BD Bruker MBT - SN040 - LIMS Integration

QM0941FM Service Note Template Rev 2
DCR-02753 Effective 06-01-2021
MALDI Biotyper
MBT Service Note 40
Internal use only

This document does not replace any training.
Information on LIMS Integration

Systems Affected: Serial Numbers : Software Version :
MALDI Biotyper (MBT) Systems all MBT 3.1
MBT 4.0
MBT Compass
MBT Compass HT
MBT Compass IVD
1. Introduction 2
2. MBT 3.x 3
3. MBT 4.0 7
4. MBT Compass RUO 13
5. MBT Compass IVD 19
6. MBT Compass HT 21
7. Transfer LIMS settings 27
8. CSV import examples 27
Please send comments and questions to

Biotyper.Support@Bruker.com or Biotyper.SW.Support@Bruker.com
Maldi.SW.Support@Bruker.com or Maldi.Support@Bruker.com
or contact a Bruker representative in your area.
Document History
Rev. Date Changes TPS Approval
A 09/06/2021 Release Karsten Krämer/ (Felix Joppe)
Karsten Krämer (TPS) Page 1 of 27

Refer to DCR (DCR-05097) for authorizations. Effective Date: 23-09-2021
MBT_SN40_LIMS Integration.docx
- confidential -
MALDI Biotyper
1. Introduction
Connecting the MBT system to a laboratory information management system (LIMS) is divided into two
major features. LIMS export is sending MBT results from the MBT to the LIMS (MBT perspective: MBT →
LIMS). LIMS import is the handling of target layouts which are created by the LIMS (MBT perspective:
LIMS → MBT). For both import and export there are two approaches to set up a connection: Either via a
transferred CSV file that is saved in a dedicated directory or directly via an ASTM socket.
For a CSV-file-based import, the LIMS writes a CSV file representing the target layout into a specific folder
(default: MBT-IN). This file gets imported by the MBT to create a target with the defined layout. For a CSV-
file-based export, the MBT writes a CSV file into a specific folder (default: MBT-OUT) after the analysis.
The LIMS collects and interprets this CSV file to process the results. Both MBT and LIMS need to have
access to the dedicated directories. The customer’s IT might need to set up network, security software and
sharing accordingly.
For an ASTM-based import, the MBT requests a target layout directly at the LIMS. If a target layout is
deposited for the inquired target ID, it is sent as an answer to the MBT. For an ASTM-based export, the
MBT contacts the LIMS after the analysis to inquire, if the LIMS expects results for the respective target ID.
If that is the case and the request is accepted, the results for the respective target ID are sent by the MBT.
To set up a LIMS connection via ASTM IP address and port of the LIMS are needed. The customer’s IT
might need to set up network and security software accordingly.
LIMS import and export are set up differently depending on the MBT version and are managed by different
parts of the software (either server or client). A combination of CSV-file-based and ASTM-based LIMS
connection is possible.
Import Export
requires IP address & port of LIMS requires IP address & port of LIMS
MBT 3.1: no ASTM import MBT 3.1, MBT 4.0, MBT Compass:
MBT 4.0, MBT Compass, MBT Compass via Web Interface
HT: via Configuration MBT Compass HT: via Configuration
ASTM MBT 4.0, MBT Compass: by client (local by server (user “Local System”)
user)
MBT Compass HT: by server (user “Local
System”)
requires shared folder (default: MBT-IN) requires shared folder (default: MBT-OUT)
MBT 3.1: via registry MBT 3.1, MBT 4.0, MBT Compass:
MBT 4.0, MBT Compass, MBT Compass via Web Interface
HT: via Configuration MBT Compass HT: via Configuration
MBT 3.1, MBT 4.0, MBT Compass: by client by server (user: “Local System”)
CSV (local user)
MBT Compass HT: by server (user “Local
System”)

- confidential -
MALDI Biotyper
2. MBT 3.x
2.1. Import
The Import is client specific, so it needs to be configured for each client individually. It is set up via Windows
registry:
- open registry editor: Windows key + R, enter “regedit”
HKEY_CURRENT_USER\Software\Bruker Daltonik\BioTyper Automation Control\Configuration
2.1.1. CSV Import

