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NPC Standard Project

A set of standardised project descriptions and data for use in unit-tests and development.

Project_Description

Files describing the study-design and composition of a project. UnitTest1 is an example project consisting of seven samples of serum and seven samples of urine from four subjects.

  • UnitTest1_metadata_PCDOC.014.xlsx - Excel manifest describing subjects, sampling events, and sample aliquots in the project.
  • UnitTest1_metadata_Unified.csv - Basic CSV version of UnitTest1
  • ISATAB-Unit-Test - ISATBAB format version of UnitTest1 sample metadata

Derived _Worklists

Worklists derived from the study design and used to define assay data names and and run order.

  • UnitTest1_MS_serum_PCSOP.021.csv - LC-MS experiment description file for UnitTest1 serum samples
  • UnitTest1_MS_serum_PCSOP.069.csv - LC-MS experiment description file for UnitTest1 serum samples
  • UnitTest1_NMR_serum_PCSOP.012.csv - NMR experiment description file for UnitTest1 serum samples
  • UnitTest1_NMR_urine_PCSOP.011.csv - NMR experiment description file for UnitTest1 urine samples
  • UnitTest3_NMR_serum_PCSOP.012.csv - NMR experiment description file for UnitTest3 serum samples
  • UnitTest1_metadata_basic_csv.csv - Description UnitTest1 including reference samples in an MS assay

Raw_Data

Raw analytical data files. Most binary data has been truncated for space, leaving text parameter files

  • ms - MS raw data

    • parameters_data Waters .raw format data files to test parameter extraction - Binary data files have been truncated
    • parameters_data Open .mzML format data files to test parameter extraction - Most scans were removed

  • nmr - NMR raw data

    • UnitTest1 Bruker format spectra of urine - Binary data files have been truncated
    • UnitTest3 Bruker format spectra of serum - Binary data files have been truncated

Derived_Data

File representing feature-extracted or otherwise processed raw data.

  • UnitTest1_PCSOP.069_Biocrates.xlsx - Excel output
  • UnitTest1_PCSOP.069_QI.csv - Cut down output from the Progenesis QI LC-MS feature extraction software
  • UnitTest1_PCSOP.069_QI_intensityData.csv
  • UnitTest1_PCSOP.069_xcms.csv - Cut down output from the XCMS LC-MS feature extraction software
  • UnitTest1_PCSOP.069_xcms_peakTable.csv - Cut down output from the XCMS LC-MS feature extraction software
  • UnitTest2_artifactualFiltering.csv
  • UnitTest3_BI-LISA.xls - Quantified lipoproteins generated by the Bruker BI-LISA platform
  • UnitTest4_targeted.xml - Targeted LCMS intergrations from TargetLynx
  • bruker_quant_BILISA.xml - XML format quantified lipoproteins generated by the Bruker BI-LISA platform
  • bruker_quant_urine.xml - XML format small-molecule quantifications generated by the Bruker BI-QuantUR platform