Efficient Database Search via Tensor Distribution Bucketing

Mongia, Mihir; Soudry, Benjamin; Davoodi, Arash Gholami; Mohimani, Hosein

In mass spectrometry-based proteomics, one needs to search billions of mass spectra against the human proteome with billions of amino acids, where many of the amino acids go through post-translational modifications. In order to account for novel modifications, we need to search all the spectra against all the peptides using a joint probabilistic model that can be learned from training data. Assuming M spectra and N possible peptides, currently the state of the art search methods have runtime of O(MN). Here, we propose a novel bucketing method that sends pairs with high likelihood under the joint probabilistic model to the same bucket with higher probability than those pairs with low likelihood. We demonstrate that the runtime of this method grows sub-linearly with the data size, and our results show that our method is orders of magnitude faster than methods from the locality sensitive hashing literature. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this chapter (10.1007/978-3-030-47436-2_26) contains supplementary material, which is available to authorized users.