Simulation of mass spectrometry-based proteomics data with Synthedia

ABSTRACT: Abstract

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

SUBMITTER:  

PROVIDER: S-EPMC9825309 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature