MaSS-Simulator: A highly configurable simulator for generating MS/MS datasets for benchmarking of proteomics algorithms

摘要

Mass Spectrometry (MS) based proteomics has become an essential tool in the study of proteins. With the advent of modern MS machines huge amounts of data is being generated which can only be processed by novel algorithmic tools. However, in the absence of data benchmarks and ground truth datasets algorithmic integrity testing and reproducibility is a challenging problem. To this end, we present MaSS-Simulator, which is an easy to use simulator and can be configured to simulate MS/MS datasets for a wide variety of conditions with known ground truths. MaSS-Simulator offers many configuration options to allow the user a great degree of control over the test datasets which can enable rigorous and large- scale testing of any proteomics algorithm. We assessed MaSS-Simulator by comparing its performance against experimentally generated spectra and spectra obtained from NIST collections of spectral library. Our results showed that MaSS-Simulator generated spectra matched closely with real-spectra and had a relative-error distribution centered around 25%. In contrast the theoretical spectra for same peptides had relative-error distribution centered around 150%. MaSS-Simulator will enable developers to specifically highlight the capabilities of their algorithms and provide a strong proof of any pitfalls they might face. Source code, executables and a user manual for MaSS-Simulator can be downloaded from