Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
Open accessAbstract
The rise of systems biology implied a growing demand for highly sensitive techniques for the fast and consistent detection and quantification of target sets of proteins across multiple samples. This is only partly achieved by classical mass spectrometry or affinity-based methods. We applied a targeted proteomics approach based on selected reaction monitoring (SRM) to detect and quantify proteins expressed to a concentration below 50 copies/cell in total S. cerevisiae digests. The detection range can be extended to single-digit copies/cell and to proteins undetected by classical methods. We illustrate the power of the technique by the consistent and fast measurement of a network of proteins spanning the entire abundance range over a growth time course of S. cerevisiae transiting through a series of metabolic phases. We therefore demonstrate the potential of SRM-based proteomics to provide assays for the measurement of any set of proteins of interest in yeast at high-throughput and quantitative accuracy.
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Prior measurements of absolute protein levels used tandem affinity purification or GFP tags (Chong et al., 2015; Ghaemmaghami et al., 2003) and selected reaction monitoring proteomics (Picotti et al., 2009).
“Absolute protein levels have been measured before using tandem affinity purification- or GFP-tagged proteins (Chong et al., 2015; Ghaemmaghamiet al., 2003) and by a targeted proteomics approach based on selected reaction monitoring (Picotti et al., 2009).”
From Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast (2017) · cites this paper as Picotti et al., 2009
Targeted MS quantification using selected reaction monitoring was recently applied to investigate the transmission of a plant virus.
“For example, the targeted MS quantification method based on selected reaction monitoring [132–134] was recently implemented to understanding the transmission of a plant virus.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [133]
SCM estimates have an average difference of 1.4-fold from SRM measurements, compared to 1.8-fold using western blotting.
“(Fig 5C, average difference of 1.4-fold between SCM estimates and SRM measurements, compared to 1.8-fold using western blotting).”
Absolute protein levels for a set of 21 proteins differing up to 25,000-fold in cellular abundance have been measured using SRM spiked with stable-isotope standards.
“Absolute protein levels for a set of 21 proteins differing up to 25,000-fold in cellular abundance have been measured using single-reaction monitoring (SRM) spiked with stable-isotope standards [57].”
SCM estimates correlate better with SRM absolute protein levels (r = 0.94) than any individual dataset.
“SCM estimates correlate better with these absolute levels (r = 0.94 between log-transformed values) than does any individual dataset.”
The dynamic range of protein expression (from fewer than 50 to more than 1,000,000 molecules per cell) is wider than that of mRNA levels (e.g., from 0.1 to 89 molecules per cell).
“The dynamic range of protein expression (from fewer than 50 to more than 1,000,000 molecules per cell [30, 57]) is wider than that of mRNA levels (e.g. from 0.1 to 89 molecules per cell in a landmark early study [36]).”
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References 36 · Cited by 744
- Authors
- Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., & Aebersold, R.
- Affiliations
- ETH Zurich (CH)
- University of Zurich (CH)
- Corresponding author
- Aebersold, Ruedi
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2009-08
- Volume
- 138
- Issue
- 4
- Pages
- 795-806
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC2825542
- OpenAlex
- W2117365920
- Cited by
- 744
- References
- 36
- Citations by year
- 2026: 4 · 2025: 13 · 2024: 10 · 2023: 10 · 2022: 15 · 2021: 10 · 2020: 19 · 2019: 20 · 2018: 33 · 2017: 43 · 2016: 45 · 2015: 68 · 2014: 66 · 2013: 76 · 2012: 123
- FWCI
- 44.42
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion)
- Funders
- Boehringer Ingelheim Fonds
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Eidgenössische Technische Hochschule Zürich
- SystemsX.ch
- National Institutes of Health (n01hv28179-12-0-0)
- National Heart, Lung, and Blood Institute (N01 HV028179, N01-HV-28179)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- targeted proteomics, multiple reaction monitoring, Saccharomyces cerevisiae, low-abundance proteins, protein quantification, yeast proteome
- MeSH terms
- Saccharomyces cerevisiae, Mass Spectrometry, Saccharomyces cerevisiae Proteins, Proteomics
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