MassIVE MSV000095615

Partial Public

Tyrosine kinase Ptk1 couples one carbon metabolism and virulence in an endogenous pathogen

Subscribe Comment Reanalyze Spectra Add Reanalysis

Description

Samples were analyzed by GelC MS using in-gel trypsinization. Digests were analyzed using an EASY nLC (ThermoFisher) UHPLC system and an Acclaim PepMap 100 trap coupled to an Acclaim PepMap RSLC 50 um separating column (ThermoFisher). The eluate was introduced into the LTQ-Orbitrap ELITE mass spectrometer using a Nanospray Flex source (ThermoElectron). A Nth Order Double Play method was created in Xcalibur v2.2. Scan event one of the method obtained an FTMS MS1 scan (normal mass range; 120,000 resolution, full scan type, positive polarity, profile data type) for the range 300 to 2000 m/z. Scan event two obtained ITMS MS2 scans (CID activation type, normal mass range, rapid scan rate, centroid data type) on up to twenty peaks that had a minimum signal threshold of 5000 counts from scan event one. The lock mass option was enabled using the 371.101236m/z polysiloxane peak as an internal calibrant. Peaks Studio Xpro (Bioinformatics Solutions) was used to analyze the data against the 9/30/2021 version of the P. gingivalis strain ATCC 33277 protein sequences from the UniProtKB (proteome identifier UP000008842) considering semi specific Trypsin (maximum two missed cleavages) with fragment tolerance (0.5 Da) from the ITMS and parent tolerance (15 ppm) from the FTMS. FDR estimation was enabled in the algorithms. A proteins.csv file was exported for curation in Microsoft Excel. Proteins and peptides were accepted at the 1% FDR threshold. [doi:10.25345/C5MK65M1V] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: affinity purification ; Bacterial PTK1 client proteins ; One carbon metabolism

Contact

Principal Investigators:
(in alphabetical order) 		Michael L. Merchant, PhD, University of Louisville, USA
Submitting User: mmerchant
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.