Metaproteomics to understand how microbiota function: The crystal ball predicts a promising future DOI Creative Commons
Jean Armengaud

Environmental Microbiology, Journal Year: 2022, Volume and Issue: 25(1), P. 115 - 125

Published: Oct. 9, 2022

In the medical, environmental, and biotechnological fields, microbial communities have attracted much attention due to their roles numerous possible applications. The study of these is challenging diversity complexity. Innovative methods are needed identify taxonomic components individual microbiota, changes over time, determine how microoorganisms interact function. Metaproteomics based on identification quantification proteins, can potentially provide this full picture. Due wide molecular panorama functional insights it provides, metaproteomics gaining momentum in microbiome holobiont research. Its potential should be unleashed coming years with progress speed cost analyses. exploratory crystal ball exercise, I discuss technical conceptual advances that expect drive innovative research next few microbiology. also debate concepts 'microbial dark matter' 'Metaproteomics-Assembled Proteomes (MAPs)' present some long-term prospects for clinical diagnostics personalized medicine, environmental monitoring, agriculture, biotechnology.

Language: Английский

Single-cell proteomics enabled by next-generation sequencing or mass spectrometry DOI
Hayley M. Bennett, William Stephenson, Christopher M. Rose

et al.

Nature Methods, Journal Year: 2023, Volume and Issue: 20(3), P. 363 - 374

Published: March 1, 2023

Language: Английский

Citations

190
Unbiased spatial proteomics with single-cell resolution in tissues DOI Creative Commons
Andreas Mund, Andreas‐David Brunner, Matthias Mann

et al.

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(12), P. 2335 - 2349

Published: June 1, 2022

Language: Английский

Citations

161
An Introduction to Mass Spectrometry-Based Proteomics DOI Open Access
Steven R. Shuken

Journal of Proteome Research, Journal Year: 2023, Volume and Issue: 22(7), P. 2151 - 2171

Published: June 1, 2023

Mass spectrometry is unmatched in its versatility for studying practically any aspect of the proteome. Because foundations mass spectrometry-based proteomics are complex and span multiple scientific fields, can be perceived as having a high barrier to entry. This tutorial intended an accessible illustrated guide technical details relatively simple quantitative proteomic experiment. An attempt made explain relevant concepts those with limited knowledge basic understanding proteins. experimental overview provided, from beginning sample preparation analysis protein group quantities, explanations how data acquired, processed, analyzed. A selection advanced topics briefly surveyed works further reading cited. To conclude, brief discussion future given, considering next-generation sequencing technologies that may complement create fruitful proteomics.

Language: Английский

Citations

122
Exploring functional protein covariation across single cells using nPOP DOI Creative Commons
Andrew Leduc, R. Gray Huffman, Joshua Cantlon

et al.

Genome biology, Journal Year: 2022, Volume and Issue: 23(1)

Published: Dec. 16, 2022

Many biological processes, such as cell division cycle and drug resistance, are reflected in protein covariation across single cells. This can be quantified interpreted by single-cell mass spectrometry with sufficiently high throughput accuracy.

Language: Английский

Citations

106
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments DOI Open Access
Laurent Gatto, Ruedi Aebersold, Jüergen Cox

et al.

Nature Methods, Journal Year: 2023, Volume and Issue: 20(3), P. 375 - 386

Published: March 1, 2023

Language: Английский

Citations

106
Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome DOI Creative Commons
Florian A. Rosenberger, Marvin Thielert, Maximilian T. Strauss

et al.

Nature Methods, Journal Year: 2023, Volume and Issue: 20(10), P. 1530 - 1536

Published: Oct. 1, 2023

Single-cell proteomics by mass spectrometry is emerging as a powerful and unbiased method for the characterization of biological heterogeneity. So far, it has been limited to cultured cells, whereas an expansion complex tissues would greatly enhance insights. Here we describe single-cell Deep Visual Proteomics (scDVP), technology that integrates high-content imaging, laser microdissection multiplexed spectrometry. scDVP resolves context-dependent, spatial proteome murine hepatocytes at current depth 1,700 proteins from cell slice. Half was differentially regulated in manner, with protein levels changing dramatically proximity central vein. We applied machine learning classes images, which subsequently inferred imaging data alone. applicable healthy diseased complements other omics technologies.

Language: Английский

Citations

86
MS-Based Proteomics of Body Fluids: The End of the Beginning DOI Creative Commons
Jakob M. Bader, Vincent Albrecht, Matthias Mann

et al.

