Defining the carrier proteome limit for single-cell proteomics. Cheung, T. K., Lee, C., Bayer, F. P., McCoy, A., Kuster, B., & Rose, C. M. Nature Methods, 18(1):76–83, January, 2021. Bandiera_abtest: a Cg_type: Nature Research Journals Number: 1 Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Mass spectrometry;Proteomic analysis;Proteomics Subject_term_id: mass-spectrometry;proteomic-analysis;proteomics![Defining the carrier proteome limit for single-cell proteomics [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Single-cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method to quantify multiplexed single-cell proteomes. While this technique has generated great excitement, the underlying technologies (isobaric labeling and mass spectrometry (MS)) have technical limitations with the potential to affect data quality and biological interpretation. These limitations are particularly relevant when a carrier proteome, a sample added at 25–500× the amount of a single-cell proteome, is used to enable peptide identifications. Here we perform controlled experiments with increasing carrier proteome amounts and evaluate quantitative accuracy, as it relates to mass analyzer dynamic range, multiplexing level and number of ions sampled. We demonstrate that an increase in carrier proteome level requires a concomitant increase in the number of ions sampled to maintain quantitative accuracy. Lastly, we introduce Single-Cell Proteomics Companion (SCPCompanion), a software tool that enables rapid evaluation of single-cell proteomic data and recommends instrument and data analysis parameters for improved data quality.
@article{cheung_defining_2021,
title = {Defining the carrier proteome limit for single-cell proteomics},
volume = {18},
copyright = {2020 The Author(s), under exclusive licence to Springer Nature America, Inc.},
issn = {1548-7105},
url = {http://www.nature.com/articles/s41592-020-01002-5},
doi = {10.1038/s41592-020-01002-5},
abstract = {Single-cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method to quantify multiplexed single-cell proteomes. While this technique has generated great excitement, the underlying technologies (isobaric labeling and mass spectrometry (MS)) have technical limitations with the potential to affect data quality and biological interpretation. These limitations are particularly relevant when a carrier proteome, a sample added at 25–500× the amount of a single-cell proteome, is used to enable peptide identifications. Here we perform controlled experiments with increasing carrier proteome amounts and evaluate quantitative accuracy, as it relates to mass analyzer dynamic range, multiplexing level and number of ions sampled. We demonstrate that an increase in carrier proteome level requires a concomitant increase in the number of ions sampled to maintain quantitative accuracy. Lastly, we introduce Single-Cell Proteomics Companion (SCPCompanion), a software tool that enables rapid evaluation of single-cell proteomic data and recommends instrument and data analysis parameters for improved data quality.},
language = {en},
number = {1},
urldate = {2021-08-10},
journal = {Nature Methods},
author = {Cheung, Tommy K. and Lee, Chien-Yun and Bayer, Florian P. and McCoy, Atticus and Kuster, Bernhard and Rose, Christopher M.},
month = jan,
year = {2021},
note = {Bandiera\_abtest: a
Cg\_type: Nature Research Journals
Number: 1
Primary\_atype: Research
Publisher: Nature Publishing Group
Subject\_term: Mass spectrometry;Proteomic analysis;Proteomics
Subject\_term\_id: mass-spectrometry;proteomic-analysis;proteomics},
pages = {76--83},
}
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