Spotlite: Web application and augmented algorithms for predicting co-complexed proteins from affinity purification - Mass spectrometry data

Dennis Goldfarb, Bridgid E. Hast, Wei Wang, Michael B. Major

Research output: Contribution to journalArticle

13 Scopus citations

Abstract

Protein-protein interactions defined by affinity purification and mass spectrometry (APMS) suffer from high false discovery rates. Consequently, lists of potential interactions must be pruned of contaminants before network construction and interpretation, historically an expensive, time-intensive, and error-prone task. In recent years, numerous computational methods were developed to identify genuine interactions from the hundreds of candidates. Here, comparative analysis of three popular algorithms, HGSCore, CompPASS, and SAINT, revealed complementarity in their classification accuracies, which is supported by their divergent scoring strategies. We improved each algorithm by an average area under a receiver operating characteristics curve increase of 16% by integrating a variety of indirect data known to correlate with established protein-protein interactions, including mRNA coexpression, gene ontologies, domain-domain binding affinities, and homologous protein interactions. Each APMS scoring approach was incorporated into a separate logistic regression model along with the indirect features; the resulting three classifiers demonstrate improved performance on five diverse APMS data sets. To facilitate APMS data scoring within the scientific community, we created Spotlite, a user-friendly and fast web application. Within Spotlite, data can be scored with the augmented classifiers, annotated, and visualized (http://cancer.unc.edu/majorlab/software.php). The utility of the Spotlite platform to reveal physical, functional, and disease-relevant characteristics within APMS data is established through a focused analysis of the KEAP1 E3 ubiquitin ligase.

Original languageEnglish
Pages (from-to)5944-5955
Number of pages12
JournalJournal of Proteome Research
Volume13
Issue number12
DOIs
StatePublished - Dec 5 2014
Externally publishedYes

Keywords

  • KEAP1
  • affinity purification mass spectrometry
  • bioinformatics
  • machine learning
  • protein-protein interactions

Fingerprint Dive into the research topics of 'Spotlite: Web application and augmented algorithms for predicting co-complexed proteins from affinity purification - Mass spectrometry data'. Together they form a unique fingerprint.

  • Cite this