Abstract

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, MaSS‐Simulator has been presented, 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. MaSS‐Simulator is assessed by comparing its performance against experimentally generated spectra and spectra obtained from NIST collections of …