The file import requires a comma-separated values (CSV file), however the file suffix can be different than
*.csv and the column arrangement can vary. The file needs at least a column with spot positions and a
column with sample ID. Example files can be found in Chapter 7The following variables and values define
composition and location of the import file:
variable (default) value function

importFolder D:\\Data\\MBT-IN Import folder
csvDelimiter ; Delimiter for import file
importSuffix in, csv File type of import file
importDeleteAfterLoaded dword:00000000 or Delete file after it has
dword:00000001 been imported
posOnScoutImportColumnNumber dword:00000001 column of spot position
(required)
externalIdImportColumnNumber dword:00000002 column of sample ID
(required)
nameImportColumnNumber dword:00000003 column of sample name
(optional)
descriptionImportColumnNumber dword:00000004 column of description
(optional)
The respective user needs at least reading permission for the import folder (in case of a network folder).
To delete the csv files after the import, writing permission is required. Only files with the specified suffix are
shown in the import list. The CSV delimiter separates columns for each row. Each row represents one spot
on the target plate. Each column is mapped to the information it contains (spot, sample ID, etc.).
2.1.2. ASTM Import

- No ASTM import possible
2.2. Export
The export is handled by the MBT server. It is set up via the web interface:
http://localhost:8080/mbt-admin/administration
- User: root
- Password: Bruker#2011
→ LIMS Integration
Web Interface MBT 3.1 – LIMS Integration

- confidential -
MALDI Biotyper
2.2.1. CSV Export
To activate a CSV file export a pre-defined export configuration needs to be activated or a new configuration
needs to be created. The file export is primarily used to create comma-separated values (CSV) files, even
though the suffix can be different than *.csv . The files are created in the given output folder either
automatically after a run has been finished or by exporting a run manually. The following settings and
menus define composition, trigger and destination of the export file:
Destination
- To set the path for a file export the destination URI needs to start with file:/// followed by the
path. To indicate a network folder, use file://///. The user “local System” needs writing
permission for that folder. The destination extension has no influence on the file composition
and can be different than *.csv.
Type and trigger
- The export file can either represent a project or an analyte. For a project export (Type: Project)
each row in the CSV file represents an analyte and the file name is the project name. For an
analyte export (Type: Analyte) each row represents an identification result and the file name
is the analyte name.
- The trigger type determines when the results are exported:
o After Analyte Result: export is triggered after each analyte result (Type: Analyte
only)
o After Project Result: export is triggered after all analyte results are finished
Manual: export is triggered manually by clicking “Export results” in the MBT client
software
o Manual And After Project Result: export is triggered after all analyte results are
finished and can additionally be triggered manually by clicking “Export results” in the
MBT client software
Transformation and composition
- The export is processed by a transformation script (see → Transformation Script). The most
recent script can be downloaded here:
ftp://ftp.bdal.de/data/Support/TOF/MaldiBiotyper/BiotyperSWSupport/Tools/LIMS_integration/
Transformation_Scripts/project2lims.xsl
- script parameters can be used to adjust the variables for the transformation script. Multiple
script parameters can be added by separating them with semicolons. For a CSV export the
following script parameter needs to be set: outputType=CSV.
- Filter expressions can be used to limit the export to analytes or projects that fulfil specific filter
criteria.
For additional information on script parameters, script adjustments or filter expressions, please contact the
MBT Software support (biotyper.sw.support@bruker.com).

- confidential -
MALDI Biotyper
Default export configuration of CSV export of MBT 3.1
2.2.2. ASTM Export

To activate an ASTM export a pre-defined export configuration needs to be activated or a new configuration
needs to be created. The ASTM export is based on a direct communication between LIMS and MBT via a
(American Society For Testing and Materials) communication protocol (see MALDI Biotyper ASTM
Communication Interface Specification Version 4.3). For this communication the LIMS acts as server and
the MBT as client. The following settings and menus define trigger and options for the ASTM socket
connection:
Destination
- To set the path for an ASTM export, the destination URI needs to start with astm:// followed by
IP address and port. This information needs to be provided by the customer. Because no file
is written in the ASTM export process, the destination extension can be “none”.
Type and trigger
- The export protocol can either represent a project (Type: Project) or an analyte (Type:
Analyte).
only)
software
MBT client software

- confidential -
MALDI Biotyper
script parameters can be added by separating them with semicolons.
criteria.
Default export configuration of ASTM export of MBT 3.1

- confidential -
MALDI Biotyper
3. MBT 4.0
3.1. Import
The import is set up via the Configuration in the MBT client:
- open configuration in MBT 4.0 client
→ Advanced screen (Windows administrator login and password)
→ Addins
Configuration MBT 4.0
3.1.1. CSV Import

