Data Processing and Analysis for DIA-Based Phosphoproteomics Using Spectronaut
Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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.
Original language | English |
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Title of host publication | Proteomics Data Analysis |
Editors | Daniela Cecconi |
Number of pages | 13 |
Publisher | Springer |
Publication date | 2021 |
Pages | 95-107 |
Chapter | 6 |
ISBN (Print) | 978-1-0716-1640-6 |
ISBN (Electronic) | 978-1-0716-1641-3 |
DOIs | |
Publication status | Published - 2021 |
Series | Methods in Molecular Biology |
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Volume | 2361 |
ISSN | 1064-3745 |
ID: 280173836