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The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
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Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform.

Fengchao Yu¹, Guo Ci Teo², Andy T Kong^2,3

¹Department of Pathology, University of Michigan, Ann Arbor, MI, USA. yufe@umich.edu.

Nature Communications

|July 12, 2023

Summary

We introduce MSFragger-DIA, a rapid and sensitive method for peptide identification in data-independent acquisition (DIA) mass spectrometry (MS) proteomics. This approach enhances quantitative proteomic analysis across diverse biological samples.

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Area of Science:

Proteomics
Mass Spectrometry
Computational Biology

Background:

Liquid chromatography-mass spectrometry (LC-MS) is vital for quantitative proteomics.
Data-independent acquisition (DIA) is a powerful MS technique for comprehensive proteome profiling.
Existing DIA analysis tools can be computationally intensive and vary in performance.

Purpose of the Study:

To develop a fast, sensitive, and reproducible method for direct peptide identification from DIA-MS data.
To integrate this new method into a user-friendly computational platform.
To evaluate the performance of the new method against existing DIA analysis tools.

Main Methods:

Development of MSFragger-DIA, a novel algorithm leveraging the MSFragger search engine for direct peptide identification from DIA-MS spectra.
Integration of MSFragger-DIA into the FragPipe computational platform for streamlined DIA data analysis and spectral library generation.
Comparative analysis of MSFragger-DIA against established DIA tools (DIA-Umpire, Spectronaut, DIA-NN, MaxDIA) using diverse proteomic datasets.

Main Results:

MSFragger-DIA demonstrates fast and sensitive peptide identification directly from DIA-MS data.
The method achieves high accuracy across various sample types, including single-cell proteomics, phosphoproteomics, and tumor proteome profiling.
Integration into FragPipe ensures ease of use and reproducibility for DIA, data-dependent acquisition (DDA), or combined data analysis.

Conclusions:

MSFragger-DIA offers a significant advancement in DIA-MS data analysis, providing a rapid and accurate solution for peptide identification.
The FragPipe platform with MSFragger-DIA enhances the accessibility and efficiency of quantitative proteomics.
This approach is broadly applicable to various proteomic research areas, facilitating deeper biological insights.