Format of Downloaded Data

Downloaded data is available in 2 formats:

  1. Table data in TSV format (Tab Separated Values)
  2. Compressed ZIP format containing mzXML files

The data contained in the downloads are available in 5 basic varieties:

  • From the Download menu at the top of every page, and from the TSV download button in the advanced search:
  • PeakData (TSV)
  • PeakGroups (TSV)
  • FCirc (TSV)
  • From the mzXMLs download button in the advanced search when performing PeakGroups and PeakData searches only:
  • mzXMLs (ZIP of mzXML files and TSV containing metadata - See the ZIP heading, below)
  • From summary tables, accessed via the links in the left sidebar^

See How to Download for more information on accessing these downloads.

TSV

The column inclusion of every TSV download is always the same, regardless of any column visibility settings that may have been applied on the Advanced Search page. This has a couple advantages:

  1. It makes downloaded data amenable to repeatable application of analysis tools outside of TraceBase.
  2. It makes it possible to share data between researchers in a consistent fashion.

Three header rows containing download-related metadata are always included in any downloaded TSV data and are preceded by the comment character #.

# Download Time # Advanced Search Query used to generate the downloaded data # Blank row

Column Names data, where one row = 1 observation

ZIP

The mzXMLs download button on the advanced search downloads a ZIP archive containing a TSV file listing the mzXML files with associated metadata and mzXML files organized into the following directory structure:

  • Mass Spec Run Date
  • Mass Spec Operator Name
    • Instrument Name
    • Liquid Chromatography Protocol Name
      • Polarity
      • Scan Range
        • *.mzXML
  • mzXML metadata in TSV format

Note that mzXML files are optional when submitting data to TraceBase, so not all rows in the PeakGroups and PeakData searches have them. Thus, mzXML downloads can contain a subset of the displayed rows: The ZIP file will include only those rows that have mzXML files available.

mzXML

The mzXML format is an external format described in this paper.