Mar 29, 2024

Public workspaceData-Independent Acquisition (DIA) Data Processing using Spectronaut/directDIA (Biognosys): Secretome Analysis

DOI
https://dx.doi.org/10.17504/protocols.io.q26g71rz3gwz/v1
  • Joanna Bons1,
  • J P Rose1,
  • M Watson1,
  • B Schilling1
  • 1Buck Institute for Research on Aging
M A Watson
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DOI: https://dx.doi.org/10.17504/protocols.io.q26g71rz3gwz/v1
Protocol Citation: Joanna Bons, J P Rose, M Watson, B Schilling 2024. Data-Independent Acquisition (DIA) Data Processing using Spectronaut/directDIA (Biognosys): Secretome Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.q26g71rz3gwz/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 26, 2024
Last Modified: March 29, 2024
Protocol Integer ID: 97355
Keywords: LC-MS/MS, DIA, Orbitrap Eclipse, Proteomics, Mass Spectrometry, Spectronaut, Human, Secretome, SASP, Conditioned Media, Ovary, secretome analysis proteolytic peptide measurement of secretome sample, secretome sample, secretome analysis, proteolytic peptide measurement, tandem mass spectrometry, orbitrap eclipse tribrid mass spectrometer, using spectronaut software, spectronaut software, dia data, processing dia data, using spectronaut, protein identification, biognosy, acquisition by data, using liquid chromatography, liquid chromatography
Abstract
Proteolytic peptide measurement of secretome samples 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