MassIVE MSV000085570

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Optimization of SWATH-MS workflow for human blood serum proteome analysis using a Design of Experiments approach

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Description

Accurate identification and quantification of the human serum proteome can help identify biomarkers of disease. SWATH (Sequential Window Acquisition of all Theoretical Spectra) is a type of Data Independent Acquisition (DIA) method which allows proteome-wide coverage and high quantification reproducibility. Optimization of the liquid chromatography (LC) and mass spectrometry (MS) parameters is essential for acquiring high quality raw data that results in precise and consistent protein quantification. We used Design of Experiments (DoE) to first identify the most important LC-MS parameters and subsequently refine them at the same time to increase the number of proteins quantified in human serum. The number of SWATH windows and the MS/MS accumulation time have the most significant impact over SWATH outcome, affecting the results in an interdependent manner. Our approach can efficiently optimize multiple parameters simultaneously and it is adaptable to different samples and equipment. [doi:10.25345/C53T47] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: SWATH, acquisition parameters, serum, proteomic quantification, design of experiments, optimization

Contact

Principal Investigators:
(in alphabetical order) 		John Isaacs, Newcastle University, United Kingdom
Submitting User: ajp1986
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.