Data Processing and Analysis for DIA-Based Phosphoproteomics Using Spectronaut
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Data Processing and Analysis for DIA-Based Phosphoproteomics Using Spectronaut. / Martinez-Val, Ana; Bekker-Jensen, Dorte Breinholdt; Hogrebe, Alexander; Olsen, Jesper Velgaard.
Proteomics Data Analysis. red. / Daniela Cecconi. Springer, 2021. s. 95-107 (Methods in Molecular Biology, Bind 2361).Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › fagfællebedømt
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TY - CHAP
T1 - Data Processing and Analysis for DIA-Based Phosphoproteomics Using Spectronaut
AU - Martinez-Val, Ana
AU - Bekker-Jensen, Dorte Breinholdt
AU - Hogrebe, Alexander
AU - Olsen, Jesper Velgaard
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
U2 - 10.1007/978-1-0716-1641-3_6
DO - 10.1007/978-1-0716-1641-3_6
M3 - Book chapter
C2 - 34236657
SN - 978-1-0716-1640-6
T3 - Methods in Molecular Biology
SP - 95
EP - 107
BT - Proteomics Data Analysis
A2 - Cecconi, Daniela
PB - Springer
ER -
ID: 280173836