MassIVE MSV000093672

Partial Public PXD047860

Exploration of adult mouse Single Cardiomyocyte Proteome using Label-Free LC-MS

Subscribe Comment Reanalyze Spectra Add Reanalysis

Description

Cardiac myocyte heterogeneity has been acknowledged based on ion channel expression, cellular electrophysiology and through transcriptomics, but the exploration of individual cardiomyocytes at the board proteome-wide level has remained challenging. We developed an entire analytical pipeline to assess the cell heterogeneity of adult primary cardiomyocytes isolated from mouse hearts. Over 700 single cell proteomes were isolated from 4 mice hearts. Each single cell image was captured by the cellenONE sorter interface and evaluated for morphological features of apoptotic cells, i.e.: hypercontracted cell shape. This imaging analysis allowed us to retain 270 rod-shaped cardiac cells for downstream single cell proteome sample processing and analysis on Bruker timsTOF SCP mass spectrometer. Final dataset UMAP dimension reduction and clustering analysis yielded 3 cardiomyocyte cell sub-populations that displayed differential: i) expression of Myh7 and Myh7b, ii) carbon metabolism signatures and iii) distribution of 7 proteins involved in calcium signaling. Single cardiomyocyte protemes demonstrated potential differences related to the metabolism and calcium ion handling between those sub-populations and could bring new insights for cardiology studies on mice. [doi:10.25345/C5NG4H33R] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Single cell proteomics ; mass spectrometry ; cardiomyocyte ; heart ; myosin ; mouse

Contact

Principal Investigators:
(in alphabetical order) 		Jennifer Van Eyk, Cedars Sinai Medical Center, United States
Submitting User: bineka
Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.