Use of the Chromatographic System Feature in Scaffold Elements

All of the details associated with the chromatography coupled to an LC-MS instrument – included but not limited to stationary phase, mobile phase, filter size, column size, pore size, gradient length, etc. – can be associated with a metabolomics experiment analyzed in Elements as a simple line of text called the “Chromatographic System”. It is up to the user to choose a textual description that makes sense to them, and that they will be able to understand in the future. Users may specify the Chromatographic System at the point in which they load data, or may associate a Chromatographic System with a completed Elements results file. Setting the Chromatographic System is optional.

Why should a User Specify Their Chromatographic System in Elements?

If a user performs a search based on mass only (ie, Match Type is set to “Mass only”), the chromatographic system is not used during the spectral library search. However, if a user performs a search based on mass and retention time (Match Type is set to “Mass and Retention Time”), the user must specify their chromatographic system, and this chromatographic system must match the chromatographic system of at least some entries in the spectral libraries they provide. To accurately compare retention times between a spectral library and input data, the chromatographic systems must be identical. Note that major public libraries distributed with Elements, such as NIST or HMDB, do not contain chromatographic system information – in fact, only personal spectral libraries generated with Elements contain chromatographic system information.

A user must first search data by mass only and save the results into a personal spectral library. When the results are saved into a personal spectral library, the chromatographic system associated with this data is recorded in the personal spectral library. The personal spectral library can be used in a subsequent analysis searching additional data (in a search by both mass and retention time).

The chromatographic system is a key component to the following workflow:

  1. A new empty spectral library can be made by following Edit > Library Manager > Create
  2. In order to add retention time information to a spectral library, raw data (typically standards) must first be processed in Elements using "Mass Only" as the Match Type. A chromatographic system can be specified at the time of loading or after the analysis is complete.
  3. If the chromatographic system was not specified during loading, one can be added using the Experiment > Set Chromatographic System dialog. The user-provided string can be any identifier that will allow the user to easily remember the details of the chromatographic system used.
  4. Select metabolites of interest in the Samples view, right click and select Add to Library..., or while the metabolites are selected, navigate to Experiment > Add Selected Metabolites to Library.
  5. A dialog will appear inviting the user to determine how to name unknown metabolites, and which spectra to copy into the personal spectral library.
  6. After the options from the dialog in (5) has been a submitted, a new dialog called the Library Preview Dialog will appear. This dialog allows the user to remove, rename, or add or modify chemical structures to metabolites, before these metabolites are added to a personal spectral library. The dropdown menu in the lower left corner of this dialog allows the user to choose an appropriate personal library to add the identified metabolites to.
  7. Now when new raw files are loaded through the Load Data workflow and Mass and Retention Time is selected as the Match Type, the chromatographic system identifier should appear in the dropdown menu.
  8. It is possible to have multiple records of the same metabolite, each from different chromatographic systems, in the same library. In this way, it is possible to limit identifications to those that match the user-specified chromatographic system only.



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