements and statistics
MS data integration
- Full integration with PerkinElmer’s TOFworks SQL database allowing access to all protein profiling experiments generated with the prOTOF 2000 MALDI O-TOF mass spectrometer
- Compatible with Waters’ MALDI micro MX data
- Compatible with Ciphergen SELDI-TOF XML
- Generic txt and csv file loading capabilities
Spectra Visualisation
- Simulated gel view with scales to show all experimental spectra as a 2D map
- Contrast and colour options to enhance the visualisation of the simulated gel view
- Scaled spectra display (individual, overlaid and stacked) with highlighted peaks
- Ability to view filtered spectra and adjust detection parameters as required
- Zooming facilities in all views
- Binning of data to speed visual display of spectra. (N.B. raw data used for all analysis)
- All displays can be printed and/or exported to other applications
Group Visualisation and Statistical Analysis
- All spectra in an experiment can be assigned to one of two customisable groups
- The spectra can be displayed by group in the spectra view
- Each group is compared and a p-value is automatically calculated for each peak
- The p-value indicates which peaks have significant differences between the groups and combined with the visualisation tools will help locate potential biomarkers
- The tabular data is filtered by p-value to show the most significant results
- A visual display of the significant peaks is also available showing the differences of the largest and most significant peaks
Clustering
- Choice of two dendrogram algorithms to distinguish how individual traces are related:
- Allows visualisation of the spectra similarity
- Assists with the identification of sub groups within the experiment and clarifies the separation (or not) of the pre-defined groups
- Outlier spectra can be identified and removed from the group statistics if required
Experiment Navigation
- “Save As” option for experiments
- View all spectra in their groups
- Rename individual spectra
- Quickly select spectra for profile display
Additional Features
- Measurements table for data display with wide range of selectable data fields
- Simple data transfer to Microsoft Excel, clipboard or file
- Comprehensive Help menu and tutorial files
- Tool tips on all features
- Printing and print preview on all data
