Progenesis MALDI - Discover the biomarkers in your proteomics data...

Progenesis MALDI is a simple to use application that gives you high quality proteomics data for biomarker discovery using MALDI-TOF or SELDI analysis. It uses the unique Progenesis workflow and technology to provide:

• Speed - Simple, rapid analysis of large data sets makes it easy for you to run enough replicates in order to minimise false discovery rates
• Objectivity - Guided workflow that helps you apply an objective, statistical-based analysis and run reproducible experiments
• Statistics - Unique spectra alignment process delivers a complete data set for multivariate statistical analysis

The first version of Progenesis MALDI allows you to try a unique workflow for biomarker discovery. Future versions will incorporate features based on your feedback; contact us to try it on your own data today.

    

 

Progenesis MALDI v1.2 - unique analysis workflow

Import data - Load mzXML files, standard text file of mass vs. intensity data and ProteinChip® SELDI System XML files for simple integration into your existing workflow. The software allows hundreds of spectra to be analysed within a single experiment, so you can easily run enough replicates for biologically relevant conclusions.

Pre-Process Spectra - This first stage of analysis removes noise and background from your spectra. Progenesis MALDI includes a noise filter and background removal methods using simple parameter settings to improve the input data for analysis.

    

Alignment - This unique step allows you to quickly align the peaks of your spectra. MALDI data is usually very well aligned but there is the possibility that data from different labs or from later batches of spectra will have the mass of the peaks unaligned. Performing this step prior to analysis allows you to overcome any variation that can occur and generate a complete data set with no missing values for robust statistical analysis.

Peak Detection - With all the spectra aligned peak detection takes place on the average spectrum and you can specify the threshold for detecting the features you want to compare. Progenesis MALDI uses isotope patterns to detect the mono-isotopic peaks. The entire isotope pattern for each peak is then measured in the same position on each spectrum to ensure no missing values in the final analysis. You can also select whole protein detection for low resolution MALDI data. Editing options mean you can define the edges of peaks, merge peaks and optimise the m/z value for a peak.

Technical Replicates - Account for the technical variation within your MALDI-TOF analysis by creating an average spectrum from any technical replicates run for each sample.

Create experimental groups - Create different groupings of the same data set to measure significant differences within the experiment based on user define criteria such as control vs. treated, male vs. female.

Review analysis results - The review stage allows you quickly review the features that have been measured as statistically significant within any groups you choose to compare. Box plots graphically represent the differences between the spectra for a selected peak. All the data at this stage can be copied or exported for you to generate presentations or for lab book information. Following the review stage, you can select peaks of interest for further investigation in Progenesis Stats.

Statistical Analysis - Progenesis Stats is a simple-to-use tool that allows you to easily apply powerful statistical analysis and make reliable conclusions. Principle Components Analysis (PCA), Correlation Analysis and Power Analysis are included to explore the trends in your data. The tests enable you to measure,

• How your data clusters within your experiment. This can validate the hypothesis used to create the experimental groups and indicate any outliers in your data.
• How similar features are in terms of their expression profile. This can help you find additional drug targets or other proteins involved in processes related to the one you're studying.
• The power of your experiment. This will tell you if you've run enough replicates for valid results and is increasingly becoming a requirement for publishing research in journals.

Contact us to evaluate Progenesis MALDI with your own data.

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 MALDI 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.

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