Dataset Information

PepDESC: A Method for the Detection of Differentially Expressed Proteins for Mass Spectrometry-Based Single-Cell Proteomics Using Peptide-level Information.

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.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC10316082 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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pepDESC: A Method for the Detection of Differentially Expressed Proteins for Mass Spectrometry-Based Single-Cell Proteomics Using Peptide-level Information.

Zhang Yutong Y

Molecular & cellular proteomics : MCP 20230524 7

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 express ...[more]

PMID: 37236439

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Project description:BackgroundThe thymus is an immune organ essential for life and plays a crucial role in the development of T cells. It undergoes a fetal to adult developmental maturation process occurring in mouse during the postnatal months. The molecular modifications underlying these ontogenic changes are essentially unknown. Here we used a differential proteomic-based technique (2D-Difference Gel Electrophoresis) coupled with matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry to search for key proteins in the postnatal development of the thymus. Eight different BALB/c mice were used in the study: four mice aged of 1 day (neonatal) and four mice aged of 60 days (adult). Protein samples derived from thymus were labeled and run in 2D-PAGE (Two-Dimensional Polyacrylamide Gel Electrophoresis). One whole-thymus tissue from each mouse was run on gels and each gel containing a pooled sample of the eight mice was run in parallel. The pooled sample was set as the internal pool, containing equal amount of each protein extract used in the experiment. Gels were matched and compared with Difference In-gel Analysis software. Differential spots were picked, in-gel digested and peptide mass fingerprints were obtained.ResultsAmong the differentially regulated proteins in neonatal thymus group, 111 proteins were identified by mass spectrometry, of which 95 proteins were up-regulated and 16 proteins were down-regulated. The identified proteins belong to several functional categories, including cell proliferation, cycle and apoptosis, transcription regulation, signal transduction, nucleotide processing, proteolysis and translation, protein folding, metabolism, oxidoreduction, cytoskeleton, immune response, and embryonic development. The major interaction networks comprised of cellular function and maintenance, cellular assembly and organization, and metabolism were also identified by STRING analysis.ConclusionsThe demonstrated molecular changes are relevant for understanding thymus development as well as neonatal immune function, and they provide the diagnostic disease markers. Further studies will be required to describe in detail the role of the identified proteins in thymus maturation and in the specific functions of neonatal thymus.

Dataset Information

PepDESC: A Method for the Detection of Differentially Expressed Proteins for Mass Spectrometry-Based Single-Cell Proteomics Using Peptide-level Information.

Publications

pepDESC: A Method for the Detection of Differentially Expressed Proteins for Mass Spectrometry-Based Single-Cell Proteomics Using Peptide-level Information.

Similar Datasets

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