Related Experiment Video
Updated: Dec 5, 2025
12:11
Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
Published on: February 27, 2020
7.2K
PASS-DIA: A Data-Independent Acquisition Approach for Discovery Studies
Dong-Gi Mun1, Santosh Renuse1,2, Mayank Saraswat1,3,4,5
1Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.
Analytical Chemistry
|October 20, 2020
Summary
Precursor ion And Small Slice-DIA (PASS-DIA) enhances proteome discovery by using small isolation windows for MS/MS spectra. This novel data-independent acquisition method significantly increases protein identification compared to traditional approaches.
Area of Science:
- Proteomics
- Mass Spectrometry
- Biochemistry
Background:
- Data-independent acquisition (DIA) is widely used for proteome identification and quantitation.
- Conventional DIA methods with wide isolation windows generate complex spectra, hindering peptide identification via database searches.
- Current DIA analysis relies on spectral libraries, limiting discovery of novel peptides and precluding its use in discovery studies.
Purpose of the Study:
- To introduce Precursor ion And Small Slice-DIA (PASS-DIA), a novel DIA strategy for enhanced proteome discovery.
- To enable direct application of conventional spectrum-centric analysis pipelines for peptide identification and quantitation.
- To improve the characterization of post-translationally modified peptides and low-abundance proteins.
Main Methods:
- PASS-DIA acquires MS/MS spectra using small isolation windows (slices).
- It interprets MS/MS spectra using accurately determined precursor ion masses.
- Conventional spectrum-centric analysis pipelines are applied for peptide identification and quantitation.
Main Results:
- PASS-DIA achieved 69% and 48% more protein identifications than data-dependent acquisition (DDA) and conventional DIA, respectively.
- It identified 77% more phosphopeptides, 56% more N-terminal acetylated peptides, and 83% more N-glycopeptides compared to DDA.
- Analysis of human fallopian tube organoids revealed 34% additional protein identifications and biologically relevant pathways, including low-abundance proteins.
Conclusions:
- PASS-DIA is a novel DIA approach that significantly outperforms DDA and conventional DIA for proteome discovery.
- This method enables deeper proteome characterization, including post-translational modifications and low-abundance proteins.
- PASS-DIA is a valuable tool for discovery-type proteomic studies requiring comprehensive characterization.
