The Current State of Single‐Cell Proteomics Data Analysis

Current Protocols, Год журнала: 2023, Номер 3(1)

Опубликована: Янв. 1, 2023

Sound data analysis is essential to retrieve meaningful biological information from single-cell proteomics experiments. This carried out by computational methods that are assembled into workflows, and their implementations influence the conclusions can be drawn data. In this work, we explore compare workflows have been used over last four years identify a profound lack of consensus on how analyze We highlight need for benchmarking standardization tools data, as well carefully designed Finally, cover current efforts aim fill gap, list remaining missing pieces, conclude with lessons learned replication published analyses. © 2023 Wiley Periodicals LLC.

Язык: Английский

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Achieving a Deeper Understanding of Drug Metabolism and Responses Using Single-Cell Technologies

Drug Metabolism and Disposition, Год журнала: 2023, Номер 51(3), С. 350 - 359

Опубликована: Янв. 10, 2023

Recent advancements in single-cell technologies have enabled detection of RNA, proteins, metabolites, and xenobiotics individual cells, the application these has potential to transform pharmacological research. Single-cell data already resulted development human model species cell atlases, identifying different cell-types within a tissue, further facilitating characterization tumor heterogeneity providing insight into treatment resistance. Research discussed this review demonstrates that distinct populations express drug metabolizing enzymes extents, indicating there may be variability metabolism not only between organs, but tissue types. Additionally, we put forth concept analyses can utilized expose underlying cellular response drugs, unique examination efficacy, toxicity, metabolism. We will outline several techniques: RNA-sequencing mass cytometry characterize distinguish types, proteomics quantify responses drug, capillary electrophoresis-ultrasensitive laser-induced fluorescence single-probe spectrometry for others. Emerging such as comprehensively both cell-type specific treatment, enhancing progress toward personalized precision medicine. Significance Statement technological advances analysis gene expression protein levels single cells. These types are important investigating mechanisms cannot elucidated on bulk level, primarily due biological systems. Here, summarize how pharmacologists utilize approaches obtain comprehensive understanding drugs.

Язык: Английский

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Multidimensional separations in top–down proteomics

Analytical Science Advances, Год журнала: 2023, Номер 4(5-6), С. 181 - 203

Опубликована: Май 29, 2023

Abstract Top–down proteomics (TDP) identifies, quantifies, and characterises proteins at the intact proteoform level in complex biological samples to understand function cellular mechanisms. However, analysing using TDP is still challenging due high sample complexity wide dynamic range. High‐resolution separation methods are often applied prior mass spectrometry (MS) analysis decrease increase throughput. These methods, however, may not be efficient enough characterise low abundance proteoforms samples. As such, multidimensional techniques (combination of two or more with orthogonality) have been developed that demonstrate improved resolution comprehensive identification TDP. A suite couple various types liquid chromatography (LC), capillary electrophoresis (CE), and/or gel electrophoresis‐based approaches analyse Here, we reviewed strategies employed for TDP, summarised current applications, discussed gaps addressed future.

Язык: Английский

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High-Throughput Proteomics Enabled by a Fully Automated Dual-Trap and Dual-Column LC-MS

Analytical Chemistry, Год журнала: 2024, Номер 96(24), С. 9761 - 9766

Опубликована: Июнь 4, 2024

This Technical Note describes a dual-column liquid chromatography system coupled to mass spectrometry (LC-MS) for high-throughput bottom-up proteomic analysis. made full use of two 2-position 10-port valves and binary pump with an integrated loading commercial LC instrument provide successive operation parallel subsystems. Each subsystem consisted set trap columns analytical column. A T-junction union was used split the mobile phase from into parts. allowed one be washed equilibrated, followed by injection next sample, while previous sample eluting being analyzed on other columns, thereby greatly increasing analysis throughput. approach showed high reproducibility HeLa tryptic digests average relative standard deviation (RSD) values 1.75%, 6.90%, 5.19% identification number proteins, peptides, peptide-spectrum matches (PSMs), respectively, across 10 consecutive runs. The capacity peptide protein identification, as well proteome depth, comparable conventional single-column system. Due its simple equipment requirements up process, this method should highly accessible laboratories.

Язык: Английский

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Droplet-Based Microfluidics with Mass Spectrometry for Microproteomics

Engineering, Год журнала: 2024, Номер unknown

Опубликована: Сен. 1, 2024

Язык: Английский

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