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Dataset Identifier

Metadata
datasetIdentifierPASS00724
datasetTypeSWATH
submitterSarah Parker <sarah.parker@cshs.org>
submitter_organizationCedars-Sinai Medical Center
lab_head_full_nameJennifer van Eyk
lab_head_emailJennifer.VanEyk@cshs.org
lab_head_organizationCedars Sinai Medical Center
lab_head_countryUnitest States
datasetTagCiRT_DIA_2015
datasetTitleRaw DIA files and libraries used in the manuscript "Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry"
publicReleaseDate2015-08-30 00:00:00
finalizedDate2015-07-21 15:18:51
summaryData independent acquisition files and corresponding library files used to demonstrate the value of a set of conserved, commonly occurring peptide sequences to align chromatographic retention time between spectral libraries and DIA files.
contributorsSarah J Parker, Hannes Rost, George Rosenberger, Ben C Collins, Lars Malmström, Dario Amodei, Vidya Venkatraman, Koen Raedschelders,Jennifer E Van Eyk, Ruedi Aebersold
publicationSarah J Parker, Hannes Rost, George Rosenberger, Ben C Collins, Lars Malmström, Dario Amodei, Vidya Venkatraman, Koen Raedschelders, Jennifer E Van Eyk, Ruedi Aebersold. Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry, Molecular and Cellular Proteomics, Accepted July 2015
growth
treatment
extractionProtein samples were lysed/extracted in 8M UREA
separationIn some samples for DDA library building, peptides were fractionated by either basic reverse phase or OFFGEL to increase analytical depth.
digestionTrypsin
acquisitionC18 reverse phase LC upstream of TripleTOF operating in either DDA mode (top 20 most intense ions fragmented) of DIA mode (25 x 32Da fixed windows with 0.5da overlap on each end).
informaticsPeptide spectral matches from DDA data were made using !XTandem and probability scores assigned using peptide prophet. Spectral libraries were assembled in SpectraST (TPP v4.6), retention time aligned using custom python script spectrast2spectrast_irt.py and assay libraries generated using the custom python script spectrast2tsv.py with subsequent conversion to .TraML format and appending of Decoy peak groups in openMS. Targeted peak group extraction and scoring in DIA files was performed by openSWATH, with FDR modeling by pyprophet.
instrumentsSCIEX TripleTOF 5600
speciesHuman, Mouse, Yeast
massModificationsstatic: C+57.021464, M+15.994915,S+79.966331, T+79.966331,Y+79.966331

Official URL for this dataset: http://www.peptideatlas.org/PASS/PASS00724
To access files via FTP, use credentials:
Servername: ftp.peptideatlas.org
Username: PASS00724
Password: PE5429zy

Or use your browser's FTP mode: ftp://PASS00724:PE5429zy@ftp.peptideatlas.org/


Listing of files:

 807K Jul 17  2015 CiRTA_114.TraML
  92K Jul 17  2015 CiRT_SW.TraML
   46 Jul 21  2015 HumanFiles
   46 Jul 15  2015 MouseFiles
  47K Jul 17  2015 OpenSWATH_iRT.TraML
 2.2K Jul 15  2015 PASS00724_DESCRIPTION.txt
   46 Jul 21  2015 YeastFiles
  303 Jul 16  2015 swaths.txt

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