ArticleNature communications2018
Deducing the presence of proteins and proteoforms in quantitative proteomics.
Article in Nature communications, 2018. 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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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.
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Who cites it
18 citing papers in PubMed, 34 citations in OpenAlex.
- ProteoForge: An Imputation-Aware Framework for Differential Proteoform Discovery in Bottom-Up Proteomics.Journal of proteome research · 2026Article
- Proteoforms as the true units of physiological function.European journal of applied physiology · 2026Review
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- Peptidomics-based identification of endogenous free peptides fromFrontiers in pharmacology · 2026Article
- In vivo conformational space and defects of misfolded CFTR variants by covalent protein painting.Nature communications · 2025Article
- Functional proteoform group deconvolution reveals a broader spectrum of ibrutinib off-targets.Nature communications · 2025Article
- Defining proteoform-specific interactions for drug targeting in a native cell signalling environment.Nature chemistry · 2025Article
- Quantitative structural proteomics in living cells by covalent protein painting.Methods in enzymology · 2023Article
- Article
- An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics.Genome biology · 2022Article
- Cancer Conformational Landscape Shapes Tumorigenesis.Journal of proteome research · 2022Article
- Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?Journal of proteome research · 2022Article
- Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs.PloS one · 2022Article
- Systematic detection of functional proteoform groups from bottom-up proteomic datasets.Nature communications · 2021Article
- Protein Footprinting via Covalent Protein Painting Reveals Structural Changes of the Proteome in Alzheimer's Disease.Journal of proteome research · 2021Article
- Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data.Journal of proteome research · 2020Article
- Monitoring protein communities and their responses to therapeutics.Nature reviews. Drug discovery · 2020Review
- Understanding molecular mechanisms of disease through spatial proteomics.Current opinion in chemical biology · 2019Review
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
The human genome harbors just 20,000 genes suggesting that the variety of possible protein products per gene plays a significant role in generating functional diversity. In bottom-up proteomics peptides are mapped back to proteins and proteoforms to describe a proteome; however, accurate quantitation of proteoforms is challenging due to incomplete protein sequence coverage and mapping ambiguities. Here, we demonstrate that a new software tool called ProteinClusterQuant (PCQ) can be used to deduce the presence of proteoforms that would have otherwise been missed, as exemplified in a proteomic comparison of two fly species, Drosophila melanogaster and D. virilis. PCQ was used to identify reduced levels of serine/threonine protein kinases PKN1 and PKN4 in CFBE41o
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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.