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MiST / mass spectrometry interaction statistics
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 relevant bait-prey pairs in a set of replicated APMS experiments. This tool provides the MiST score which is a weighted sum of three features: (1) normalized protein abundance (abundance); (2) invariability of abundance over replicated experiments (reproducibility) and (3) a measure of how unique a bait-prey pair is compared to all other baits (specificity).
SAINT / Significance Analysis of INTeractome
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 compute interaction probabilities with an incorporation of negative controls. Theses controls are commonly generated as a part of the experimental study but can be applied to large datasets in the absence of such data. SAINT can also estimate the spectral count distribution for false interactions directly from the negative controls.
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 experiments and multiple purifications can be directly compared in a ‘Blot’ plot representation. It aims to provide an analysis tool for biologists to identify and interpret protein complexes in their pull-down studies, more particularly the combination and visualization of quantitative and connectivity data.
SFINX / Straightforward Filtering INdeX
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) datasets. SFINX maintains the reliability and user-friendliness of the SFINX web site interface but is faster, unlimited in input size, and can be run locally within R. It is not only useful for the filtering of AP-MS data, but also for similar types of data resulting from other co-complex interatomic technologies, such as TAP-MS, Virotrap and BioID.
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 scoring methods on novel data sets. So, the resulting protein interactions are annotated for function, model organism phenotype and human disease relevance. It employs a logistic regression classifier that integrates gene coexpression patterns, functional annotations, proteins domains and homologous interactions.
PIPINO / Protein-Protein Interaction Optimizer
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 binding partners and to compare the dynamic of interaction networks. Also, a comprehensive interaction network is created and used for the data analysis of a specific protein of interest. PIPINO use a large amount of data formats while enlarging the information space through curated interaction databases.
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