How to Submit Data

The Upload Submit page instructs researchers on where to put their data and how to npotify curators that data is ready to be checked and loaded by a TraceBase curator. It also describes a recommended directory structure for their submission.

Submissions include a mix of the following types of files:

  • Study Doc (an Excel file)
  • Peak annotation files
  • mzXML and RAW files

General File Guidelines

  • The name of the Study Doc should reflect the name of the study, but there are no strict guidelines.
  • It is suggested that all file and directory names should avoid spaces, when possible.
  • Refrain from editing the content of the Peak Annotation Files

Other files are allowed, but are not used in the load.

Associating mzXML/RAW Files with Peak Annotation Files

You can arrange the study directory however you want, but where possible, it is best to colocate peak annotation files (e.g. AccoCor files) with the raw files that were used to generate them, ideally with one peak annotation file per directory. This will make resolving which same-named mzXML files go with which peak annotation files easier.

Peak annotation files are automatically associated only with the mzXML/RAW files in the immediate directory (not those in subdirectories), however there are exceptions.

If a peak annotation file was generated with a mix of mzXML files, some (but not all) of which were used to generate other peak annotation files, place the peak annotation files in a common parent directory, under which multiple subdirectories contain all of its mzXML/RAW files, even though it may include unassociated raw files. Arranging them this way will usually avoid the ambiguities created by multiple mzXML files with the same name, but only having 1 file of that name under the peak annotation file's current directory.

If 2 mzXML files of the same name exist under a parent directory that contains a peak annotation file in which one of the 2 was used, a curator will populate the mzXML file names column in the Peak Annotation Details sheet of the Study Doc for you, to contain the relative path of the one that was used to generate the peak annotation file, but they may need to reach out to you to know which same-named mzXML goes with which peak annotation file.