ArticleProteomes2022
Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance.
Article in Proteomes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Article
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- Dual genomic localizations and gene regulatory functions of MBD-2 with and without NuRD in Caenorhabditis elegans which lacks DNA methylation.Nature communications · 2026Article
- Mass Spectrometry Proteomics: A Key to Faster Drug Discovery.Journal of medicinal chemistry · 2026Review
- The Microbial Anti-Inflammatory Molecule (MAM) is a key protein processed and exported toGut microbes · 2025Article
- Protein Carrier Adeno-Associated Virus.ACS nano · 2025Article
- Calculating and Reporting Coefficients of Variation for DIA-Based Proteomics.Journal of proteome research · 2024Review
- Proteomics: An Essential Tool to Study Plant-Specialized Metabolism.Biomolecules · 2024Review
- Dual Fractions Proteomic Analysis of Silica Nanoparticle Interactions with Protein Extracts.Materials (Basel, Switzerland) · 2024Article
- Protein Carrier AAV.bioRxiv : the preprint server for biology · 2024Article
- Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience.Proteomes · 2024Article
- From the outer space to the inner cell: deconvoluting the complexity ofMicrobiology spectrum · 2024Article
- Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias.Molecular & cellular proteomics : MCP · 2023Article
- Quantitative Aspects of the Human Cell Proteome.International journal of molecular sciences · 2023Review
- Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803.Photosynthesis research · 2023Article
- A proteome scale study reveals how plastic surfaces and agitation promote protein aggregation.Scientific reports · 2023Article
- Tear Proteome Revealed Association of S100A Family Proteins and Mesothelin with Thrombosis in Elderly Patients with Retinal Vein Occlusion.International journal of molecular sciences · 2022Article
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Authors and funding
5 authors.
Funding
Abstract
In proteomics, it is essential to quantify proteins in absolute terms if we wish to compare results among studies and integrate high-throughput biological data into genome-scale metabolic models. While labeling target peptides with stable isotopes allow protein abundance to be accurately quantified, the utility of this technique is constrained by the low number of quantifiable proteins that it yields. Recently, label-free shotgun proteomics has become the "gold standard" for carrying out global assessments of biological samples containing thousands of proteins. However, this tool must be further improved if we wish to accurately quantify absolute levels of proteins. Here, we used different label-free quantification techniques to estimate absolute protein abundance in the model yeast Saccharomyces cerevisiae. More specifically, we evaluated the performance of seven different quantification methods, based either on spectral counting (SC) or extracted-ion chromatogram (XIC), which were applied to samples from five different proteome backgrounds. We also compared the accuracy and reproducibility of two strategies for transforming relative abundance into absolute abundance: a UPS2-based strategy and the total protein approach (TPA). This study mentions technical challenges related to UPS2 use and proposes ways of addressing them, including utilizing a smaller, more highly optimized amount of UPS2. Overall, three SC-based methods (PAI, SAF, and NSAF) yielded the best results because they struck a good balance between experimental performance and protein quantification.
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