Data Processing and Analysis for DIA-Based Phosphoproteomics Using Spectronaut
Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › fagfællebedømt
Data-independent acquisition (DIA) for liquid chromatography tandem mass spectrometry (LC-MS/MS) can improve the depth and reproducibility of the acquired proteomics datasets. DIA solves some limitations of the conventional data-dependent acquisition (DDA) strategy, for example, bias in intensity-dependent precursor selection and limited dynamic range. These advantages, together with the recent developments in speed, sensitivity, and resolution in MS technology, position DIA as a great alternative to DDA. Recently, we demonstrated that the benefits of DIA are extendable to phosphoproteomics workflows, enabling increased depth, sensitivity, and reproducibility of our analysis of phosphopeptide-enriched samples. However, computational data analysis of phospho-DIA samples have some specific challenges and requirements to the software and downstream processing workflows. A step-by-step guide to analyze phospho-DIA raw data using either spectral libraries or directDIA in Spectronaut is presented here. Furthermore, a straightforward protocol to perform differential phosphorylation site analysis using the output results from Spectronaut is described.
Originalsprog | Engelsk |
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Titel | Proteomics Data Analysis |
Redaktører | Daniela Cecconi |
Antal sider | 13 |
Forlag | Springer |
Publikationsdato | 2021 |
Sider | 95-107 |
Kapitel | 6 |
ISBN (Trykt) | 978-1-0716-1640-6 |
ISBN (Elektronisk) | 978-1-0716-1641-3 |
DOI | |
Status | Udgivet - 2021 |
Navn | Methods in Molecular Biology |
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Vol/bind | 2361 |
ISSN | 1064-3745 |
ID: 280173836