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Dataset Identifier

Metadata
datasetIdentifierPASS00093
datasetTypeSRM
submitterAleksey Filimonov <filimonov.a.d@gmail.com>
submitter_organizationIMSB
lab_head_full_nameAlexander Archakov
lab_head_emailalexander.archakov@ibmc.msk.ru
lab_head_organizationIMSB
lab_head_countryRussia
datasetTagIBMC-JPR-2012-QC1
datasetTitleHuman Chr18. Transition groups for 25 light synthetic and 17 heavy peptides corresponding to 21 proteins.
publicReleaseDate2012-11-01 00:00:00
finalizedDate2012-12-11 18:06:26
summary
Dataset QC1 was acquired to elaborate the transition groups for the proteotypic peptides of 21 human proteins encoded by chromosome 18.
contributors
Victor Zgoda
Arthur Kopylov
Alexander Moisa
Olga Tikhonova
Andrey Lisitsa
Aleksey Filimonov
Ekaterina Ilgisonis
Alexander Archakov
publication
Zgoda, VG, Kopylov, AT, Archakov, AI, et al, "Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells", Journal of Proteome Research, submitted 2012-08-31
growth
treatment
extraction
separation
digestion
acquisition
  1. Preliminary transition groups were extracted from the results of MRM scouting of depleted plasma and liver and organized into 9 MRM assays by groups named A to E with least overlapping of RT-window of proteotypic peptides separately for light (L) and heavy (H). Decoy transitions were generated for each assay by ADD_RANDOM algorithm of mGen.
  2. MassHunter Data Acquisition software (Agilent Technologies) was used to create the separate method files for the assays A..E. Target (T) and associated decoy transitions (F) were included into the same method file.
  3. Data acquisition for each assay was conducted using the synthetic peptide mixtures in five technical runs on the triple-quadrupole mass-spectrometer, operating under the conditions specified below.
    • Fragmentor voltage was varied from 107 to 135 V
    • and the capillary voltage to -1970 - 2050 V,
    • drying gas flow 5 L/min, drying gas temperature 280C.
    • Cell accelerating voltage was set to -6.0 V.
    • The collision energies for precursor ions were calculated according the formula
      CE(eV) = (([m/z]/100*3.6) - 4.8)+lg(m/z)*(m/z*0.00062)+(L/2.58),
      where
      m/z - is mass-to-charge value of precursor ion,
      L - is length of peptide in number of amino acid residues,
      and 0.00062 - is correction coefficient.
    • The dwell time per fragment ion was varied from 30 to 60 ms depending on number of concurrent transitions in acquisition method while the full cycle time was within 1.2 seconds.
  4. The aquired transitions with MassHunter correspoing method files (*.m) was stored in the MassHunter data files (*.d) named with metanotation
    [A-E]-{L,H}-TF-r00[1-5].d
    (FreeBSD glob routine).
See also the detailed general Separation and Acquisition Protocol at
http://msr.ibmc.msk.ru/jpr2012/SepAndAcqProt
informatics
  1. Peak groups for synthetic peptides and corresponding profiles of relative intensities of transitions were extracted using manual inspection of the acquired raw spectra in MassHunter Qualitative Analysis (Agilent Technologies). Peak apexes were used to estimate the transitions relative intensity.
  2. Alternatively candidate peak groups were extracted via processing the same raw spectra by in-house extended version of mQuest\mProphet which generates ms2prot-reports with traces and detected peptides.
  3. Manual inspection found candidate peak groups and separation of them onto the true and false peak group categories by comparing with the peak groups proposed by expert on step 1.
  4. Extracting boundaries of RT-windows of proteotypic peptides by analysis of the stability-over-time in aggregate intervals of the trace relative intensities of the transition from the true peak groups.
  5. Calculating most probable relative intensities for each transition in a series of repeated runs and assigning relative intensity profiles to transition groups in final multiplex protein assays A..E, prepared for further measurements in biomaterial.
See the result page with links to the online ms2prot-reports which contain dataset descriptions, traces, peak groups, detected peptides and mProphet output histograms and files, protocols and measurements statistics at
http://msr.ibmc.msk.ru/jpr2012
instrumentsAgilent Triple Quadrupole LC-MS/MS 6410
speciesHuman
massModificationsstatic: L+6.38

Official URL for this dataset: http://www.peptideatlas.org/PASS/PASS00093
To access files via FTP, use credentials:
Servername: ftp.peptideatlas.org
Username: PASS00093
Password: EH9754q

Or use your browser's FTP mode: ftp://PASS00093:EH9754q@ftp.peptideatlas.org/


Listing of files:

 3.7K Aug 28  2012 PASS00093_DESCRIPTION-2012-07-28_075514.txt
 4.4K Dec 11  2012 PASS00093_DESCRIPTION.txt
 4.0K Nov  1  2012 assay
 4.0K Aug 29  2012 raw data
 1.7K Nov  1  2012 read.me
   96 Nov  1  2012 result

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