Proteomics  Print-icon

GenePattern provides the following support for the analysis of proteomic data:

AuDIT

Multiple reaction monitoring-mass spectrometry (MRM-MS) of peptides with stable isotope-labeled internal standards (SIS) is a quantitative assay for measuring proteins in complex biological matrices. These assays can be highly precise and quantitative, but the frequent occurrence of interferences require that MRM-MS data be manually reviewed by an expert. The AuDIT module implements an algorithm that, in an automated manner, identifies inaccurate transition data based on the presence of interfering signal or inconsistent recovery between replicate samples. AuDIT reduces the time required for manual, subjective inspection of data, improves the overall accuracy of data analysis, and is easily implemented into the standard data analysis workflow.

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ESP Predictor

Development of targeted MS-based assays for detecting and quantifying changes in protein levels requires identification of peptides to use as quantitative surrogates for each candidate protein. The enhanced signature peptide predictor (ESPPredictor module) provides a means of predicting such 'signature peptides' from sequence alone.

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PEPPeR (LC-MS)

For the analysis of LC-MS data, GenePattern provides support for the algorithms defined by PEPPeR, a Platform for Experimental Proteomic Pattern Recognition:

The PEPPeR modules are based on work published by Jaffe, Mani, et al in PEPPeR, a Platform for Experimental Proteomic Pattern Recognition (Molecular & Cellular Proteomics 5:1927-1941, 2006).

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ProteoArray (LC-MS)

GenePattern's ProteoArray module provides the following support for the analysis of LC-MS data:

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SELDI/MALDI

GenePattern provides the following support for the analysis of SELDI/MALDI data:

The modules for the analysis of SELDI/MALDI data are based on work published by Mani and Gillette in Proteomic Data Analysis: Pattern Recognition for Medical Diagnosis and Biomarker Discovery (Mehmed Kantardzic and Jozef Zurada (Eds.) Next Generation of Data Mining Applications, Wiley-IEEE Press).

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Data Formats

Proteomics analysis modules are designed for easy access:

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Modules

View current GenePattern proteomics modules

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Updated on July 22, 2012 13:54