The checkbox for “CSV File Import” needs to be checked and the client needs to be restarted to access the
CSV Import Configuration. The file import requires a comma-separated values (CSV file) (see MALDI
Biotyper2 LIMS-Integration (Version 1.1.1, KOK, 2008-10-10)), however the file suffix can be different than
column with sample ID. Example files can be found in Chapter 7 The following settings and menus define
Run name
- The run name can either be the file name plus a prefix (which can be empty) or the default run
name given by the MBT.
- confidential -
MALDI Biotyper
Import folder
- Import folder and import suffix can be adjusted. The respective user needs at least reading
permission for the import folder (in case of a network folder). To delete the csv files after the
import, writing permission is required. Only files with the specified suffix are shown in the import
list.
CSV file composition (column mapping)
- The CSV delimiter separates columns for each row. Each row represents one spot on the target
plate. Each column is mapped to the information it contains (spot, sample ID, etc.). An example
import file can be loaded to check and adjust the current column mapping. The column for each
information can be changed manually via the dropdown menu.
CSV Import MBT 4.0

- confidential -
MALDI Biotyper
3.1.2. ASTM Import
The checkbox for “Lims Server Import” needs to be checked and the client needs to be restarted to access
the ASTM Import Configuration. The ASTM import is based on a direct communication between LIMS and
MBT via a (American Society For Testing and Materials) communication protocol (see MALDI Biotyper
ASTM Communication Interface Specification Version 4.3). For this communication the LIMS acts as server
and the MBT as client. The following settings and menus define options for the ASTM socket connection:
LIMS server
- To specify the ASTM connection the IP address (or PC name) of the LIMS server needs to be
entered as well as the used port at the LIMS server. This information needs to be provided by
the customer.
Run name
- The run name can either be the sent project name plus a prefix (which can be empty) or the
default run name given by the MBT.
ASTM Import MBT 4.0

- confidential -
MALDI Biotyper
3.2. Export
- User: Administrator
- Password: smovxai6
→ Export Configuration
Web Interface MBT 4.0 – Export Configuration
3.2.1. CSV Export

Destination
Type and trigger
only)
software
MBT client software
- confidential -
MALDI Biotyper
criteria.
Default export configuration of CSV export of MBT 4.0
3.2.2. ASTM Export

connection:
Destination

- confidential -
MALDI Biotyper
Type and trigger
Analyte).
only)
software
MBT client software
criteria.
Default export configuration of ASTM export of MBT 4.0

- confidential -
MALDI Biotyper
4. MBT Compass RUO

4.1. Import
The Import is client specific, so it needs to be configured for each client individually. It is set up via the
Configuration in the MBT client:
- open configuration in MBT Compass RUO client
→ Advanced screen (Windows administrator login and password)
→ Addins
Configuration MBT Compass RUO
4.1.1. CSV Import

The checkbox for “CSV File Import” needs to be checked and the client needs to be restarted to access the
CSV Import Configuration. The file import requires a comma-separated values (CSV file) (see MALDI
Biotyper2 LIMS-Integration (Version 1.1.1, KOK, 2008-10-10)), however the file suffix can be different than
column with sample ID. Example files can be found in Chapter 7 The following settings and menus define

- confidential -
MALDI Biotyper
Run name
- The run name can either be the file name plus a prefix (which can be empty) or the default run
name given by the MBT.
Import folder
list.
information can be changed manually via the dropdown menu.
CSV Import MBT Compass RUO

- confidential -
MALDI Biotyper
4.1.2. ASTM Import

The checkbox for “Lims Server Import” needs to be checked and the client needs to be restarted to access
the ASTM Import Configuration. The ASTM import is based on a direct communication between LIMS and
MBT via a (American Society For Testing and Materials) communication protocol (see MALDI Biotyper
ASTM Communication Interface Specification Version 4.3). For this communication the LIMS acts as server
and the MBT as client. The following settings and menus define options for the ASTM socket connection:
LIMS server
the customer.
Run name
- The run name can either be the sent project name plus a prefix (which can be empty) or the
default run name given by the MBT.
ASTM Import MBT Compass RUO

- confidential -
MALDI Biotyper
4.2. Export
- Password: smovxai6
Web Interface MBT Compass – Export Configuration
4.2.1. CSV Export

Destination
Type and trigger
only)
software
MBT client software
- confidential -
MALDI Biotyper
criteria.
Default export configuration of CSV export of MBT Compass
4.2.2. ASTM Export

connection:
Destination

- confidential -
MALDI Biotyper
Type and trigger
Analyte).
only)
software
MBT client software
criteria.
Default export configuration of ASTM export of MBT Compass

