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Single Cell Proteomics and the Carrier Proteome Effect

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) comprise technical limitations with the potential to effect data quality and biological interpretation. These limitations are particularly relevant when a carrier proteome, a sample added at 25-500x single cell proteomes, 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 a program that enables rapid evaluation of single cell proteomics data and recommends instrument and data analysis parameters for improved data quality.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Christopher Rose

PROVIDER: MSV000085959 | MassIVE | Sun Aug 16 16:23:00 BST 2020

REPOSITORIES: MassIVE

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Single Cell Proteomics and the Carrier Proteome Effect

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