Adding / Editing Metadata of MALDI-TOF Mass Spectral Data

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Introduction

When analyzing MALDI-TOF mass spectra from microorganisms it is often important to have direct access to taxonomic information, parameters of cultivation, of the sample preparation method and other relevant data associated with mass spectra acquisition in the context of microbiology. Historically, MALDI-TOF mass spectrometry was developed in the late 1980s and beginning of the 1990s from physicists for physicists and chemists. None of the developers at these times could imagine that MALDI-TOF MS could be relevant for classification and identification of microorganisms. Therefore, most of MS data formats developed in these years (which often are used today in almost unchanged form) offer no possibilities for storing such additional microbiological (non-spectrometric) metadata.
Metadata information is extensively used in MicrobeMS. With this tutorial it is intended to describe a methodology aiming to circumvent the limitations associated with the manufacturer's original spectra file format.

Requirements


What is required?

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
FlexControl screenshot - write the file ID into comment line II


 

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 pulldown menu of the MicrobeMS 
     program
MicrobeMS screenshot - write metadata to files (comment line I)


  5. Check the radio button comment line II


  6. Open Microsoft Excel and load the document MALDI fields.xls
MicrobeMS screenshot - write metadata to files (comment line II)


  7. In Microsoft Excel select the spreadsheet CMT2 and copy 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.jpg)
MicrobeMS screenshot - write metadata to files (comment line III)


  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 in 
     the same way as it was done in step 8 (see also figure
     export-header-info-2.jpg)


  11.Repeat the procedure for data contained in the spreadsheet 
     CMT3
MicrobeMS screenshot - view/edit metadata


  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 pulldown menu. Alternatively, the same 
     information can be obtain from the context menus of 
     individual mass spectra (main figure of MicrobeMS).