MassIVE MSV000093796

Partial Public PXD048334

Quantitative analysis of ribosomal protein expression in bacteria

Subscribe Comment Convert Spectra Reanalyze Spectra Add Reanalysis

Description

Analysis of ribosomal proteins purified as ribosome particles. Two set of samples were analyzed: 1) ribosomes purified from bacteria expressing sgRNA that does not target any ribosomal RNA gene (control); 2) ribosomes purified from bacteria expressing sgRNA targeting three ribosomal RNA genes. The aim of the project is to quantify the peptides and compare both sets of samples. The ribosomal peptides prepared from the bacteria expressing the sgRNA targeting the rRNA genes are expected to be less abundant than in the control samples. The two sample sets are the following: A-D (four biological replicates) are the samples from the bacteria expressing functional sgRNA downregulating three rRNA genes. E-H (four biologicial replicates) are the control samples from the bacteria expressing sgRNA that do not target any rRNA gene. All the sampes were spiked with an almost equivalent amount of ribosomes from a WT strain grown in almost 100% 13C and 15N labelled minimum medium. Ribosomes were purified according to published protocols. Basically, the ribosome particles are sedimented by ultra-centrifugation in a saccharose-rich medium. The recovered pellets were resuspended for electrophoretic migration (stacking gel only) for later in-gel trypsinolysis. The obtained peptides were extracted from the gel according to standard procedures and analyzed by LC-MS/MS on a QExactivePlus Orbitrap mass spectrometer (Thermo scientific). The raw data were converted to mzXML (raw data files) and processed using our proteomics software suite (i2MassChroQ, see http://pappso.inrae.fr/en/bioinfo/). The database search engine was X!Tandem, that produces, for each MS run file analyzed, a corresponding XML file, that we submit here as the database search identification data files). The X!Tandem program was first configured to run without accounting for labelled peptides (one set of "light-only" XML files were thus generated by X!Tandem). Then, X!Tandem was configured to account for all the residues labelled 100% with 13C and 15N (one set of "heavy-only" XML files were thus generated by X!Tandem). We loaded first the "light-only" X!Tandem-generated XML files in i2MassChroq, checked the quality of the data and wrote to disk an XPIP (i2MassChroq project file) file for the four replicates of both sample sets all taken together. Then we did this likewise for the "heavy-only" X!Tandem-generated XML files (at this time we configured i2MassChroQ to look for heavy-isotope-labelled peptides). We finally open the two XPIP files (light-only and heavy-only) and save the combination of the data to a new XPIP file (light-and-heavy). The quantitative analysis was performed inside the i2MassChroq's MassChroQ module which is then directed to write a spreadsheet file with all the identification/quantification data of the peptides. That spreadsheet file was then used within GNU-R to perform data reformatting and peptide quantification work (comparison of the amount of selected peptides belonging to known ribosome subunits between the two data sets). [doi:10.25345/C5MW28R5D] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: bacteria ; ribosome ; quantification

Contact

Principal Investigators:
(in alphabetical order) 		Michel Arthur, Centre de Recherche des Cordeliers, INSERM, France
Submitting User: rusconi
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
Browse Quantification Results
 
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.