ArticleF1000Research2013
The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics.
Article in F1000Research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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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.
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Who cites it
36 citing papers in PubMed.
- Unveiling the Proteomic Landscape of Extracellular Vesicles: Implications for Neurodegeneration and Neuroprotection.Journal of neurochemistry · 2026Review
- Tear fluid proteomics: a comparative study of DIA and DDA mass spectrometry.Journal of mass spectrometry and advances in the clinical lab · 2025Article
- Blood proteome profiling for biomarker discovery in broilers with necrotic enteritis.Scientific reports · 2025Article
- SpectroPipeR-a streamlining post Spectronaut® DIA-MS data analysis R package.Bioinformatics (Oxford, England) · 2025Article
- Instrumentation at the Leading Edge of Proteomics.Analytical chemistry · 2024Review
- Dietary Mg Supplementation Decreases Oxidative Stress, Inflammation, and Vascular Dysfunction in an Experimental Model of Metabolic Syndrome with Renal Failure.Antioxidants (Basel, Switzerland) · 2023Article
- Quantitative Proteomics at Early Stages of the Symbiotic Interaction Between Oryza sativa and Nostoc punctiforme Reveals Novel Proteins Involved in the Symbiotic Crosstalk.Plant & cell physiology · 2022Article
- Label-free quantitative SWATH-MS proteomic analysis of adult myocardial slices in vitro after biomimetic electromechanical stimulation.Scientific reports · 2022Article
- Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi.Current issues in molecular biology · 2022Article
- Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens.Clinical proteomics · 2022Article
- Arabidopsis fibrillin 1-2 subfamily members exert their functions via specific protein-protein interactions.Journal of experimental botany · 2022Article
- The metabolic growth limitations of petite cells lacking the mitochondrial genome.Nature metabolism · 2021Article
- Ultra-fast proteomics with Scanning SWATH.Nature biotechnology · 2021Article
- Dataset for proteomic analysis ofData in brief · 2020Article
- A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics.Scientific data · 2020Article
- PHOSPHO1 is a skeletal regulator of insulin resistance and obesity.BMC biology · 2020Article
- Article
- Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition.Molecular & cellular proteomics : MCP · 2020Article
- SWATH-based proteomics reveals processes associated with immune evasion and metastasis in poor prognosis colorectal tumours.Journal of cellular and molecular medicine · 2019Article
- The Core Proteome of Biofilm-Grown ClinicalCells · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The combination of qualitative analysis with label-free quantification has greatly facilitated the throughput and flexibility of novel proteomic techniques. However, such methods rely heavily on robust and reproducible sample preparation procedures. Here, we benchmark a selection of in gel, on filter, and in solution digestion workflows for their application in label-free proteomics. Each procedure was associated with differing advantages and disadvantages. The in gel methods interrogated were cost effective, but were limited in throughput and digest efficiency. Filter-aided sample preparations facilitated reasonable processing times and yielded a balanced representation of membrane proteins, but led to a high signal variation in quantification experiments. Two in solution digest protocols, however, gave optimal performance for label-free proteomics. A protocol based on the detergent RapiGest led to the highest number of detected proteins at second-best signal stability, while a protocol based on acetonitrile-digestion, RapidACN, scored best in throughput and signal stability but came second in protein identification. In addition, we compared label-free data dependent (DDA) and data independent (SWATH) acquisition on a TripleTOF 5600 instrument. While largely similar in protein detection, SWATH outperformed DDA in quantification, reducing signal variation and markedly increasing the number of precisely quantified peptides.
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Registered trials
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.