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Diamond: a multi-modal DIA mass spectrometry data processing pipeline.

Chenxin Li1, Mingxuan Gao1, Wenxian Yang2

  • 1Department of Computer Science, School of Informatics, Xiamen University, 361005 Xiamen, China.

Bioinformatics (Oxford, England)
|January 8, 2021
PubMed
Summary
This summary is machine-generated.

A new pipeline called Diamond offers a unified solution for data-independent acquisition (DIA) mass spectrometry (MS) data processing. It integrates spectrum-centric scoring (SCS) and peptide-centric scoring (PCS) for both library-based and library-free modes.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Current data-independent acquisition (DIA) mass spectrometry (MS) data processing relies on separate tools for spectrum-centric scoring (SCS) and peptide-centric scoring (PCS).
  • A need exists for a comprehensive, automated, and accessible pipeline integrating both SCS and PCS strategies for DIA-MS analysis.

Purpose of the Study:

  • To develop Diamond, a Nextflow-based, containerized, multi-modal pipeline for DIA-MS data processing.
  • To integrate both SCS and PCS workflows within a single, user-friendly platform.
  • To support both library-based and library-free DIA-MS data analysis.

Main Methods:

  • Development of a Nextflow-based pipeline for DIA-MS data processing.
  • Containerization using Docker for reproducibility and accessibility.
  • Integration of spectrum-centric scoring (SCS) and peptide-centric scoring (PCS) algorithms.
  • Implementation of support for both library-based and library-free analysis modes.

Main Results:

  • Diamond provides a unified platform for peptide identification and quantification in DIA-MS data.
  • The pipeline successfully integrates both SCS and PCS strategies.
  • Diamond supports both library-based and library-free DIA-MS workflows.
  • The developed tool is designed for large-scale data processing, offering versatility and ease of use.

Conclusions:

  • Diamond addresses the lack of a fully automated, reproducible, and accessible pipeline for DIA-MS data processing.
  • The multi-modal pipeline enhances efficiency and flexibility in analyzing DIA-MS data.
  • Diamond serves as a valuable, extendable toolbox for the scientific community, facilitating large-scale proteomic studies.