Dataset Information

The DIALib-QC software tool for the systematic assessment of spectral library quality in data-independent acquisition proteomics

ABSTRACT: DIALib-QC (DIA library quality control) tool is used for the systematic evaluation of a spectral library’s characteristics, completeness and mass-accuracy ensuring correct identification and accurate quantitation of peptides and proteins from DIA/SWATH processing tools.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Erythrocyte, Acute Myeloid Leukemia Cell Line

SUBMITTER: Mukul Midha

LAB HEAD: Prof. Robert L. Moritz

PROVIDER: PXD020953 | Pride | 2020-10-16

REPOSITORIES: Pride

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Publications

DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics.

Midha Mukul K MK Campbell David S DS Kapil Charu C Kusebauch Ulrike U Hoopmann Michael R MR Bader Samuel L SL Moritz Robert L RL

Nature communications 20201016 1

Data-independent acquisition (DIA) mass spectrometry, also known as Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH), is a popular label-free proteomics strategy to comprehensively quantify peptides/proteins utilizing mass spectral libraries to decipher inherently multiplexed spectra collected linearly across a mass range. Although there are many spectral libraries produced worldwide, the quality control of these libraries is lacking. We present the DIALib-QC (DIA library qu ...[more]

PMID: 33067471

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Project description:Chronic lymphocytic leukaemia (CLL) is renowned for its variable clinical course and response to therapy, suggesting a role for precision medicine. However, the molecular basis of CLL variability remains incompletely understood. Recent developments in data independent acquisition (DIA) -MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. This report describes the sample replication and data handling requirements for SWATH-MS analysis of clinical samples. A CLL-specific spectral library compromising over 1,500,000 spectra with digital information for over 150,000 peptides has been generated to enable the quantification of up to 7736 proteins. To assess the reproducibility of the assay, SWATH-MS analysis was performed on 6 cryopreserved CLL patient samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins (<1% FDR) across 54 SWATH-MS acquisitions. These analyses showed that SWATH-MS is a highly reproducible technique. However, replicate sample preparations on different days was identified as the main source of variation. To overcome the effect of variation between sample preparation batches, different computational approaches for batch correction were tested. All approaches successfully removed technical variability whilst retaining proteomic differences between clinical subgroups. Functional enrichment analysis of proteins associated to IGHV mutational status highlighted the importance of metabolic remodelling in the biology of CLL and overlapped significantly with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was developed. This approach could be used to drive the design of future CLL SWATH-MS studies. These fundamental requirements for DIA approaches should be widely applicable to other clinical proteomics studies.

Dataset Information

The DIALib-QC software tool for the systematic assessment of spectral library quality in data-independent acquisition proteomics

Publications

DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics.

Similar Datasets

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