ArticleAnalytical chemistry2013
Optimized nonlinear gradients for reversed-phase liquid chromatography in shotgun proteomics.
Article in Analytical chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups.Nature communications · 2026Article
- Toward an Integrated Machine Learning Model of a Proteomics Experiment.Journal of proteome research · 2023Review
- Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases.International journal of molecular sciences · 2022Review
- Reconsidering adsorption in hemodialysis: is it just an epiphenomenon? A narrative review.Journal of nephrology · 2022Review
- Article
- Quantification of Cardiovascular Disease Biomarkers in Human Platelets by Targeted Mass Spectrometry.Proteomes · 2017Article
- Dinosaur: A Refined Open-Source Peptide MS Feature Detector.Journal of proteome research · 2016Article
- Improving the Sensitivity, Resolution, and Peak Capacity of Gradient Elution in Capillary Liquid Chromatography with Large-Volume Injections by Using Temperature-Assisted On-Column Solute Focusing.Analytical chemistry · 2016Article
- Exploring the potential of public proteomics data.Proteomics · 2016Review
- Challenges and Strategies for Proteome Analysis of the Interaction of Human Pathogenic Fungi with Host Immune Cells.Proteomes · 2015Review
- Heat shock proteins and hormesis in the diagnosis and treatment of neurodegenerative diseases.Immunity & ageing : I & A · 2015Review
- GOAT--a simple LC-MS/MS gradient optimization tool.Proteomics · 2014Article
Corrections and comments
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Reversed-phase liquid chromatography has become the preferred method for separating peptides in most of the mass spectrometry-based proteomics workflows of today. In the way the technique is typically applied, the peptides are released from the chromatography column by the gradual addition of an organic buffer according to a linear function. However, when applied to complex peptide mixtures, this approach leads to unequal spreads of the peptides over the chromatography time. To address this, we investigated the use of nonlinear gradients, customized for each setup at hand. We developed an algorithm to generate optimized gradient functions for shotgun proteomics experiments and evaluated it for two data sets consisting each of four replicate runs of a human complex sample. Our results show that the optimized gradients produce a more even spread of the peptides over the chromatography run, while leading to increased numbers of confident peptide identifications. In addition, the list of peptides identified using nonlinear gradients differed considerably from those found with the linear ones, suggesting that such gradients can be a valuable tool for increasing the proteome coverage of mass spectrometry-based experiments.
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