FCAP Array is designed for use with multiplex microsphere kits from any source

The FCAP Array software uses unique partitional type clustering technology that attempts to directly decompose the microsphere data set into a set of disjoint clusters. The software assignes clusters to peaks in the probability density function defined on one or two clustering fluorescence parameters.

Because the used classification algorythm works without any strict pre-assumption about the cluster structure of the data set, FCAP Array can be used with any multiplex assay kit in which the microsperes form resolvable, non-overlapping clusters. Essentially all commercial microsphere kits satisfy these requirements.

FCAP Array supports any instrument that saves data is standard FCS format

FCAP Array allows you to design, develop and analyze multiplex assays

With FCAP Array software, you create Experiments that define multiplex bead assays, and then analyze the acquired FCS data files.

While an experiment can have more than one Plex, each test sample is associated with a unique Plex. When you add test samples in the main window, you associate them with an Experiment Plex.

When used with the BD FACSArray flow cytometer, the FCAP Array Experiment document can be exported to coordinate data acquisition.

You can use any number of analytes (bead clusters)

The number of capture bead clusters, and consequently the number of analytes per assay are not limited by FCAP Array. However, the number of resolvable clusters depends on the SD (standard deviation) of the clustering fluorescence peaks and the number of events acquired from the same capture bead population.

FCAP Array was tested with a mixture of more than 70 bead-analyte specificities. In order to identify an individual cluster by FCAP Array, the cluster must contain a minimum number – typically 50 to 100 events of capture beads.

Because the bead size can also be used as clustering parameter, FCAP Array can easily resolve the data sets of 300 to 400 mircosphere clusters.

The list of analytes is associated to the pattern of cluster centroids but not to pre-determined locations of the clusters. Consequently, the association fails if one or more clusters (elements of the cluster centroid pattern) are missing, and FCAP Array reports a ''Clustering Error''.

Download assay protocols (Plexes) for manufactured kits

The Plex is a crucial element of data processing with FCAP Array. A Plex defines the bead-analyte specificities, the instrument specific pattern of cluster centroids, as well as the standards, controls and the mathematical model of the data analysis. A Plex is an FCAP Array construct that contains everything to perform an Experiment and analyze the acquired data, except the sample specifications/definitions.

If the Plex of a manufactured kit is available, you need only two steps to design an experiment:

1. Select the Plex, and
2. Define the samples to be analyzed.

The Plex needs to be imported by FCAP Array before use. The Plex of a commercial kit may be available from the manufacturer of the kit.

We also maintain a database of Plex files that can be downloaded for use with FCAP Array. We are eager to save well defined Plexes in our database, or to provide customized services for Plex definiton of both personalized and commercial assays.

Create your own assays (Plexes) and export for use by colleagues

You can export Plexes in a file to be imported by another FCAP Array software user. In this way, laboratories can share Plex definitions. The exported Plex document file can be sent as e-mail attachment for use by colleagues.

We are also eager to save well defined Plexes of your personalized assay in our database. For customized services, please download the Plex Definiton Form, provide the requested information and return it to us via e-mail.

Use any number of assays (Plexes) in one experiment

Each FCAP Experiment can contain one or more Plexes. An Experiment is essentially a list of Plexes and the set of samples to be measured by the assays represented by the Plexes. A Plex defines the Beads used in analyte testing, as well as the standards or controls. Beads associate the distinct fluorescence characteristcs of a capture bead with an analyte. A Plex also specifies the instrument parameters used to distinguish clusters and quantify analyte concentration.

Customize reporting templates/preferences

You can easily customize the form and content of the Experiment Report Document to be printed. FCAP array allows you to define and store several Report Document Templates that can be selected from a pull-down menu. Printing preferences determining the type, style, and size of the fonts to be used in the report can also be customized.

When analysis and review of an Experiment are complete, an authorized user can electronically sign and finalize it. The Report generated and printed from a finalized Experiment becomes locked. An internally generated ID is attached to the finalized Experiment that is written into all output documents generated by FCAP Array software. In this way, the Experimental setup and the data processing details can be subsequently reviewed. The authorized user''s name appears on the printed version of the Report document as well.

Export raw data for MS Excel®

Raw data can be exported and saved as a comma delimited text file (comma separated values format). This format allows you to import the data into standard spreadsheet applications such as Microsoft Excel® for further processing.

Clustering is based on single or dual color and/or size of beads

The classification performed by FCAP Array results in a set of clusters (peaks) identified on the histogram or dot plot (one- or two-parameter probability distribution) of clustering parameters. FCAP Array was tested with a mixture of more than 70 bead populations (beads) with discrete and distinct fluorescence intensities. In addition, FCAP Array can recognize several distinct bead sizes allowing this way to resolve several hundred bead clusters from the same data set.

Fully automatic quantitative and qualitative analysis

FCAP Array software facilitates the design and data analysis of bead assays. These assays can detect presence of, or determine concentrations for multiple analytes such as proteins and peptides in a sample. Quantitative analysis determines analyte concentrations based on known concentration values of a set of standards. Qualitative analysis determines whether a specific type of analyte exists in a sample.

With FCAP Array software, analyte concentrations or existence can be determined for many analytes per sample.

Eleven selectable fitting equations (standard curves)

In FCAP Array, you can use eleven curve fitting models for quantitative analysis. The built in fitting models include:

• 5 parameter logistic
• 4 parametes logistic
• Linear
• Quadratic
• Cubic
• 2 parameter power
• 4 parameter power
• Logarithmic
• 2 parameter exponential
• 3 parameter exponential
• Exponential sigmoid

The fitting model is a Plex component. Changing the fitting model defines a new Plex. You can set the required degree of accuracy when fitting standard curves. Fitting accuracy is expressed by the regression coefficient, whose values range from 0–1 (0–100). Fitting accuracy affects both the feasibility and the number of computation iterations needed for a standard curve fit.

Unlimited number of samples, plates, replicates

The number of test samples, plates and replicates is not limited in FCAP Array Experiments.

Suitable for research and drug discovery applications

FCAP Array enables researchers and laboratories to perform multiplex microbead bioassays more quickly and easily than with other systems. FCAP Array has also been designed for supporting drug discovery industry to use the extensive list of cytometric bead array applications for high througput screening. The software package was designed/developed with worldwide regulatory requirements in mind. The software supported experiment design, the key-word supported sample-data assignment and the fully automatic data analysis and reporting can significantly increase the safety of processing the generated huge amount of data.

Soft Flow also offers a custom Pex development service for the multiplex assays designed to your individual specifications.

Easy to use: Experiment and Plex Wizard

Experiments are created with either the Experiment Wizard or the standard Experiment document interface (main activity window). Experiments can also be saved and reused, often by making a few quick edits. A Plex can be created or modified from within an Experiment. Plexes can also be saved for reuse. Plex development is also supported with a New Plex Wizard and a Plex Modification Wizard.

Multi-user login, electronic signature

Only authorized users can work with FCAP Array. Some users may have special rights:

• Administrator has access to the user management tools.
• Authorized users can sign and finalize an Experiment. When analysis and review are complete, you can prevent additional modifications to an Experiment by finalizing it. Experiments can only be finalized by users authorized to sign Report documents. When an Experiment is finalized, the authorized user''s electronic signature is added to the Experiment and Report documents.

Users without special rights can use all FCAP Array software features except user management and finalizing an Experiment.

ENGOREPROD 1283-3938 20091122