ArticleJournal of the American Society for Mass Spectrometry2023
The Edge Effect in High-Throughput Proteomics: A Cautionary Tale.
Article in Journal of the American Society for Mass Spectrometry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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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.
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Who cites it
11 citing papers in PubMed.
- MSstatsQC-ML: A Supervised Machine Learning Approach to Monitor System Suitability and Quality Control in Mass Spectrometry-Based Proteomics.Journal of proteome research · 2026Article
- Development and Validation of a Streamlined Workflow for Proteomic Analysis of Proteins and Post-translational Modifications from Dried Blood.Journal of proteome research · 2026Article
- A High-Throughput Automation Platform for Accelerated AAV Stability Optimization.Pharmaceutics · 2026Article
- MR-SPJournal of proteome research · 2026Article
- Harnessing New Tools for Old Challenges: Optimising Neat Plasma Proteomics with Automation and Gas-Phase Fractionation.ACS measurement science au · 2026Article
- Covariate balanced allocation of samples to batches to mitigate the impacts of technical variability.Bioinformatics advances · 2026Article
- Proteomic Analysis of COVID-19 Infection.Advances in experimental medicine and biology · 2026Article
- Development and validation of a streamlined workflow for proteomic analysis of proteins and post-translational modifications from dried blood.bioRxiv : the preprint server for biology · 2025Article
- Automation of a Capillary-Wave Microbioreactor Platform to Enhance Phage Sensitivity Screen Efficiency.Engineering in life sciences · 2025Article
- Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer.Journal of biomolecular techniques : JBT · 2024Article
- Use of Nonhuman Sera as a Highly Cost-Effective Internal Standard for Quantitation of Multiple Human Proteins Using Species-Specific Tryptic Peptides: Applicability in Clinical LC-MS Analyses.Journal of proteome research · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In order for mass spectrometry to continue to grow as a platform for high-throughput clinical and translational research, careful consideration must be given to quality control by ensuring that the assay performs reproducibly and accurately and precisely. In particular, the throughput required for large cohort clinical validation in biomarker discovery and diagnostic screening has driven the growth of multiplexed targeted liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) assays paired with sample preparation and analysis in multiwell plates. However, large scale MS-based proteomics studies are often plagued by batch effects: sources of technical variation in the data, which can arise from a diverse array of sources such as sample preparation batches, different reagent lots, or indeed MS signal drift. These batch effects can confound the detection of true signal differences, resulting in incorrect conclusions being drawn about significant biological effects or lack thereof. Here, we present an intraplate batch effect termed the edge effect arising from temperature gradients in multiwell plates, commonly reported in preclinical cell culture studies but not yet reported in a clinical proteomics setting. We present methods herein to ameliorate the phenomenon including proper assessment of heating techniques for multiwell plates and incorporation of surrogate standards, which can normalize for intraplate variation.
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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.