Mar 22, 2024

Public workspaceData-Independent Acquisition (DIA) Data Processing using Spectronaut/directDIA (Biognosys): Whole Proteome Analysis of Human Whole Lung Tissue

DOI
https://dx.doi.org/10.17504/protocols.io.261ge5p8og47/v1
  • Joanna Bons1,
  • J P Rose1,
  • M Watson1,
  • B Schilling1
  • 1Buck Institute for Research on Aging
  • Cellular Senescence Network (SenNet) Method Development Community
M A Watson
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DOI: https://dx.doi.org/10.17504/protocols.io.261ge5p8og47/v1
Protocol Citation: Joanna Bons, J P Rose, M Watson, B Schilling 2024. Data-Independent Acquisition (DIA) Data Processing using Spectronaut/directDIA (Biognosys): Whole Proteome Analysis of Human Whole Lung Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.261ge5p8og47/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 22, 2024
Last Modified: March 22, 2024
Protocol Integer ID: 97130
Keywords: LC-MS/MS, DIA, Orbitrap Eclipse, Proteomics, Mass Spectrometry, Spectronaut, Lung , Human, proteolytic peptide measurement of human, proteolytic peptide measurement, whole proteome analysis of human whole lung tissue, tandem mass spectrometry, whole proteome analysis, orbitrap eclipse tribrid mass spectrometer, using spectronaut software, protein identification, spectronaut software, using spectronaut, processing dia data, dia data, biognosy, acquisition by data, human whole lung tissue, using liquid chromatography, liquid chromatography
Funders Acknowledgements:
NIH Grant
Grant ID: 5U54AG075932-02
NIH Grant
Grant ID: 5U54AG075932-03
Abstract
Proteolytic peptide measurement of Human whole lung tissue using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) Acquisition by Data-Independent Acquisition (DIA) on an Orbitrap Eclipse Tribrid Mass Spectrometer for peptide/protein identification and quantification by processing DIA data using Spectronaut software.
Materials
  • Spectronaut software (version 17.6.230428.55965; Biognosys)
Troubleshooting
Search the DIA data with Spectronaut using the spectral library-free directDIA algorithm against a Human UniProt-SwissProt proteome database (https://www.uniprot.org/proteomes), applying the settings described in Table 1.






Table 1. Settings for the data-independent acquisition data processing with Spectronaut/directDIA