- confidential -
MALDI Biotyper
5. MBT Compass IVD

5.1. Import
The Import is client specific, so it needs to be configured for each client individually. It is set up via LIMS
import tools:
- See Chapter 5.1.1. & 5.1.2.
5.1.1. CSV Import

To set up a CSV file import in MBT Compass IVD, please use the following tool:
ftp://ftp.bdal.de/data/Support/TOF/MaldiBiotyper/BiotyperSWSupport/Tools/LIMS integration/
MBT-Compass-IVD-Activate-CSVImport.exe
The file import requires a comma-separated values (CSV file) (see MALDI Biotyper2 LIMS-Integration
(Version 1.1.1, KOK, 2008-10-10)), however the file suffix can be different than *.csv and the column
arrangement can vary. The file needs at least a column with spot positions and a column with sample ID.
Example files can be found in Chapter 7 The following settings and menus define composition and location
of the import file:
Import folder
list.
CSV Import tool MBT Compass IVD
5.1.2. ASTM Import

To set up a ASTM import connection, please use the following tool:
ftp://ftp.bdal.de/data/Support/TOF/MaldiBiotyper/BiotyperSWSupport/Tools/LIMS
integration/MBT-Compass-IVD-Activate-LIMSImport.exe
The ASTM import is based on a direct communication between LIMS and MBT via a (American Society For
Testing and Materials) communication protocol (see MALDI Biotyper ASTM Communication Interface
Specification Version 4.3). For this communication the LIMS acts as server and the MBT as client. The
following settings define options for the ASTM socket connection:
- confidential -
MALDI Biotyper
LIMS server
the customer.
ASTM Import tool MBT Compass IVD
5.2. Export
- Password: smovxai6-IVD
5.2.1. CSV Export

- See Chapter 4.2.1.
5.2.2. ASTM Export

- See Chapter 4.2.2.

- confidential -
MALDI Biotyper
6. MBT Compass HT
6.1. Import
The import is set up via the Configuration in the MBT client:
- open configuration in MBT Compass HT client (Laboratory Manager role)
→ Import
6.1.1. CSV Import

The switch for “CSV Import Enabled” needs to be activated. Multiple import configurations can be set up.
The file import requires a comma-separated values (CSV file) (see MALDI Biotyper2 LIMS-Integration
(Version 1.1.1, KOK, 2008-10-10)), however the file suffix can be different than *.csv and the column
arrangement can vary. The file needs at least a column with spot positions and a column with sample ID.
Example files can be found in Chapter 7 The following settings and menus define composition and location
of the import file:
Effective Computers & Users

- The import can be set up individually for different users and clients (PCs).
Import folder
list.
information can be changed manually via the move buttons.

- confidential -
MALDI Biotyper
CSV Import MBT Compass HT

- confidential -
MALDI Biotyper
6.1.2. ASTM Import
The switch for “Lims Import Enabled” needs to be activated. Multiple import configurations can be set up.
The ASTM import is based on a direct communication between LIMS and MBT via a (American Society
For Testing and Materials) communication protocol (see MALDI Biotyper ASTM Communication Interface
Specification Version 4.3). For this communication the LIMS acts as server and the MBT as client. The
following settings and menus idefine options for the ASTM socket connection:
LIMS server
the customer.
Sample type
- The sample type can be transferred via the ASTM socket and needs to be matched to the
sample types defined in the MBT Compass HT configuration for this feature to be used.
ASTM Import MBT Compass HT
6.2. Export
The export is set up via the Configuration in the MBT client:
- open configuration in MBT Compass HT client (Laboratory Manager role)
→ Export
6.2.1. CSV Export

Destination

- confidential -
MALDI Biotyper
Trigger
-
The trigger type determines when the results are exported:
o AUTOMATICALLY: export is triggered after all analyte results are finished
MANUAL: export is triggered manually by clicking “Export results” in the MBT client
software
o MANUAL_AND_AUTOMATICALLY: export is triggered after all analyte results are
MBT client software
- The export is processed by a transformation script. The most recent script can be downloaded
here:
criteria.
Default export configuration of CSV export of MBT Compass HT

- confidential -
MALDI Biotyper
6.2.2. ASTM Export
connection:
Destination
Trigger
o AUTOMATICALLY: export is triggered after all analyte results are finished
MANUAL: export is triggered manually by clicking “Export results” in the MBT client
software
o MANUAL_AND_AUTOMATICALLY: export is triggered after all analyte results are
MBT client software
- The export is processed by a transformation script. The most recent script can be downloaded
here:
criteria.

