MassIVE MSV000093703

Partial Public

A chemoproteomics method for direct and comprehensive characterization of cysteine reversible oxidation

Subscribe Comment Convert Spectra Add Reanalysis

Description

Cysteine oxidation is a series of protein modifications caused by reactive oxygen species (ROS) in cells and can regulate protein functions and cellular activities. Comprehensive and site-specific characterization of the cysteine oxidation is critical for understanding the role of ROS regulating cellular events. Here we developed a chemoproteomics method to directly and systematically detect the reversible cysteine oxidation sites. Different from the commonly used methods for indirect detection of cysteine oxidation, this method allows for direct targeting of oxidized cysteine for MS analysis. The method was validated using small molecules containing oxidized cysteines and the whole cell lysate treated with the probe, demonstrating that it specifically targets reversible oxidized cysteines. In total, 3000-4000 proteins containing cysteine oxidation sites were identified from Jurkat, MCF7 and HEP G2 cells, respectively. Combining with multiplexed proteomics, we applied the method to quantify cysteine oxidation changes in the livers from mice fed with the high or low fat diet (HFD/LFD). It was found that the overall cysteine oxidation in mouse liver was dramatically upregulated with HFD, and the upregulation is correlated with protein distribution, functions, and the flanking residues of the oxidation sites. Many biological processes critical in the pathology of fatty liver diseases are also significantly enriched among the oxidized proteins with higher abundance in the HFD samples, suggesting the potential regulatory role of cysteine oxidation in the diseases. Additionally, the method was applied to study the cysteine oxidation change in THP-1 cells with the lipopolysaccharide treatment, and among >15000 cysteine oxidation sites quantified in THP-1 cells, many of them were upregulated under the treatment. For the oxidized proteins with upregulated oxidation sites, they are associated with inflammation and immune response, indicating the potential role of cysteine oxidation in regulating cellular response to bacterial infection. This chemoproteomics method can be widely applied to comprehensively study cysteine oxidation events in various samples. [doi:10.25345/C5N87395H] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: proteomics ; protein modifications ; Cysteine oxidation

Contact

Principal Investigators:
(in alphabetical order) 		Ronghu Wu, Georgia Institute of Technology, United States
Submitting User: xusenhan
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.