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Differential protein expression software tools | Mass spectrometry-based untargeted proteomics

Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein's associated spectral peaks.

Source text:
(Wang et al., 2012) A hybrid approach to protein differential expression in mass spectrometry-based proteomics. Bioinformatics.

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EBprot
A probabilistic framework that directly models the peptide-protein hierarchy and rewards the proteins with reproducible evidence of differential expression (DE) over multiple peptides. To evaluate its performance with known DE states, we conducted a simulation study to show that the peptide-level analysis of EBprot provides better receiver-operating characteristic and more accurate estimation of the false discovery rates than the methods based on protein-level ratios. We also demonstrate superior classification performance of peptide-level EBprot analysis in a spike-in dataset. EBprot is a robust alternative to the existing statistical methods for the DE analysis of labeling-based quantitative datasets.
SPIQuE / Statistical Processing for Isobaric Quantitation Evaluation
Assists in the determination of differentially expressed proteins from isobaric tag-labelled proteomics data by the calculation of quality-weighted statistics and ratios. SPIQuE is a web application that allows users to upload their own data and uses a defined multi-feature weighing model to maximize the emphasis of those quantitations. It includes options for normalization, statistical testing, group testing and peptide spectrum match (PSM).
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