ReviewProteomics2012
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments.
Review in Proteomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Protocol for analyzing protein interactomes under starvation in fission yeast using in vivo cross-linking.STAR protocols · 2026Article
- Article
- Characterizing host-microbe interactions with bacterial effector proteins using proximity-dependent biotin identification (BioID).Communications biology · 2025Review
- CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data.Molecular biology of the cell · 2021Article
- Global mapping of Salmonella enterica-host protein-protein interactions during infection.Cell host & microbe · 2021Article
- From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants.International journal of molecular sciences · 2021Review
- A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations.BMC genomics · 2019Article
- Experimental Analysis of Viral-Host Interactions.Frontiers in physiology · 2019Review
- Functional equivalence of germ plasm organizers.PLoS genetics · 2018Article
- PAF1 complex interactions with SETDB1 mediate promoter H3K9 methylation and transcriptional repression ofOncotarget · 2018Article
- Mapping of Plasma Membrane Proteins Interacting WithFrontiers in plant science · 2018Article
- Functional diversity of topological modules in human protein-protein interaction networks.Scientific reports · 2017Article
- Unravelling the biology of chromatin in health and cancer using proteomic approaches.Expert review of proteomics · 2017Review
- A two-step framework for inferring direct protein-protein interaction network from AP-MS data.BMC systems biology · 2017Article
- Automated multigroup outlier identification in molecular high-throughput data using bagplots and gemplots.BMC bioinformatics · 2017Article
- Proteome-Scale Human Interactomics.Trends in biochemical sciences · 2017Review
- Revealing Higher Order Protein Structure Using Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2016Article
- Article
- PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data.BioMed research international · 2016Article
- Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy.Methods in molecular biology (Clifton, N.J.) · 2016Article
Corrections and comments
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1 author.
Funding
Abstract
Analysis of protein interaction networks and protein complexes using affinity purification and mass spectrometry (AP/MS) is among most commonly used and successful applications of proteomics technologies. One of the foremost challenges of AP/MS data is a large number of false-positive protein interactions present in unfiltered data sets. Here we review computational and informatics strategies for detecting specific protein interaction partners in AP/MS experiments, with a focus on incomplete (as opposite to genome wide) interactome mapping studies. These strategies range from standard statistical approaches, to empirical scoring schemes optimized for a particular type of data, to advanced computational frameworks. The common denominator among these methods is the use of label-free quantitative information such as spectral counts or integrated peptide intensities that can be extracted from AP/MS data. We also discuss related issues such as combining multiple biological or technical replicates, and dealing with data generated using different tagging strategies. Computational approaches for benchmarking of scoring methods are discussed, and the need for generation of reference AP/MS data sets is highlighted. Finally, we discuss the possibility of more extended modeling of experimental AP/MS data, including integration with external information such as protein interaction predictions based on functional genomics data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.