ArticleMolecular biology of the cell2015
Reproducible quantitative proteotype data matrices for systems biology.
Article in Molecular biology of the cell, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Analytical Techniques as Indicators of Biomarkers in Proteomics Cancer Diagnosis.Anti-cancer agents in medicinal chemistry · 2026Review
- The Role of Clinical Glyco(proteo)mics in Precision Medicine.Molecular & cellular proteomics : MCP · 2023Article
- Review
- Precision periodontal care: from omics discoveries to chairside diagnostics.Clinical oral investigations · 2023Review
- Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression.Nature communications · 2023Article
- Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology.Molecular cell · 2022Review
- From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions.Molecular systems biology · 2021Article
- An extended catalogue of tandem alternative splice sites in human tissue transcriptomes.PLoS computational biology · 2021Article
- diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition.Nature methods · 2020Article
- HyperQuant-A Computational Pipeline for Higher Order Multiplexed Quantitative Proteomics.ACS omega · 2020Article
- Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation.Molecular systems biology · 2020Article
- Multibatch TMT Reveals False Positives, Batch Effects and Missing Values.Molecular & cellular proteomics : MCP · 2019Article
- Beyond Genes: Re-Identifiability of Proteomic Data and Its Implications for Personalized Medicine.Genes · 2019Review
- MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides.Molecular & cellular proteomics : MCP · 2019Article
- Alternative Splicing and Protein Diversity: Plants Versus Animals.Frontiers in plant science · 2019Review
- BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes.Nature methods · 2018Article
- Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system.Scientific reports · 2017Article
- Quantitative proteomics: challenges and opportunities in basic and applied research.Nature protocols · 2017Article
- Most Alternative Isoforms Are Not Functionally Important.Trends in biochemical sciences · 2017Article
- Undiscovered Physiology of Transcript and Protein Networks.Comprehensive Physiology · 2016Review
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Historically, many mass spectrometry-based proteomic studies have aimed at compiling an inventory of protein compounds present in a biological sample, with the long-term objective of creating a proteome map of a species. However, to answer fundamental questions about the behavior of biological systems at the protein level, accurate and unbiased quantitative data are required in addition to a list of all protein components. Fueled by advances in mass spectrometry, the proteomics field has thus recently shifted focus toward the reproducible quantification of proteins across a large number of biological samples. This provides the foundation to move away from pure enumeration of identified proteins toward quantitative matrices of many proteins measured across multiple samples. It is argued here that data matrices consisting of highly reproducible, quantitative, and unbiased proteomic measurements across a high number of conditions, referred to here as quantitative proteotype maps, will become the fundamental currency in the field and provide the starting point for downstream biological analysis. Such proteotype data matrices, for example, are generated by the measurement of large patient cohorts, time series, or multiple experimental perturbations. They are expected to have a large effect on systems biology and personalized medicine approaches that investigate the dynamic behavior of biological systems across multiple perturbations, time points, and individuals.
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