pepDESC: A Method for the Detection of Differentially Expressed Proteins for Mass Spectrometry-Based Single-Cell Proteomics Using Peptide-level Information.
Mol Cell Proteomics
; 22(7): 100583, 2023 07.
Article
em En
| MEDLINE
| ID: mdl-37236439
ABSTRACT
Single-cell proteomics as an emerging field has exhibited potential in revealing cellular heterogeneity at the functional level. However, accurate interpretation of single-cell proteomics data suffers from challenges such as measurement noise, internal heterogeneity, and the limited sample size of label-free quantitative mass spectrometry. Herein, the author describes peptide-level differential expression analysis for single-cell proteomic (pepDESC), a method for detecting differentially expressed proteins using peptide-level information designed for label-free quantitative mass spectrometry-based single-cell proteomics. While, in this study, the author focuses on the heterogeneity among the limited number of samples, pepDESC is also applicable to regular-size proteomics data. By balancing proteome coverage and quantification accuracy using peptide quantification, pepDESC is demonstrated to be effective in real-world single-cell and spike-in benchmark datasets. By applying pepDESC to published single-mouse macrophage data, the author found a large fraction of differentially expressed proteins among three types of cells, which remarkably revealed distinct dynamics of different cellular functions responding to lipopolysaccharide stimulation.
Palavras-chave
Texto completo:
1
Bases de dados:
MEDLINE
Assunto principal:
Peptídeos
/
Proteômica
Tipo de estudo:
Diagnostic_studies
Limite:
Animals
Idioma:
En
Revista:
Mol Cell Proteomics
Assunto da revista:
BIOLOGIA MOLECULAR
/
BIOQUIMICA
Ano de publicação:
2023
Tipo de documento:
Article