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AP-MS analysis software tools | MS-based targeted proteomics

Identifying the interactions established by a protein of interest can be a critical step in understanding its function. This is especially true when an unknown protein of interest is demonstrated to physically interact with proteins of known…
MiST
Web
Desktop

MiST mass spectrometry interaction statistics

Discovers protein interactions in an unbiased manner. MiST allows to perform…

Discovers protein interactions in an unbiased manner. MiST allows to perform quality controls, to process raw affinity purification mass spectrometry (APMS) data, and to prioritize biologically…

compPASS
Desktop

compPASS comparative proteomic analysis software suite

Allows to analyze proteomic data. The compPASS method gives confidence…

Allows to analyze proteomic data. The compPASS method gives confidence measurements to interactions from parallel non-reciprocal proteomic datasets in using unbiased metrics. This tool is applicable…

SAINT
Desktop

SAINT Significance Analysis of INTeractome

A computational tool assigning confidence scores to protein-protein…

A computational tool assigning confidence scores to protein-protein interactions based on affinity purification-mass spectrometry (AP-MS) data. SAINT is a method able to analyse a specific dataset to…

CRAPome
Dataset

CRAPome Contaminant Repository for Affinity Purification

A resource to score protein-protein interactions. CRAPome stores, annotates and…

A resource to score protein-protein interactions. CRAPome stores, annotates and standardizes negative controls generated by the proteomics research community and enables their use for scoring…

SFINX
Web
Desktop

SFINX Straightforward Filtering INdeX

Provides access to the straightforward filtering index (SFINX) for the…

Provides access to the straightforward filtering index (SFINX) for the separation of true positive from false positive protein interactions in affinity purification – mass spectrometry (AP-MS)…

compleXView
Web

compleXView

Offers interactive graphical features for the manipulation and interpretation…

Offers interactive graphical features for the manipulation and interpretation of the interaction maps. With compleXView user can colour preys based on their relative abundances in single-bait…

PIPINO
Desktop

PIPINO Protein-Protein Interaction Optimizer

A software to identify protein-protein interactions based on affinity…

A software to identify protein-protein interactions based on affinity purified-mass spectrometry (AP-MS) data. PIPINO is an automatic data analyser able to facilitate the selection of bona fide…

Spotlite
Web

Spotlite

A platform to reveal physical, functional and disease-relevant characteristics…

A platform to reveal physical, functional and disease-relevant characteristics within affinity purification mass spectrometry (APMS) data. Spotlite tool executes both the enhance and original APMS…

Reinforce
Desktop

Reinforce Rank aggrEgatIon aNd False discOvery Rate Control based prEdiction

Assists users to check the quality of generated protein-protein interaction…

Assists users to check the quality of generated protein-protein interaction (PPI) networks. Reinforce is an algorithm that runs on three steps: (1) data pre-processing; (2) rank aggregation; (3) and…

Decontaminator
Desktop

Decontaminator

A confidence assessment algorithm identifying false-positive protein-protein…

A confidence assessment algorithm identifying false-positive protein-protein interactions in affinity purification-mass spectrometry (AP-MS) experiments. Decontaminator use a limited number of high…

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