TY - JOUR
T1 - Implementing the reuse of public DIA proteomics datasets
T2 - from the PRIDE database to Expression Atlas
AU - Walzer, Mathias
AU - García-Seisdedos, David
AU - Prakash, Ananth
AU - Brack, Paul
AU - Crowther, Peter
AU - Graham, Robert L
AU - George, Nancy
AU - Mohammed, Suhaib
AU - Moreno, Pablo
AU - Papatheodorou, Irene
AU - Hubbard, Simon J
AU - Vizcaíno, Juan Antonio
N1 - © 2022. The Author(s).
PY - 2022/6/14
Y1 - 2022/6/14
N2 - The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets.
AB - The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets.
KW - Data Analysis
KW - Databases, Protein
KW - Datasets as Topic
KW - Mass Spectrometry/methods
KW - Proteomics/methods
KW - Software
U2 - 10.1038/s41597-022-01380-9
DO - 10.1038/s41597-022-01380-9
M3 - Article
C2 - 35701420
SN - 2052-4463
VL - 9
SP - 335
JO - Scientific Data
JF - Scientific Data
IS - 1
ER -