Proteomics

Dataset Information

0

Single Cell Proteomics and the Carrier Proteome Effect

ABSTRACT: Single cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method that utilizes isobaric labels to quantify multiplexed single cell proteomes. While this technique has generated great excitement, the technologies underlying SCoPE-MS - isobaric labels and mass spectrometry - comprise technical limitations with the potential to unfavorably impact data quality and biological interpretation. These limitations are due to the carrier proteome, a sample added at 25-500x single cell proteomes to enable peptide identifications. Here, we perform SCoPE-MS experiments with increasing amounts of carrier proteome 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 – we term this the carrier proteome effect. Based on our findings, we provide guidance on experimental design, data collection, and data analysis to limit the impact of the carrier proteome effect within SCoPE-MS measurements.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Christopher Rose  

LAB HEAD: Christopher M. Rose

PROVIDER: PXD016573 | Pride | 2020-12-16

REPOSITORIES: Pride

Json Xml
altmetric image

Publications

Defining the carrier proteome limit for single-cell proteomics.

Cheung Tommy K TK   Lee Chien-Yun CY   Bayer Florian P FP   McCoy Atticus A   Kuster Bernhard B   Rose Christopher M CM  

Nature methods 20201207 1

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 us  ...[more]

Similar Datasets

Proteomics Single Cell Proteomics and the Carrier Proteome Effect
2020-08-16 | MSV000085959 | MassIVE
Proteomics Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
2017-01-23 | MSV000080489 | MassIVE
Proteomics Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
2018-02-19 | MSV000082077 | MassIVE
Transcriptomics Transcription profiling by high throughput sequencing of HeLa human cancer cell line
2011-11-12 | E-MTAB-823 | biostudies-arrayexpress
Proteomics E.coli and Human proteome
2019-05-14 | PXD011913 | JPOST Repository
Proteomics Quantitative accuracy and precision in multiplexed single-cell proteomics.
2022-01-28 | PXD027912 | Pride
Proteomics A Bioorthogonal Chemical Reporter for the Detection and Identification of Protein Lactylation
2022-06-23 | PXD033454 | Pride
Proteomics An improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) strategy for precise quantitative single-cell proteomics
2020-03-05 | PXD017626 | JPOST Repository
Transcriptomics Integrating single-cell RNA-seq and imaging with SCOPE-seq2
2020-06-28 | GSE151137 | GEO
Transcriptomics Single-cell Transcriptomes Reveal Diverse Regulatory Strategies for Olfactory Receptor Expression and Axon Targeting
2020-01-04 | GSE143038 | GEO