Defining the carrier proteome limit for single-cell proteomics.
Tommy K CheungChien-Yun LeeFlorian P BayerAtticus McCoyBernhard KusterChristopher M RosePublished in: Nature methods (2020)
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.
Keyphrases
- single cell
- mass spectrometry
- rna seq
- data analysis
- liquid chromatography
- high throughput
- high resolution
- high performance liquid chromatography
- electronic health record
- capillary electrophoresis
- gas chromatography
- multiple sclerosis
- label free
- quantum dots
- tandem mass spectrometry
- quality improvement
- deep learning
- risk assessment
- water soluble