iSwathX 2.0 for processing DDA spectral libraries for DIA data analysis

Zainab Noor, Abidali Mohamedali, Shoba Ranganathan*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    2 Citations (Scopus)
    16 Downloads (Pure)


    The iSwathX web application processes and normalizes mass spectrometry−based proteomics spectral libraries generated in the data-dependent acquisition (DDA) approach. These libraries are stored in various proteomics repositories such as PeptideAtlas and NIST, or are user-generated and provide reference data for data-independent acquisition (DIA) targeted data extraction and analysis. iSwathX 2.0 can efficiently normalize DDA data from different instruments, gathered at different instances, and make it compatible with specific DIA experiments. Novel functions for parallel processing of DDA libraries and DIA report files, along with various data visualizations, are available in iSwathX 2.0. The step-by-step protocols provided here describe how the libraries are uploaded, processed, visualized, and downloaded using various modules of the application. They also provide detailed guidelines on the use of DIA report files for data analysis and visualization.

    Original languageEnglish
    Article numbere101
    Pages (from-to)1-13
    Number of pages13
    JournalCurrent Protocols in Bioinformatics
    Issue number1
    Publication statusPublished - Jun 2020


    • mass spectrometry
    • proteomics
    • protein identification
    • protein characterization
    • bioinformatics tools
    • proteome


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