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Updated: Aug 12, 2025

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes
Published on: May 4, 2020
Simulation of mass spectrometry-based proteomics data with Synthedia
Michael G Leeming1, Ching-Seng Ang1, Shuai Nie1
1Bio21 Molecular Science & Biotechnology Institute, Melbourne Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, VIC 3052, Australia.
Motivation:
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 (DIA) strategies.
Results:
Here, we present Synthedia-a software package to simulate DIA liquid chromatography-mass spectrometry for bottom-up proteomics experiments. Synthedia can generate datasets with known peptide precursor ions and fragments and allows for the customization of a wide variety of chromatographic and mass spectrometry parameters.
Availability And Implementation:
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 Information:
Supplementary data are available at Bioinformatics Advances online.
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