Single-cell proteomics differentiates Arabidopsis root cell types

Montes, Christian; Zhang, Jingyuan; Nolan, Trevor M.; Walley, Justin W.

doi:10.1101/2024.04.09.588771

Cited by 3 publications

(1 citation statement)

References 61 publications

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“…For example, the 2024 preprint from Montes et al, closely follows the SCOPE2 method, as FACs sorted plant cells were analyzed on a Q Exactive Plus system following labeling with low cost robotics. 59 This enabled a group's first entry in the world of SCP to be a study of nearly 800 single cells with the lowest estimated cost/cell in any publication reviewed here in the last 6 years. However, the use of high precision instrumentation such as the CellenOne coupled to today's newest instruments for label free analysis compound to increase the relative cost per cell by more than an order of magnitude.…”

Section: Throughput In Published Studies Are Decreasing Over Time Whi...mentioning

confidence: 99%

The current economics and throughput of single cell proteomics by liquid chromatography mass spectrometry

Smythers,

Orsburn

2024

Preprint

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Single cell proteomics by mass spectrometry (SCP) is an emerging field of study that has captured the interest and imagination of biologists in a wide array of disciplines. In the pursuit of this new field a dizzying array of technologies and techniques have demonstrated the ability to quantify hundreds to a few thousand proteins in single mammalian cells of typical size. One striking characteristic of these methods is the wide range of relative costs associated with the analysis of each single cell. We have attempted to estimate the cost per cell across 17 different studies based on quotes we have obtained for hardware, reagents and instrument support plans in relation to number of cells that can be analyzed per day. Before including labor or facilities, we find that the cost to analyze a single mammalian cell of typical size can range from less than <$2 per cell to over $50 per cell. The increase in cost appears directly related to the decrease in relative throughput as measured in theoretical maximum number of cells analyzed per day. Perhaps the most surprising observation is that the average number of single cells analyzed across these studies appears to decrease each year. This is striking when compared to the emergence of single cell RNA sequencing where throughput increased, and cost/cell decreased exponentially over the first 7 years of the field’s emergence. While we have made many assumptions to obtain these estimates, we hope that these will be informative for scientists interested in obtaining SCP data and for mass spectrometrists who are considering entering this new field. We have provided a spreadsheet with a simple calculator in the supplemental data to allow others to adjust our calculations based on other variables and new methods which will inevitably be described in the future.

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Section: Throughput In Published Studies Are Decreasing Over Time Whi...mentioning

confidence: 99%

The current economics and throughput of single cell proteomics by liquid chromatography mass spectrometry

Smythers,

Orsburn

2024

Preprint

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Pleiotropy, a feature or a bug? Toward co-ordinating plant growth, development, and environmental responses through engineering plant hormone signaling

Ferreira Neres,

Wright

2024

Current Opinion in Biotechnology

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Exploring the feasibility of a single-protoplast proteomic analysis

Vu,

Lee,

Kim

et al. 2024

J Anal Sci Technol

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Background Recent advances in high-resolution mass spectrometry have now enabled the study of proteomes at the single-cell level, offering the potential to unveil novel aspects of cellular processes. Remarkably, there has been no prior attempt to investigate single-plant cell proteomes. In this study, we aimed to explore the feasibility of conducting a proteomic analysis on individual protoplasts. Findings As a result, our analysis identified 978 proteins from the 180 protoplasts, aligning with well-known biological processes in plant leaves, such as photosynthetic electron transport in photosystem II. Employing the SCP package in the SCoPE2 workflow revealed a notable batch effect and extensive missing values in the data. Following correction, we observed the heterogeneity in single-protoplast proteome expression. Comparing the results of single-protoplast proteomics with those of bulk leaf proteomics, we noted that only a small fraction of bulk data was detected in the single-protoplast proteomics data, highlighting a technical limitation of the current single-cell proteomics method. Conclusions In summary, we demonstrated the feasibility of conducting a single-protoplast proteomic experiment, revealing heterogeneity in plant cellular proteome expression. This underscores the importance of analyzing a substantial number of plant cells to discern statistically significant changes in plant cell proteomes upon perturbation such as abscisic acid treatment in future studies. We anticipate that our study will contribute to advancing single-protoplast proteomics in the near future.

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Single-cell proteomics differentiates Arabidopsis root cell types

Cited by 3 publications

References 61 publications

The current economics and throughput of single cell proteomics by liquid chromatography mass spectrometry

The current economics and throughput of single cell proteomics by liquid chromatography mass spectrometry

Pleiotropy, a feature or a bug? Toward co-ordinating plant growth, development, and environmental responses through engineering plant hormone signaling

Exploring the feasibility of a single-protoplast proteomic analysis

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