- confidential -
MALDI Biotyper
Default export configuration of ASTM export of MBT Compass HT

- confidential -
MALDI Biotyper
7. Transfer LIMS settings

The Export settings are stored in the MBT database and are therefore conserved when updating a database
from MBT 3.1→MBT4.0→MBT Compass or when restoring a database backup. Because MBT Compass
RUO and MBT Compass IVD use different databases, the LIMS settings cannot be transferred from RUO
to IVD or vice versa via a database backup. The MBT Compass web interface offers the function “Transfer
LIMS Settings” to save and load the LIMS settings including the export configuration as a xml file. This
function can be used to transfer LIMS settings between MBT Compass RUO and MBT Compass IVD. The
Import settings are client specific and cannot be transferred reliably.
Transfer LIMS Settings MBT Compass
8. CSV import examples

8.1. Minimal requirement CSV import example for the two mandatory columns:
Position, ID
A1;BTS
A2;00001-1
A3;00002-1
A4;00003-1
A5;00003-2
A6;00004-1
A7;00005-1
A8;00006-1
A9;00007-1
8.2. CSV import example for the column mapping: Position, ID, Name; Sample
Type, Description
A1;BTS;Standard;Bts;This is the standard
A2;00001-1;Name A;Sample;This is sample A
A3;00002-1;Name B;Sample;This is sample B
A4;00003-1;Name C;Sample;This is sample C
A5;00003-2;Name C;Sample;This is also sample C
A6;00004-1;Name D;Bloodculture;This is blood culture sample D
A7;00005-1;Name E;MycobacteriaSample;This is mycobacteria sample E
A8;00006-1;Name F;FilamentousFungiSample;This is filamentous fungi sample F
A9;00007-1;Name G;NetgativeIonModeSample;This is negative iron mo

- confidential -

BD Bruker MBT - SN040 - LIMS Integration

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

BD Bruker MBT - SN040 - LIMS Integration

Uploaded by

Copyright:

Available Formats

QM0941FM Service Note Template Rev 2

DCR-02753 Effective 06-01-2021

MBT Service Note 40

Internal use only

Information on LIMS Integration

Please send comments and questions to

Karsten Krämer (TPS) Page 1 of 27

Karsten Krämer (TPS) Page 2 of 27

2.1.1. CSV Import

variable (default) value function

2.1.2. ASTM Import

Web Interface MBT 3.1 – LIMS Integration

Karsten Krämer (TPS) Page 3 of 27

Karsten Krämer (TPS) Page 4 of 27

Default export configuration of CSV export of MBT 3.1

2.2.2. ASTM Export

Karsten Krämer (TPS) Page 5 of 27

Default export configuration of ASTM export of MBT 3.1

Karsten Krämer (TPS) Page 6 of 27

Configuration MBT 4.0

3.1.1. CSV Import

CSV Import MBT 4.0

Karsten Krämer (TPS) Page 8 of 27

ASTM Import MBT 4.0

Karsten Krämer (TPS) Page 9 of 27

Web Interface MBT 4.0 – Export Configuration

3.2.1. CSV Export

Default export configuration of CSV export of MBT 4.0

3.2.2. ASTM Export

Karsten Krämer (TPS) Page 11 of 27

Default export configuration of ASTM export of MBT 4.0

Karsten Krämer (TPS) Page 12 of 27

4. MBT Compass RUO

Configuration MBT Compass RUO

4.1.1. CSV Import

Karsten Krämer (TPS) Page 13 of 27

CSV Import MBT Compass RUO

Karsten Krämer (TPS) Page 14 of 27

4.1.2. ASTM Import

ASTM Import MBT Compass RUO

Karsten Krämer (TPS) Page 15 of 27

Web Interface MBT Compass – Export Configuration

4.2.1. CSV Export

Default export configuration of CSV export of MBT Compass

4.2.2. ASTM Export

Karsten Krämer (TPS) Page 17 of 27

Default export configuration of ASTM export of MBT Compass

Karsten Krämer (TPS) Page 18 of 27

5. MBT Compass IVD

5.1.1. CSV Import

CSV Import tool MBT Compass IVD

5.1.2. ASTM Import

ASTM Import tool MBT Compass IVD

5.2.1. CSV Export

5.2.2. ASTM Export

Karsten Krämer (TPS) Page 20 of 27

6.1.1. CSV Import

Effective Computers & Users

Karsten Krämer (TPS) Page 21 of 27

CSV Import MBT Compass HT

Karsten Krämer (TPS) Page 22 of 27

ASTM Import MBT Compass HT

6.2.1. CSV Export