MALDI-TOF biomarker discovery using the Progenesis PG600 software solution

What is Biomarker discovery?

The major goal of biomarker discovery (or protein profiling) is to identify disease specific proteins/peptides, primarily from easily accessible bodily fluids such as serum, plasma and saliva. The technique of MALDI TOF mass spectrometry is a reliable and efficient method of acquiring highly sensitive proteomic data from complex biological samples and is increasingly being used to gain insights into the mechanisms of disease and to monitor the success of a therapy.

Widespread implementation of this technique is hampered by the lack of accurate, platform independent software available to researchers. Progenesis PG600 has been developed specifically for this application and simplifies the process of discovering specific and sensitive biomarkers from this abundance of MALDI TOF spectral data.

Using the Progenesis PG600 software in your biomarker discovery research

The PG600 software currently supports the following platforms:

• PerkinElmer’s prOTOF 2000 MALDI O-TOF
• Waters’ MALDI micro MX.
• Ciphergen’s Protein Chip Biomarker System II SELDI TOF

PG600 has a data loader for the PerkinElmer and Waters instruments which automates the process of data importation, experimental set-up, treatment definition and specifying analysis parameters.

Spectral data and peak lists can be imported from Ciphergen’s ProteinChip Biomarker System II (PSB-II) SELDI TOF (in an XML format). Users are able to import, visualise, match, cluster and perform differential analysis of their SELDI spectral data using Ciphergen’s peak detection.

The PG600 software is a completely open analysis platform allowing you to freely interact with your data. It employs a simple and intuitive user interface for data pre-processes (binning, re-sampling), visualising spectral data, monoisotopic peak detection, alignment, normalisation, performing statistic calculations and clustering.

Key feature summary:

Below are some of the key features in Nonlinear Dynamics’ PG600 software. As leading innovators in software development for the Life Science researcher, we are continually developing new solutions ensuring our users are at the cutting edge of research technologies. To find out the up to date information on the Progenesis range, including the PG600 software, please visit our website.

• Fully automated data handling and processing of MALDI TOF spectral traces using sophisticated alignment and peak detection algorithms
  
  • You can adjust the binning size for improved performance whilst visualising the data, although all processing is done on the raw data
    
  • Peak detection and alignment is carried out in a single step without any further intervention. Adjustable alignment parameters allow full control over the automatic process
    
  • Peak data can be normalised for the accurate comparison of traces
• Intelligent detection of the monoisotopic protein / peptide peak
  
  • Intensity calculations accurately determine the total intensity under all of the peaks in the peptide group
    
• Automatic generation of a simulated gel view from the trace data for advanced visualisation
  
  • There are adjustable settings for contrast, colour and trace display allowing a completely customised view
    
• Range of options available for the display of trace data
  
  • Traces can be stacked or overlaid and/or grouped according to the sample class
    
  • Mono-isotopic peak labelling can be switched on or off
    
  • The simulated gel view is positioned alongside the trace data to facilitate visual comparison
• Rapid identification of data clusters using the dendrogram view
  
  • Dendrograms can be generated from the traces to provide an instant visualisation of data clusters
    
  • There is a choice of Neighbour Joining or UPGMA methods
• Straightforward grouping and averaging of traces according to sample class
  
  • Adjustable parameters allow you to have full control over the averaging of measurements within each sample class
• Simple but effective tools to display differences between sample classes
  
  • Sample class differences are shown for instant viewing of changes in the data which reflect potential biomarkers and areas for further investigation
    
  • Statistical measurements (p-values) are calculated and displayed in measurements tables alongside all other trace data
    
  • Tables can be re-ordered to rank results by statistical significance for convenient viewing

The Progenesis PG600 software for biomarker discovery is rapidly evolving. Please visit these pages regularly to see the latest developments or contact us to receive further information.