PXD000574

PXD000574 is an original dataset announced via ProteomeXchange.

Title	Dectin-1/Syk pathway activates autophagy-dependent unconventional protein secretion from human macrophages
Description	Before stimulation, the cells were washed and the culture media was changed to RPMI-1640. After stimulation, cell culture media were collected, concentrated, and the proteins were precipitated with 2-D Clean-Up Kit (GE Healthcare) followed by protein alkylation, trypsin digestion and iTRAQ labelling of the resulting peptides according to manufacturer´s instructions (Applied Biosystems). Control sample was labeled with 114, LPS-stimulated with 115, Curdlan-stimulated with 116, and GBY-stimulated with 117 isobaric tag. After labelling the samples were pooled and dried, and the peptides were fractionated by strong cation exchange chromatography using an Ettan HPLC system (Amersham Biosciences) connected to a PolySULFOETHYL A column. Each SCX-fraction containing labelled peptides was analyzed twice with nano-liquid chromatography-tandem mass spectrometry using Ultimate 3000 nano-liquid chromatograph (Dionex) and QSTAR Elite hybrid quadrupole time-of-flight mass spectrometer (Applied Biosystems / MDS Sciex) with nano-ESI ionization as previously described (Lietzén et al., 2011). MS data were acquired automatically using Analyst QS 2.0 software. Protein identification and relative quantitation were performed with ParagonTM search algorithm (Shilov et al., 2007) using ProteinPilot 2.0 interface (AB Sciex). Data files from both technical replicates of an iTRAQ sample set were processed together. Database searching was done against UniProt human database (version 2008-01-28 with 20330 human sequences) and ´decoy` database (the reverse amino acid sequence for false discovery rate estimation). The search criteria were: cysteine alkylation with MMTS, trypsin digestion, biological modifications allowed, thorough search and detected protein threshold of 95% confidence (Unused ProtScore > 1.3). Importantly, automatic bias correction was not used in quantitation. The false discovery rates were calculated as previously described (Elias and Gygi, 2007) and were 1.4% and 2% for the two biological replicates.
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_03:48:17.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tuula Nyman
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iTRAQ4plex-116 reporter+balance reagent acylated residue; methylthiolated residue
Instrument	QSTAR

Revision	Datetime	Status	ChangeLog Entry
0	2013-11-08 06:40:27	ID requested
1	2014-05-12 02:39:37	announced
⏵ 2	2014-07-24 03:48:18	announced	Updated project metadata.

Ö, hman T, Teiril, ä L, Lahesmaa-Korpinen AM, Cypryk W, Veckman V, Saijo S, Wolff H, Hautaniemi S, Nyman TA, Matikainen S, Dectin-1 pathway activates robust autophagy-dependent unconventional protein secretion in human macrophages. J Immunol, 192(12):5952-62(2014) [pubmed]

curator keyword: Biological

submitter keyword: Human, macrophages, dectin-1, iTRAQ

Tuula Nyman
contact affiliation	Institute of Biotechnology
contact email	tuula.nyman@helsinki.fi
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000574
     1. Label: PRIDE project
     2. Name: Dectin-1/Syk pathway activates autophagy-dependent unconventional protein secretion from human macrophages