Simulation of mass spectrometry-based proteomics data with Synthedia


 
 
 A large number of experimental and bioinformatic parameters must be set to identify and quantify peptides in mass spectrometry experiments and each of these will impact the results. An ability to simulate raw data with known contents would allow researchers to rapidly explore the effects of varying experimental parameters and systematically investigate downstream processing software. A range of data simulators are available for established data-dependent acquisition methodologies but these do not extend to the rapidly developing field of data-independent acquisition strategies.
 
 
 
 Here, we present Synthedia—a software package to simulate data-independent acquisition liquid chromatography mass spectrometry for bottom-up proteomics experiments. Synthedia can generate datasets with known peptide precursor ions and fragments and allows for customisation of a wide variety of chromatographic and mass spectrometry parameters.
 
 
 
 Synthedia is freely available via the internet and can be used through a graphical website (https://synthedia.org/) or locally via the command line (https://github.com/mgleeming/synthedia/)
 
 
 
 Supplementary data are available at Bioinformatics online.
