MassIVE MSV000082833

Imported Reanalysis Dataset Public PXD000343

SWATH analysis of 1433B_HUMAN affinity purifications from HEK293 cells after time course treatment with IGF1

Subscribe Comment Reanalyze Spectra Add Reanalysis

Description

Protein complexes and protein interaction networks are essential mediators of most biological functions. Complexes supporting transient functions such as signal transduction processes are frequently subject to dynamic remodeling. Currently, the majority of studies into the composition of protein complexes are carried out by affinity purification and mass spectrometry (AP-MS) and present a static view of the system. Therefore, to better understand inherently dynamic biological processes, methods to reliably quantify temporal changes of protein interaction networks are essential. In this study we used affinity purification combined with SWATH mass spectrometry (AP-SWATH) to study the dynamics of the 14-3-3B scaffold protein interactome after stimulation of the insulin/PI3K/AKT pathway.. The consistent and reproducible quantification of 1967 proteins across all stimulation time points provided new insights into the 14-3-3B interactome and its dynamic change following IGF1 stimulation. We therefore establish AP-SWATH as a tool to quantify dynamic changes in protein complex interaction networks. Data analysis: Profile mode wiff files from shotgun data acquisition were centroided and converted to mzML using the AB Sciex Data Converter v1.3, and further converted to mzXML using ProteoWizard67 MSConvert v3.04.238. Mass spectra were queried against the canonical UniProt complete proteome database for human (July 2011) appended with common contaminants and reversed sequence decoys (40,548 protein sequences including decoys) using XTandem with kscore plugin46, and additionally XTandem with native scoring47. Carbamidomethyl was set as fixed modification for cysteines, and methionine oxidation and phosphorylation on serine/threonine/tyrosine were set as variable modification. Semi-tryptic peptides and peptides with up to 2 missed cleavages were allowed, and mass error was set as 30 ppm and 75 ppm for precursor and product ions respectively. Results from both search engines were individually converted to the pepXML format using Tandem2XML v4.6.0, analysed with PeptideProphet48 v4.6.0, and combined using iProphet49 v4.6.0 including false identification rate calculation. Phosphosite localisation probabilities were estimated using PTMProphet v4.6.1 . [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: quantitative interaction proteomics ; affinity purificaiton ; AP-MS ; AP-SWATH

Contact

Principal Investigators:
(in alphabetical order) 		None Listed
Submitting User: ccms

Publications

Collins BC, Gillet LC, Rosenberger G, Röst HL, Vichalkovski A, Gstaiger M, Aebersold R.
Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system.
Nat. Methods. 2013 Dec;10(12):1246-53. Epub 2013 Oct 27.

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.