Adding / Editing Metadata of MALDI-TOF Mass Spectral Data
Introduction
When analyzing MALDI-TOF mass spectra of microorganisms, it is often important to have direct access to taxonomic information, cultivation parameters, sample preparation methods, and other relevant data associated with the acquisition of mass spectra in the context of microbiology. Historically, MALDI-TOF mass spectrometry was developed by physicists for physicists and chemists in the late 1980s and early 1990s. At that time, it was difficult for the developers to imagine that MALDI-TOF MS could be relevant to the classification and identification of microorganisms. As a result, most of the MS data formats developed in those years (and often still used today in almost unchanged form) do not provide any way to store additional microbiological (non-spectrometric) metadata.
However, metadata information is important for the evaluation of identification results, so this data is extensively used in MicrobeMS. Therefore, the purpose of this tutorial is to describe a methodology to circumvent the limitations associated with the original manufacturer's spectra file format.
Requirements
What will be required?
- MS Excel worksheets CMT1-CMT3, the respective template file can be downloaded here (MALDI-Fields.xls)
- Matlab(TM) version 2014a or later (see http://www.mathworks.com) and the MicrobeMS pcode toolbox (see MicrobeMS), or
- MicrobeMS stand-alone version
Complete the MS Excel template „MALDI fields.xls“:
This template consists of three separate spreadsheets labeled as CMT1, CMT2 and CMT3.
In the cells of spreadsheet CMT1 enter the following information for each of the measured spectra:
| Three letter code | Description |
|---|---|
| GEN | genus information |
| SPE | species info |
| STR | strain info |
| TYP | type |
| UID | Uniprot species ID |
| UIE | Uniprot strain ID |
| GTI | cultivation conditions: growth time |
| TEM | cultivation conditions: cultivation temperature |
| AIR | cultivation conditions: cultivation under aerobic or anaerobic conditions |
| MED | cultivation conditions: cultivation medium |
| SPO | spore formers (YES or NO) |
Use cells of horizontal rows to enter the appropriate information of a given MALDI-TOF mass spectrum. For example the genus information should be indicated in column B of the spreadsheet „CMT1“. Note that rows 1-4 are locked and cannot be modified.
Spreadsheet „CMT2“
This spreadsheet is reserved for data that are used to compose the spectrum id:
| Three letter code | Description |
|---|---|
| DAT | date of measurement |
| OPE | name of the operator |
| NUM | measurement number |
Please carefully check the data content of spreadsheet “CMT2”! Incorrect spectra id’s can result in flawed spectra designation and lead to misclassifications.
Spreadsheet „CMT3“
| Three letter code | Description |
|---|---|
| CON | sample concentration |
| TRT | sample treatment |
| EXT | extra information |
| LAS | laser parameters (power, diameter, frequency, etc.) |
| CAL | calibration info |
| CUS | customer info |
It is important to enter the spectra description info of a given mass spectrum into identical rows of all three spreadsheets (see example below). Once all data have been entered completely, the Excel worksheet processes the information by updating the content of cells in column A. Copy the cell content of column A (column A of spreadsheet „CMT2“) into the field "Line 2" of the FlexControl program (Bruker Daltonics) when the MALDI measurement has been completed and the spectrum is stored (see screenshot below).
Processing information from the spreadsheets „CMT1“ and „CMT3“
The information from columns A of the Microsoft Excel spreadsheets CMT1-CMT3 can be automatically exported into the original MALDI-TOF mass spectral data files (original Bruker Daltonics data format, note that this function does not support exporting metadata to mzXML data files!). This procedure can be carried out by using the function write metadata to files of the MicrobeMS software. This tutorial describes the steps that are taken in order to write the information to the spectra data files.
1. It is strongly recommended to test the procedure on a copy of the original mass spectra: Copy the original mass spectra into a separate folder (for example into C:\test)
2. Start MicrobeMS (stand-alone version or the Matlab pcode version)
3. In MicrobeMS load the spectral data files you wish to update. Note that each mass spectrum should contain a valid spectral id (i.e. the information of spreadsheet CMT2, see section 1. of this tutorial)
4. Select write metadata to file from the edit menu bar of the MicrobeMS program
5. Check the radio button comment line II
6. Open Microsoft Excel and load the document MALDI fields.xls
7. In Microsoft Excel select the spreadsheet CMT2 and copy the cell content of row A with the id’s of mass spectra to be updated. Do not copy the complete column!
8. In MicrobeMS press button paste. The content of the cells should now appear in the active figure (cf. figure export-header-info-1.png)
9.Switch back to Microsoft Excel and copy cells of column A of spreadsheet CMT1. ATTENTION: It is important to copy information from exactly the same lines as it was done in step 7. Failure will result in processing of wrong metadata information!
10.Switch back to MicrobeMS and paste the data in the same way as it was done in step 8 (see also figure export-header-info-2.png)
11.Repeat the procedure for data contained in the spreadsheet CMT3
12.When completed the button edit is activated (this button was grayed out before). Note that the button remains inactive in cases where the number of lines in fields CMT1-CMT3 are different (for clarity these numbers are displayed below the radio buttons comment line I-III, see screenshot above)
13.Press button edit. MicrobeMS is now comparing the id’s of mass spectra in workspace and the information content of comment line II. In case of identical id’s the data of comment line I and III are added to the original Bruker Daltonics spectral data files (acqu, acqus, pdata/proc and pdata/procs).
14.Close MicrobeMS and re-load the mass spectra. The mass spectra should now contain extra fields with the information added. This information is accessible through the button edit (lower left corner of the main user interface or via the command view/edit metadata of the Edit menu bar. Alternatively, the same information can be obtain from the context menus of individual mass spectra (main figure of MicrobeMS).