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

11 June 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


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.


Single cell proteomics
single cell sequencing

Supplementary materials

Supplemental Data
Supplemental Data 1: A summary of all studies reviewed in this work with relevant characteristics Supplemental Data 2: The step by step calculations for how the cost for analyzing each cell was determined for each study Supplemental Data 3: Extracted data from Svennson et al., used for scSeq data presented in Figure 1B Supplemental Data 4: A simple calculator sheet to estimate the cost/cell for other studies.


Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.