A deeper look at carrier proteome effects for single-cell proteomics.
Zilu YeTanveer S BatthPatrick Leopold RütherJesper Velgaard OlsenPublished in: Communications biology (2022)
Multiplexing approaches using tandem mass tags with a carrier proteome to boost sensitivity have advanced single cell proteomics by mass spectrometry (SCoPE-MS). Here, we probe the carrier proteome effects in single cell proteomics with mixed species TMTpro-labeled samples. We demonstrate that carrier proteomes, while increasing overall identifications, dictate which proteins are identified. We show that quantitative precision and signal intensity are limited at high carrier levels, hindering the recognition of regulated proteins. Guidelines for optimized mass spectrometry acquisition parameters and best practices for fold-change or protein copy number-based comparisons are provided.
Keyphrases
- mass spectrometry
- single cell
- copy number
- liquid chromatography
- rna seq
- high resolution
- gas chromatography
- capillary electrophoresis
- mitochondrial dna
- high performance liquid chromatography
- high throughput
- healthcare
- primary care
- genome wide
- multiple sclerosis
- transcription factor
- label free
- computed tomography
- tandem mass spectrometry
- gene expression
- ms ms
- pet ct