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. 2012 Apr 6;11(4):2619-24.
doi: 10.1021/pr201185r. Epub 2012 Mar 2.

SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments

Hyungwon Choi  1 , Timo Glatter, Mathias Gstaiger, Alexey I Nesvizhskii
Affiliations

SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments

Hyungwon Choi et al. J Proteome Res. .

Abstract

We present a statistical method SAINT-MS1 for scoring protein-protein interactions based on the label-free MS1 intensity data from affinity purification-mass spectrometry (AP-MS) experiments. The method is an extension of Significance Analysis of INTeractome (SAINT), a model-based method previously developed for spectral count data. We reformulated the statistical model for log-transformed intensity data, including adequate treatment of missing observations, that is, interactions identified in some but not all replicate purifications. We demonstrate the performance of SAINT-MS1 using two recently published data sets: a small LTQ-Orbitrap data set with three replicate purifications of single human bait protein and control purifications and a larger drosophila data set targeting insulin receptor/target of rapamycin signaling pathway generated using an LTQ-FT instrument. Using the drosophila data set, we also compare and discuss the performance of SAINT analysis based on spectral count and MS1 intensity data in terms of the recovery of orthologous and literature-curated interactions. Given rapid advances in high mass accuracy instrumentation and intensity-based label-free quantification software, we expect that SAINT-MS1 will become a useful tool allowing improved detection of protein interactions in label-free AP-MS data, especially in the low abundance range.

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Figures

Figure 1
Figure 1
Intensity plotted against spectral count in the QUBIC and Drosophila-Insulin datasets. Peptides with intensity but missing MS/MS identification were removed. Dots under the dashed lines indicate observations with spectral counts but missing intensity values. All axes were drawn in the natural log scale.
Figure 2
Figure 2
The ROC curves for Drosophila-Insulin dataset comparing SAINT-MS1 (intensity) and SAINT (spectral count). The selected interactions were benchmarked against (a) orthologous interaction partners and (b) interactions previously catalogued in the literature (BioGRID database).
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