Data Independent Acquisition (DIA) Proteomics Resources

Proteome Software wants to help you make the best use of its products through effective support and informational resources. We have compiled the list below to assist you in getting starting doing DIA proteomics. Please let us know if there are any additional resources you find useful and we'll be happy to update this page for the community.

White Papers and Publications

Designing DIA mass spectrometry methods
A white paper that describes how to set up DIA MS methods on Thermo instruments.

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
An experimental workflow that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic peak shape and retention time for every detectable peptide in a proteomics experiment.

Generating high-quality libraries for DIA-MS with empirically-corrected peptide predictions
A library generation workflow that leverages fragmentation and retention time prediction to build libraries containing every peptide in a proteome, and then refines those libraries with empirical data.

Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries
An illustration on how to acquire, queue, and validate DIA data without spectrum libraries, and provide a workflow to efficiently generate DIA-only chromatogram libraries using gas-phase fractionation (GPF)

Online Resources

Prosit-derived spectral libraries
A repository of spectral libraries for common organisms which are available below. If you would like us to make a specific Prosit library for you, please contact us with an organism-specific FASTA

Scaffold DIA video tutorials
Three-part tutorial, from getting started to loading your data into Scaffold DIA

An ABRF study to evaluate data-independent acquisition
An in-depth look at how DIA is being used, including software applications, in core facilities around the globe, with an aim to eliminate barriers to adoption.

Thermo windowing schemes for DIA proteomics
Here is a spreadsheet outlining the preferred LC-MS methods for performing reference library runs and experimental runs for DIA experiments.

Software and Tools

Scaffold DIA: data-independent analysis of proteomics experiments
Scaffold DIA is an identification and quantification program for data independent acquisition (DIA) proteomics and is designed to help researchers identify, organize, summarize, refine, quantitate, and visualize experiment results.

EncyclopeDIA: library searching for data independent acquisition
Comprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries. Searle et al, Nat Commun 9, 5128 (2018)

DIA-Umpire: computational analysis for mass spectrometry-based proteomics data
Produces MGFs from DIA data that can be searched in DDA search engines such as Mascot and Sequest (Proteme Discoverer), the results of which can be loaded into Scaffold. Tsou, C, Avtonomov, D, Larsen, B et al, Nat Methods 12, 258–264 (2015).

Skyline: SRM, MRM, PRM, DIA-SWATH, and targeted DDA
Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), DIA/SWATH and targeted DDA quantitative methods and analyzing the resulting mass spectrometer data. Brendan MacLean, et al, Bioinformatics, Volume 26, Issue 7, 1 April 2010, Pages 966–968