PXD000410

PXD000410 is an original dataset announced via ProteomeXchange.

Title	Peatland Soil Community Proteomics
Description	These samples were collected from Stordalen Mire in Abisko Sweden on August 2010 from a core at 24-27cm. Microbial proteins were extracted from an in situ lysis protocol with 5% SDS and boiling. Peptides were analyzed by 22hr 2D-LC-MS/MS. A 22-hr 11-step two-dimensional separation was performed with a U3000 HPLC and ionized into the MS via nanospray ionization. During the full chromatographic runs, the MS oscillated between full scans in the Orbitrap at 30K resolution and 20 data-dependent MS/MS spectra in the dual linear ion trap. The entire run was controlled by Xcalibur, with dynamic exclusion on, and 2 microscans averaged for both the full scans and MS/MS scans . Three technical replicates were analyzed. Data analysis: The resultant MS/MS spectra were analyzed by an automated proteome informatics pipeline that uses SEQUEST and DTASelect. Raw spectra are extracted via readW program (ISB version 4.3.1), MS/MS spectra were searched against a database consisting of (i) metagenomic contigs from the same sample (consisting of 3,348,142 proteins predicted using Prodigal 2.50 (ii) wheat (NCBI February 2010, Protein sequences from NCBI taxonomy ID 4565) and (iii) with the common contaminants trypsin and human keratin. SEQUEST Searches using these databases were performed with the following parameters: Parent Mass Tolerance, 3.0; Fragment Ion Tolerance, 0.5; up to 4 missed cleavages allowed, and fully tryptic peptides only. No other modifications were analyzed. SEQUEST outputs were sorted and filtered via DTASelect with the following parameters: delta CN, >0.08; Xcorr, >1.8 (+1), 2.5 (+2), >3.5 (+3); +1 minimum charge state, +3 maximum charge state; and 2 peptides/protein.
HostingRepository	PRIDE
AnnounceDate	2017-09-13
AnnouncementXML	Submission_2017-09-13_02:00:54.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eun-Hae Kim
SpeciesList	scientific name: unidentified soil organism; NCBI TaxID: 46465;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2013-08-13 01:54:29	ID requested
1	2014-02-03 02:52:17	announced
2	2014-07-24 03:49:39	announced	Updated project metadata.
⏵ 3	2017-09-13 02:00:55	announced	Updated project metadata.

Mondav R, Woodcroft BJ, Kim EH, McCalley CK, Hodgkins SB, Crill PM, Chanton J, Hurst GB, VerBerkmoes NC, Saleska SR, Hugenholtz P, Rich VI, Tyson GW, Discovery of a novel methanogen prevalent in thawing permafrost. Nat Commun, 5():3212(2014) [pubmed]

curator keyword: Metaproteomics, Biological

submitter keyword: Peatland, soil microbial community, metaproteomics, wetland community

Eun-Hae Kim
contact affiliation	Soil, Water, and Environmental Science
contact email	eunhaekim@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/02/PXD000410

PRIDE project URI

• PRIDE
  1. PXD000410
     1. Label: PRIDE project
     2. Name: Peatland Soil Community Proteomics