Mar 28, 2024

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

DOI
dx.doi.org/10.17504/protocols.io.q26g71rz3gwz/v1
  • 1Buck Institute for Research on Aging
  • Metabolomics Protocols & Workflows
    Tech. support email: bbmisraccb@gmail.com
M A Watson
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DOI: dx.doi.org/10.17504/protocols.io.q26g71rz3gwz/v1
Protocol Citation: Joanna Bons, J P Rose, M A 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 25, 2024
Last Modified: March 28, 2024
Protocol Integer ID: 97355
Keywords: LC-MS/MS, DIA, Orbitrap Eclipse, Proteomics, Mass Spectrometry, Spectronaut, Human, Secretome, SASP, Conditioned Media, Ovary
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)
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