Proteomic analysis involves comparing and quantifying differences in protein expression among several conditions. To perform such analyses, most laboratories utilize mass spectrometry, a robust, unbiased, and reliable technology that allows for the identification and characterization of peptides and proteins.
The most common approach applies shotgun proteomics, using data-independent acquisition (DIA), data-dependent acquisition (DDA), or a combination of both strategies. Both DDA and DIA are considered discovery-based approaches in bottom-up proteomics. This means that in both cases, proteins are enzymatically digested into smaller peptides and information is extracted from peptides to infer conclusions at the protein level.
This blog post will briefly introduce both DDA and DIA approaches in proteomic analysis and highlight innovative products that are available to apply them effectively.
In DIA virtually all peptides are fragmented together and then analyzed using mass spectrometry. This technique results in complex fragmentation (MS2) spectra, but collects MS2 data for all peptides across the entire retention time range. After these initial steps, DIA approaches employ a spectral library to extract information from the highly rich data and allow for quantification at MS2 level. Because of these characteristics, DIA offers unmatched precision and quantitative accuracy, improved replicability, and a more comprehensive peptide sampling than DDA.
Biognosys’ Spectronaut® software performs DIA data analysis with the most advanced algorithms available, allowing deep proteome coverage and comprehensive measurements. This can characterize thousands of proteins, making it ideal for large-scale experiments.
In contrast to DIA, the mass spectrometer in DDA mode selects only certain peptides and then fragments them, ideally one at a time. While DIA is the superior acquisition method for quantitative goals, DDA is the preferred method for library generation and database searches due to its near peptide-specific MS2 spectra. This is particularly true when combined with deep fractionation. DDA can speedily provide identification results based on search engine algorithms applied to existing protein databases.
Biogynosys’ software developers created SpectroMine™ specifically for DDA applications. SpectroMine is suitable for both label-free and labeled approaches like TMT, and can give precise analytical measurements on a peptide level. Its workflow is designed as an all-in-one system integrating spectral data processing, identifications, visualizations, and quantification abilities. The latest version of SpectroMine features search engine capabilities with powerful deep learning augmentation, which greatly expands the performance of DDA in proteomics research.
Biognosys is an industry leading developer of solutions for mass spectrometry proteomics. By developing advanced DDA and DIA solutions for proteomics, Biognosys is at the frontier of protein studies.
The Biognosys team is dedicated to continuously upgrading the company’s products to support the most recent advances in proteomics technology. The recently released Spectronaut 15 for DIA data analysis is equipped with the most advanced deep learning technology and a comprehensive protein modification analysis workflow.
Biognosys also launched an updated version of the SpectroMine software last year. SpectroMine 3 raises the standards for DDA data acquisition and analysis with its industry-leading identification performance and processing speed.
Research laboratories in both academic and industrial spheres can benefit from the innovative Biognosys DDA and DIA products and services. In doing so, the scientific and technological communities can amplify the power of proteomics to transform life sciences.
To find out more about Biognosys proteomics software solutions, contact us today.