Increasing the throughput of sensitive proteomics by plexDIA

Nature Biotechnology, Год журнала: 2022, Номер 41(1), С. 50 - 59

Опубликована: Июль 14, 2022

Язык: Английский

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High-throughput proteomics: a methodological mini-review

Laboratory Investigation, Год журнала: 2022, Номер 102(11), С. 1170 - 1181

Опубликована: Авг. 3, 2022

Язык: Английский

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Single-cell proteomics enabled by next-generation sequencing or mass spectrometry

Nature Methods, Год журнала: 2023, Номер 20(3), С. 363 - 374

Опубликована: Март 1, 2023

Язык: Английский

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Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments

Nature Methods, Год журнала: 2023, Номер 20(3), С. 375 - 386

Опубликована: Март 1, 2023

Язык: Английский

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Exploring functional protein covariation across single cells using nPOP

Genome biology, Год журнала: 2022, Номер 23(1)

Опубликована: Дек. 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.

Язык: Английский

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Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics

Molecular & Cellular Proteomics, Год журнала: 2022, Номер 21(4), С. 100219 - 100219

Опубликована: Фев. 25, 2022

In the young field of single-cell proteomics (scMS), there is a great need for improved global proteome characterization, both in terms proteins quantified per cell and quantitative performance thereof. The recently introduced real-time search (RTS) on Orbitrap Eclipse Tribrid mass spectrometer combination with SPS-MS3 acquisition has been shown to be beneficial measurement samples that are multiplexed using isobaric tags. Multiplexed scMS requires high ion injection times high-resolution spectra quantify signal; however, carrier channel facilitates peptide identification thus offers opportunity fast on-the-fly precursor filtering before committing time-intensive quantification scan. Here, we compared classical MS2 against RTS-SPS-MS3, MS FAIMS Pro mobility interface present new strategy termed RETICLE (RTS enhanced quant single spectra) makes use searched linear trap scans preselect MS1 precursors acquisition. We show outperformed by RTS-SPS-MS3 through increased accuracy at similar coverage, higher latter enabling over 1000 an time 750 ms 2 h gradient.

Язык: Английский

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Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics

Nature Methods, Год журнала: 2023, Номер 20(5), С. 714 - 722

Опубликована: Апрель 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 .

Язык: Английский

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Sampling the proteome by emerging single-molecule and mass spectrometry methods

Nature Methods, Год журнала: 2023, Номер 20(3), С. 339 - 346

Опубликована: Март 1, 2023

Язык: Английский

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Pan-cancer proteogenomics connects oncogenic drivers to functional states

Cell, Год журнала: 2023, Номер 186(18), С. 3921 - 3944.e25

Опубликована: Авг. 1, 2023

Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here, our multi-omics pan-cancer analysis uncovers insights into the impacts of cancer drivers by identifying significant cis-effects and distal trans-effects quantified at RNA, protein, phosphoprotein levels. Salient observations include association point mutations copy-number alterations with rewiring protein interaction networks, notably, most genes converge toward similar states denoted sequence-based kinase activity profiles. A correlation between predicted neoantigen burden measured T cell infiltration suggests potential vulnerabilities for immunotherapies. Patterns hallmarks vary polygenic abundance ranging from uniform heterogeneous. Overall, work demonstrates value comprehensive proteogenomics in understanding functional oncogenic links development, surpassing limitations studying individual types.

Язык: Английский

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Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 22, 2023

Single-cell resolution analysis of complex biological tissues is fundamental to capture cell-state heterogeneity and distinct cellular signaling patterns that remain obscured with population-based techniques. The limited amount material encapsulated in a single cell however, raises significant technical challenges molecular profiling. Due extensive optimization efforts, single-cell proteomics by Mass Spectrometry (scp-MS) has emerged as powerful tool facilitate proteome profiling from ultra-low amounts input, although further development needed realize its full potential. To this end, we carry out comprehensive orbitrap-based data-independent acquisition (DIA) for proteomics. Notably, find difference between optimal DIA methods high- low-load samples. We improve our low-input method relying on high-resolution MS1 quantification, thus enhancing sensitivity more efficiently utilizing available mass analyzer time. With input tailored method, are able accommodate long injection times high resolution, while keeping the scan cycle time low enough ensure robust quantification. Finally, demonstrate capability approach mouse embryonic stem culture conditions, showcasing global proteomes highlighting differences key metabolic enzyme expression subclusters.

Язык: Английский

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