View source for Adding / Editing Metadata of MALDI-TOF Mass Spectral Data

== 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.<br>
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 ==
<br> 
'''What is required?'''
* MS Excel worksheets CMT1-CMT3, the respective template file can be downloaded [[download_MicrobeMS|here (MALDI-Fields.xls)]]
* Matlab(TM) version 2014a or later (see http://www.mathworks.com) and the MicrobeMS pcode toolbox (see [[Main_Page|MicrobeMS]]), or
* MicrobeMS stand-alone version <br>

== 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 <b>spreadsheet CMT1</b> enter the following information for each of the measured spectra:
&nbsp;<br>

<ul>
{| class="wikitable" width=600
!width=150| Three letter code
!width=450| 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)
|}
</ul>

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.

<b>Spreadsheet „CMT2“</b>

This spreadsheet is reserved for data that are used to compose the spectrum id: 

<ul>
{| class="wikitable" width=600
!width=150| Three letter code
!width=450| Description
|-
|DAT
|date of measurement
|-
|OPE
|name of the operator
|-
|NUM
|measurement number
|}
</ul>

Please carefully check the data content of spreadsheet “CMT2”! Incorrect spectra id’s can result in flawed spectra designation and lead to misclassifications.

<b>Spreadsheet „CMT3“</b>

<ul>
{| class="wikitable" width=600
!width=150| Three letter code
!width=450| Description
|-
|CON
|sample concentration
|-
|TRT 
|sample treatment
|-
|EXT 
|extra information
|-
|LAS 
|laser parameters (power, diameter, frequency, etc.)
|-
|CAL 
|calibration info
|-
|CUS
|customer info
|}
</ul>

[[File:assign-id.jpg|400px|thumb|right|FlexControl screenshot - write the file ID into comment line II]] 
<br> &nbsp; <br>

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

[[File:edit-comment-I.jpg|600px|thumb|right|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''

[[File:edit-comment-II.jpg|600px|thumb|right|MicrobeMS screenshot - write metadata to files (comment line II)]] 


   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.jpg)

[[File:edit-comment-III.jpg|600px|thumb|right|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

[[File:edit-header-info.jpg|500px|thumb|right|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'' menu bar. Alternatively, the same 
      information can be obtain from the context menus of 
      individual mass spectra (main figure of MicrobeMS).