Analysis of proteomics data
Proteomics is the large-scale study of proteins, particularly their expression and physical properties. Commonly quantitative methods used in proteomics are 2D gel, LC-MS and LC-MS/MS 2D gel electrophoresis is an established technique considered to be a very good option for high-resolution profiling of low abundance proteins in complex biological samples. More recent methods are liquid chromatography-mass spectrometry (LC-MS) methods and associated tandem mass spectrometry (LC-MS/MS). Tandem mass spectrometry, or MS/MS, involves a second analysis within the instrument after a molecular dissociative event in order to obtain structural information including but not limited to sequence information. Key functionality Qlucore Omics Explorer lets the researcher freely examine and analyze data from protemics experiments. For protein analysis the following functionality will be of specific interest - Investigate any structure in data using variance filtering combined with PCA.
- Perform statistical filtering using ANOVA to enhance results.
- Generate a list of proteins that classifies data based on a selection of statistical tests: F-test, t-tests or regression.
- Use hierarchical clustering or PCA to indentify subgroups.
- Work with Variable PCA plots to find correlation and networks among selected proteins.
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Platform specific data import
Qlucore Omics Explorer supports data import from various sources. If you have used the analysis software from any of the companies listed below, a brief description of the required import steps is provided. Note that Qlucore Omics Explore expects data to be normalized before input. If you have data from other sources please see the general data import section.
SearchLight® Array Analyst Software (www.aushon.com) is software for image capture and image alignment. Data can be exported to Excel. After export, follow the instructions in the General data import section below to convert data to a ".gedata" file.
Ludesi: By using the Ludesi Redfin software (www.ludesi.com), it is easy to export your data into Excel. This is done by pressing the Excel icon at the top right of the user interface. The Excel file will then require some simple editing. For instance, you will have to remove the initial rows and replace them with the Qlucore ".gedata" header rows. See the section general data import below.
Nonlinear dynamics (www.nonlinear.com) provides the Samespots software. From Samespots the user can export analyzed data into Excel for downstream analysis. See the Samespots user documentation for details. When the file is exported, you can use the description provided in the General Data Import section below.
General data import
Use generic formats: If your file match the simple or compact text file formats supported, data can be imported directly, see the features section (menu at top right) and the document How to import data for more details.
Convert manually: Most data generated from protein array experiments can easily be converted to the Qlucore platform independent data format ".gedata" or to the compact text or the simple text format supported by Qlucore Omics Explorer. The ".gedata" format allows both data and annotations in the same file, the simple text format supports data. The annotations can be imported separately. Conversion is at best done in a spread sheet program as Excel. More information about the ".gedata" and the simple and compact text formats can be found in the features section (menu at top right) and the document How to import data.