SAINTq: Scoring protein-protein interactions in affinity purification - mass spectrometry experiments with fragment or peptide intensity data.
SAINT (Significance Analysis of INTeractome) is a probabilistic method for scoring bait-prey interactions against negative controls in affinity purification - mass spectrometry (AP-MS) experiments. Our published SAINT algorithms use spectral counts or protein intensities as the input for calculating the probability of true interaction, which enables objective selection of high-confidence interactions with false discovery control. With the advent of new protein quantification methods such as Data Independent Acquisition (DIA), we redeveloped the scoring method to utilize the reproducibility information embedded in the peptide or fragment intensity data as a key scoring criterion, bypassing protein intensity summarization required in the previous SAINT workflow. The new software package, SAINTq, addresses key issues in the interaction scoring based on intensity data, including treatment of missing values and selection of peptides and fragments for scoring each prey protein. We applied SAINTq to two independent DIA AP-MS data sets profiling the interactome of MEPCE and EIF4A2 and that of 14-3-3β, and benchmarked the performance in terms of recovering previously reported literature interactions in the iRefIndex database. In both data sets, the SAINTq analysis using the fragment-level intensity data led to the most sensitive detection of literature interactions at the same level of specificity. This analysis outperforms the analysis using protein intensity data summed from fragment intensity data that is equivalent to the model in SAINTexpress.
Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore.
Guoci
G
Teo
Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore.
Hiromi
H
Koh
Department of Pathology, Yale University, New Haven, CT, USA.
Damian
D
Fermin
Lunenfeld-Tanenbaum Research Institute, Sinai Health Service, Ontario, Canada.
Jean-Philippe
JP
Lambert
Lunenfeld-Tanenbaum Research Institute, Sinai Health Service, Ontario, Canada.
James D R
JD
Knight
Lunenfeld-Tanenbaum Research Institute, Sinai Health Service, Ontario, Canada.|Department of Molecular Genetics, University of Toronto, Ontario, Canada.
Anne-Claude
AC
Gingras
Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore.|Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.
Hyungwon
H
Choi
D002846:Chromatography, Affinity / Q000379:methods*; D019295:Computational Biology; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000032:analysis*; D011485:Protein Binding
D010455:Peptides
Bioinformatics; Interaction; Protein-protein