MassIVE MSV000082430

Complete Public PXD010009

SamavarchiTehrani_P112_VS4_Viral_BioID_Benchmark_human

Subscribe Comment Convert Spectra Reanalyze Spectra Compare Results Add Reanalysis

Description

This submission contains the mass spectrometry files for the manuscript by Samavarchi-Tehrani et al. that describes the use of lentiviral delivery of BirA*-tagged transgenes into HeLa, BJ and MEF cells or in comparison to stably integrated transgene in Flp-In T-REx HeLa cell lines. This submission contains the human files from a set of 56 raw MS files and associated peak lists and result files, acquired on a TripleTOF 6600 spectrometer (AB SCIEX, Concord, Ontario, Canada) operated in Data Dependent Acquisition mode. Samples were generated by Payman Samavarchi-Tehrani. This massIVE submission contains the files for the mouse samples. Please see accompanying submission for the human samples. Raw files are deposited here in MassIVE. For questions, please contact Anne-Claude Gingras (gingras@lunenfeld.ca) or Payman Samavarchi-Tehrani (payman@lunenfeld.ca). Table 1 describes the composition of this dataset Table 2 lists all the peptide identification evidence (as per iProphet) Table 3 lists the SAINTexpress interactions Internal reference from the Gingras lab ProHits implementation: Project 112, Export versions VS4 (Viral BioID Benchmark) SAINT Task ID: Flp-HeLa:3596; HeLa:3139; BJ:3140; MEF:3141 [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Affinity purification ; BioID ; Proximity-dependent biotinylation ; Protein-protein interaction ; AP-MS ; Lentivirus

Contact

Principal Investigators:
(in alphabetical order) 		Anne-Claude Gingras, LTRI, Canada
Submitting User: gingraslab

Publications

Samavarchi-Tehrani P, Abdouni H, Samson R, Gingras AC.
A versatile lentiviral delivery toolkit for proximity-dependent biotinylation in diverse cell types.
Mol. Cell Proteomics. Epub 2018 Jul 10.

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 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.