PXD000343

PXD000343 is an original dataset announced via ProteomeXchange.

Title	SWATH analysis of 1433B_HUMAN affinity purifications from HEK293 cells after time course treatment with IGF1
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 .
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_03:49:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ben Collins
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; phosphorylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-16 01:41:10	ID requested
1	2013-09-25 09:53:53	announced
1	2013-11-21 06:58:28	announced
⏵ 2	2014-07-24 03:49:07	announced	Updated project metadata.

Collins BC, Gillet LC, Rosenberger G, R, ö, st HL, Vichalkovski A, Gstaiger M, Aebersold R, Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat Methods, 10(12):1246-53(2013) [pubmed]

curator keyword: Biomedical

submitter keyword: quantitative interaction proteomics, affinity purificaiton, AP-MS, AP-SWATH,

Ben Collins
contact affiliation	ETH Zurich
contact email	collins@imsb.biol.ethz.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000343
     1. Label: PRIDE project
     2. Name: SWATH analysis of 1433B_HUMAN affinity purifications from HEK293 cells after time course treatment with IGF1