Evidence map›Paper›PMID 34384350›Full record

ArticleClinical proteomics2021

Robust optimization of SWATH-MS workflow for human blood serum proteome analysis using a quality by design approach.

Edith Serrano-Blesa, Andrew Porter, Dennis W Lendrem, Costantino Pitzalis, Anne Barton, Achim Treumann, John D Isaacs

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Clinical proteomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.5field-weighted citation impact, top 42% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 4 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 5 institutions in 1 country.

Edith Serrano-BlesaNational Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
Andrew PorterNewcastle University Protein and Proteome Facility, Newcastle upon Tyne, UK.
Dennis W LendremNational Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
Costantino PitzalisCentre for Experimental Medicine and Rheumatology, Queen Mary University of London, London, UK.
Anne BartonVersus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre,, The University of Manchester, Manchester, UK.
Achim TreumannNewcastle University Protein and Proteome Facility, Newcastle upon Tyne, UK.
John D IsaacsNational Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK. john.isaacs@ncl.ac.uk.ORCID http://orcid.org/0000-0002-6103-7056
Newcastle University · GBNIHR Newcastle Biomedical Research Centre · GBManchester Academic Health Science Centre · GBNewcastle upon Tyne Hospitals NHS Foundation Trust · GBQueen Mary University of London · GB

Funding

Medical Research Council MR/K015346/1
6 · The paper itself

Abstract

backgroundIt is not enough to optimize proteomics assays. It is critical those assays are robust to operating conditions. Without robust assays, proteomic biomarkers are unlikely to translate readily into the clinic. This study outlines a structured approach to the identification of a robust operating window for proteomics assays and applies that method to Sequential Window Acquisition of all Theoretical Spectra Mass Spectroscopy (SWATH-MS).

methodsWe used a sequential quality by design approach exploiting a fractional screening design to first identify critical SWATH-MS parameters, then using response surface methods to identify a robust operating window with good reproducibility, before validating those settings in a separate validation study.

resultsThe screening experiment identified two critical SWATH-MS parameters. We modelled the number of proteins and reproducibility as a function of those parameters identifying an operating window permitting robust maximization of the number of proteins quantified in human serum. In a separate validation study, these settings were shown to give good proteome-wide coverage and high quantification reproducibility.

conclusionsUsing design of experiments permits identification of a robust operating window for SWATH-MS. The method gives a good understanding of proteomics assays and greater data-driven confidence in SWATH-MS performance.

Indexed as

Design of experimentsOptimizationProteomic quantificationQuality by designRobustnessScreeningSWATH-MS

Identifiers

PMID34384350
PMCPMC8359389
OpenAlexW3180748073

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.