Molecular & Cellular Proteomics, Journal Year: 2023, Volume and Issue: 22(7), P. 100577 - 100577

Published: May 19, 2023

Accurate biomarkers are a crucial and necessary precondition for precision medicine, yet existing ones often unspecific new have been very slow to enter the clinic. Mass spectrometry (MS)-based proteomics excels by its untargeted nature, specificity of identification, quantification, making it an ideal technology biomarker discovery routine measurement. It has unique attributes compared affinity binder technologies, such as OLINK Proximity Extension Assay SOMAscan. In in previous review 2017, we described technological conceptual limitations that had held back success. We proposed 'rectangular strategy' better separate true minimizing cohort-specific effects. Today, this converged with advances MS-based technology, increased sample throughput, depth quantification. As result, studies become more successful, producing candidates withstand independent verification and, some cases, already outperform state-of-the-art clinical assays. summarize developments over last years, including benefits large cohorts, which acceptance. Shorter gradients, scan modes, multiplexing about drastically increase cross-study integration, proxies absolute levels. found multiprotein panels inherently robust than current single analyte tests capture complexity human phenotypes. Routine MS measurement clinic is fast becoming viable option. The full set proteins body fluid (global proteome) most important reference best process control. Additionally, increasingly all information could be obtained from targeted analysis although latter may straightforward way regular use. Many challenges remain, not least regulatory ethical but outlook applications never brighter.

Language: Английский

Citations

72
Mass spectrometry‐based high‐throughput proteomics and its role in biomedical studies and systems biology DOI Creative Commons
Christoph B. Messner, Vadim Demichev, Ziyue Wang

et al.

PROTEOMICS, Journal Year: 2022, Volume and Issue: 23(7-8)

Published: Nov. 9, 2022

Abstract There are multiple reasons why the next generation of biological and medical studies require increasing numbers samples. Biological systems dynamic, effect a perturbation depends on genetic background environment. As consequence, many conditions need to be considered reach generalizable conclusions. Moreover, human population clinical only sufficient statistical power if conducted at scale with precise measurement methods. Finally, proteins remain without functional annotations, because they have not been systematically studied under broad range conditions. In this review, we discuss latest technical developments in mass spectrometry (MS)‐based proteomics that facilitate large‐scale by fast efficient chromatography, scanning spectrometers, data‐independent acquisition (DIA), new software. We further highlight recent which demonstrate how high‐throughput (HT) can applied capture diversity, annotate gene functions or generate predictive prognostic models for diseases.

Language: Английский

Citations

71
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics DOI Creative Commons
R. Gray Huffman, Andrew Leduc, Christoph Wichmann

et al.

Nature Methods, Journal Year: 2023, Volume and Issue: 20(5), P. 714 - 722

Published: April 3, 2023

Major aims of single-cell proteomics include increasing the consistency, sensitivity and depth protein quantification, especially for proteins modifications biological interest. Here, to simultaneously advance all these aims, we developed prioritized Single-Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands peptides across single cells (thus data completeness) while maximizing instrument time spent analyzing identifiable peptides, thus proteome depth. These strategies increased sensitivity, completeness coverage over twofold. The gains enabled quantifying variation in untreated lipopolysaccharide-treated primary macrophages. Within each condition, covaried within functional sets, including phagosome maturation proton transport, similarly both treatment conditions. This covariation is coupled phenotypic variability endocytic activity. also proteolytic products, suggesting a gradient cathepsin activities condition. freely available widely applicable, interest without sacrificing coverage. Support at http://scp.slavovlab.net/pSCoPE .

Language: Английский

Citations

66
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel DOI Creative Commons
Marvin Thielert, Corazon Ericka Mae M. Itang, Constantin Ammar

et al.

Molecular Systems Biology, Journal Year: 2023, Volume and Issue: 19(9)

Published: Aug. 21, 2023

Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited proteomic depth, throughput, robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated complete dimethyl labeling bulk or single-cell samples, without losing depth. Lys-N digestion enables five-plex quantification MS1 MS2 level. Because channels are quantitatively isolated from each other, mDIA accommodates reference channel that does not interfere with target channels. Our algorithm RefQuant takes advantage this confidently quantifies twice as many per single cell compared our previous work (Brunner et al, PMID 35226415), while allows routine analysis 80 cells day. Finally, combined spatial increase throughput Deep Visual Proteomics seven-fold for microdissection four-fold MS analysis. Applying primary cutaneous melanoma, discovered signatures within distinct tumor microenvironments, showcasing its potential precision oncology.

Language: Английский

Citations

61