ArticleMolecular & cellular proteomics : MCP2016
Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring.
Article in Molecular & cellular proteomics : MCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- Link Between Individual Codon Frequencies and Protein Expression: Going Beyond Codon Adaptation Index.International journal of molecular sciences · 2024Article
- A genome-to-proteome atlas charts natural variants controlling proteome diversity and forecasts their fitness effects.bioRxiv : the preprint server for biology · 2024Article
- Paralogous translation factors target distinct mRNAs to differentially regulate tolerance to oxidative stress in yeast.Nucleic acids research · 2023Article
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- AlacatDesigner─Computational Design of Peptide Concatamers for Protein Quantitation.Journal of proteome research · 2023Article
- Estimating Total Quantitative Protein Content inInternational journal of molecular sciences · 2023Article
- Intelligent host engineering for metabolic flux optimisation in biotechnology.The Biochemical journal · 2021Review
- Construction of à la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins.BMC biology · 2021Article
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- Factors affecting the rapid changes of protein under short-term heat stress.BMC genomics · 2021Article
- Nutrient Signaling, Stress Response, and Inter-organelle Communication Are Non-canonical Determinants of Cell Fate.Cell reports · 2020Article
- Review
- Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon,Microorganisms · 2020Article
- Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics.Journal of proteome research · 2020Article
- Incorporation of a unified protein abundance dataset into the Saccharomyces genome database.Database : the journal of biological databases and curation · 2020Article
- Translation factor mRNA granules direct protein synthetic capacity to regions of polarized growth.The Journal of cell biology · 2019Article
- Extension of the yeast metabolic model to include iron metabolism and its use to estimate global levels of iron-recruiting enzyme abundance from cofactor requirements.Biotechnology and bioengineering · 2019Article
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13 authors.
Funding
Abstract
Defining intracellular protein concentration is critical in molecular systems biology. Although strategies for determining relative protein changes are available, defining robust absolute values in copies per cell has proven significantly more challenging. Here we present a reference data set quantifying over 1800Saccharomyces cerevisiaeproteins by direct means using protein-specific stable-isotope labeled internal standards and selected reaction monitoring (SRM) mass spectrometry, far exceeding any previous study. This was achieved by careful design of over 100 QconCAT recombinant proteins as standards, defining 1167 proteins in terms of copies per cell and upper limits on a further 668, with robust CVs routinely less than 20%. The selected reaction monitoring-derived proteome is compared with existing quantitative data sets, highlighting the disparities between methodologies. Coupled with a quantification of the transcriptome by RNA-seq taken from the same cells, these data support revised estimates of several fundamental molecular parameters: a total protein count of ∼100 million molecules-per-cell, a median of ∼1000 proteins-per-transcript, and a linear model of protein translation explaining 70% of the variance in translation rate. This work contributes a "gold-standard" reference yeast proteome (including 532 values based on high quality, dual peptide quantification) that can be widely used in systems models and for other comparative studies.
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