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Image Optimization and Visualization

PDQuest includes tools to optimize the acquired gel image to perfection. Publication-quality images are easily generated with a comprehensive range of image optimization tools.

* Adjustment of brightness, contrast, and image filtering
* Full incremental image rotation
* Color palette for realistic color representation
* Multichannel image merging of 3 images to independent color channels for convenient viewing of multicolor merged data
* 3D Viewer for 3-D modeling of any user-defined area of the gel
* Image Stacking for aligned viewing of multiple gel images

Spot Detection and Matching

PDQuest software"s Automated Spot Detection and Matching feature allows you to select the gels you want to analyze, detect spots of interest, create a MatchSet experiment, and match gels, all automatically. The Spot Detection wizard guides you through the process of identifying and quantitating the spots in gel images.

* Spot Detection wizard allows rapid, accurate spot detection
* Automated detection and Gaussian modeling allow separation of merged, overlapping spots, eliminating the need for manual editing
* Automatic spot-matching uses proprietary mathematical algorithms for superior accuracy, eliminating the need for manual intervention
* Spot Detection and Matching Summary reports help define optimal spot detection and matching parameters
* Replicate Group Consensus tool allows spot matching information across replicate gels to be leveraged to find and correct spot detection errors
* Auto-recognition of background speckles by application of a proprietary SYPRO Ruby filter
* Auto-add to Standard function allows fast, automated construction of composite reference gels from experimental gels


Quantitation

PDQuest software offers powerful quantitative analysis and is specifically designed for laboratories that analyze many gels at once. Sophisticated analysis tools reveal subtle differences among gels being analyzed (for example, studying the effects of variables such as heat shock, growth media, dose-response, and time course).

* Several normalizing methods eliminate experimental errors across gels for more accurate comparative results, including multiplex dye normalization
* Sophisticated variable background removal ensures quantitative accuracy even for low-abundance spots
* Choice of Replicate group, Sample Class, or individual gel-based quantitation modes allows statistically representative quantitative accuracy
* Volume Freehand and Auto-contour tools that allow users to manually override Gaussian spot quantitation
* Sortable quantity reports include precalculated ratios for all gel spots against reference member spots


Statistical Analysis

Sophisticated statistical analysis tools in PDQuest software identify experimentally significant spots.

* User-adjustable significance levels on statistical analysis sets
* Intuitive data mining tools help user to identify expression outliers
* Boolean queries allow results from multiple analyses to be combined and compared
* Wilcoxon paired-sample algorithm for statistical comparison of sample pairs


Data Visualization

PDQuest software offers a wide variety of tools to visualize results and data on the gel, in graphs, and in tabular reports.

* Color-coded labeling of matched and unmatched spots in all gel images
* Match-offset vectors that indicate outliers in red for better visibility when editing matching of spots
* "Cyber gel" composite views built from multiple gels that resolve different pI or molecular weight ranges
* Scatter Plot tool dynamically linked to spots in image, allowing easy identification of variant proteins
* Color-coded graphs to differentiate samples according to replicate group or sample class attributes
* Flexible annotation capabilities that allow extensive rich text comments, URL addresses, or data files to be linked to spots


Integration

PDQuest software integrates with key workflow elements for proteomic discovery research for sample tracking, spot excision, mass spectrometric protein identification, and bioinformatics. Automatically imports protein identification results from mass spectrometers.

* Fully integrated automation with ProteomeWorks, ProteomeWorks Plus, and EXQuest spot cutters