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Differential protein expression software tools | MS-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…
Perseus
Desktop

Perseus

Aims to proteomics data analyses. Perseus extracts biologically meaningful…

Aims to proteomics data analyses. Perseus extracts biologically meaningful information from processed raw files. It uses bioinformatic analyses from MaxQuant output and completes the proteomics…

RankProd
Desktop

RankProd

Allows detection of differentially expressed features in molecular profiling…

Allows detection of differentially expressed features in molecular profiling experiments. RankProd is a non-parametric method that provides a robust and reliable implementation of the Rank Product…

binda
Desktop

binda

A simple yet effective approach for identifying differentially expressed…

A simple yet effective approach for identifying differentially expressed proteins using binary discriminant analysis. This approach works by data-adaptive thresholding of protein expression values…

ProteoSign
Web

ProteoSign

Offers a user-friendly, web based interface, dedicated in protein differential…

Offers a user-friendly, web based interface, dedicated in protein differential expression analysis. The ProteoSign platform is made for protein differential expression/abundance analysis. It was…

EBprot
Desktop

EBprot

A probabilistic framework that directly models the peptide-protein hierarchy…

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…

QPROT
Desktop

QPROT

A statistical framework with computational software tool for comparative…

A statistical framework with computational software tool for comparative quantitative proteomics analysis. QPROT features various extensions of QSPEC method originally built for spectral count data…

xuan_code
Desktop

xuan_code

A statistical method for protein differential expression, based on a simple…

A statistical method for protein differential expression, based on a simple Binomial likelihood. This enables the researcher to extract more information from a quantitative proteomic dataset than…

MZDASoft
Desktop

MZDASoft

Allows implementation of PeakLink for multiple sample comparison. MZDASoft aims…

Allows implementation of PeakLink for multiple sample comparison. MZDASoft aims to allow higher protein comparison coverage across multiple samples. It is composed of two modules. MZDASoft PPE saves…

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