As mentioned in our email to you regarding new opportunities for NMR especially for 600 MHz users, we want to give more details.

As you probably are aware, Human metabolomics has seen a rapid rise in the world of Omics and currently is a major source of funding in many countries worldwide. NMR is one of the 2 main tools in Metabolomics, highly synergistic to mass spectrometry, which is the other tool in use.

At Bruker we have developed a standardized approach to generate high quality spectra of human bodyfluids and analysis of the spectra in terms of quantification from the mixture spectra and also statistical analysis. This is all centered on our IVDr platform and covers currently Urine, Plasma, Serum, CSF and Methanol extracts (from bodyfluids, tissues, cells).

As you can see from below, the complete solution is consisting of 4 levels. Level 1 and 2 are requirements to use the enabling tools and assays in level 3 and 4. In level 4 the grey and yellow boxes describe collaborative developments with partners currently in progress. Everything listed in the blue boxes is available for ordering. Detailed descriptions can be obtained clicking on the boxes.

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We have a base of more than 75 users worldwide working with our standards already and such creating exchangeable spectra for large scale epidemiology research or clinical trials. Amongst those users are also hospitals, biobanks and the members of the International Phenome Center Network (IPCN).

In case you are interested yourself in entering this field, we can inform you, what would be needed to progress to the IVDr platform standard. Since shared use with other applications will be a need for such upgraded systems, we want to assure you, that you are not losing the shared capabilities of the instrument. The IVDr system itself is a fully functional NMR spectrometer, if your system has 3 or more channels, no problem, we can also adapt an existing TCI cryoprobe, even so our first choice are 5mm inverse probes e.g. BBI or TXI.  This however is related to minimum down time for probe exchange and ease of use. In hospitals we want a MTA to be able to run the system in daily routine and avoid non-availability of the systems due to regular warm up procedures as needed on CryoProbes. In addition it should be mentioned, that the sensitivity gain using a cryoprobe for the typical bodyfluid screening experiments is at maximum a factor of 1.6 due to the high salt content.

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We also want to point out, that we already had discussions with several users, where a medical or clinical/translational research department or biobank is in the same organization and was interested to get access to NMR based metabolomics. Such a source of income could be opened to the NMR owners and access to high ranking publications assured. We can support you in identifying potential partners in the human metabolomics field in your environment.

Below you can see typical use cases of the IVDr platform in the clinical/translational value chain.

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Licenses and Packages of Layer 3 Enabling Tools on the IVDr platform

Level 2 - Bruker IVDr Methods: B.I.Methods 2.0

As you are surely aware, there is a strong need for standardization, guaranteeing highest spectral performance, reproducibility and transferability of routines used. This defines, what our   level 2, the B.I.Methods 2.0 has to ensure. The following features are integral part of the procedures

Preanalytics

  • Advice on sample collection, storage and transfer to magnet
  • SOP for sample preparation for 3 and 5mm tubes

 

Spectral properties

  • Generated under fully automated data acquisition and processing conditions
  • Flat baseline without any offset
  • High quality signal suppression for water and methanol at low presaturation power
  • 90 degree pulse and presaturation power are adjusted for every sample, the latter making sure, if integral correction factors are need for signals close to solvent lines being suppressed, they are always the same
  • Automatic transfer of optimized parameters to the 2D-Jres experiment done on every sample
  • Residual solvent signals are always in phase with all non-suppressed signals
  • Automatic phase correction works without errors
  • Daily QC samples to ensure integral calibration, absolute temperature and solvent suppression are correct and integral value for 1 proton is stored in the dataset
  • QC reports for every sample

As you can imagine, such routines can also be of importance for best performance in other applications you run in Water or Methanol. So you can multiply benefit here.

Bruker IVDr Methods B.I.Methods Figure 1
Example of a Methanol Extract of human urine with fourfold suppression of Methanol (including main methanol signal, methanol carbon satellites and water)
Below a series of 34 spectra is shown, produced from the same urine sample in 34 aliquots prepared individually, measured and processed under full automation, no baseline correction applied, the expansion of the TSP signal on the right
Bruker IVDr Methods B.I.Methods Figure 2
Based on the spectra obtained with B.I.Methods 2.0 (available on AVIIIHD and AV-NEO) the enabling tools (layer 3) can be applied

Level 3 - Bruker IVDr Lipoprotein Subclass Analysis: B.I.LISA

With Version 2.0 41 Metabolites are quantified under full automation from serum and plasma. For each metabolite the reference range as obtained from NMR is shown again with grey bars, the black bar shows the person`s values superimposed. In order to improve our quantification results, we have now introduced the raw  concentration (r), which can also be below LOD. TMAO and branched chain amino acids are known to contribute to the risk of cardiovascular disease as well. So with B.I.LISA and B.I.QUANT-PS we offer 2 viewpoints with one experiment and further improved cardio risk analysis is obtained.

An extract showing 1 page of the quantification report including the Aminoacid part of the quantification is displayed below. In case of doubt, an interactive plot can be obtained showing the real spectrum versus the fit.

All Metabolites have undergone wet spiking according to DIN-ISO norm.

Bruker IVDr Lipoprotein Subclass Analysis B.I.LISA Figure 1
Looking in detail to the LDL-Cholesterol on the right side as given below shows the person is in model range, looking to the LDL Cholesterol subfractions, a clear risk profile is visible.
Bruker IVDr Lipoprotein Subclass Analysis B.I.LISA Figure 2
With exactly the same experiment done for lipoproteins, also small molecules in plasma and serum can be quantified using our B.I.QUANT-PS 2.0 tool.

Level 3 – Bruker IVDr Quantification in Plasma/Serum: B.I.QUANT-PS 2.0 new

With Version 2.0 41 Metabolites are quantified under full automation from serum and plasma. For each metabolite the reference range as obtained from NMR is shown again with grey bars, the black bar shows the person`s values superimposed. In order to improve our quantification results, we have now introduced the raw concentration (r), which can also be below LOD. TMAO and branched chain amino acids are known to contribute to the risk of cardiovascular disease as well. So with B.I.LISA and B.I.QUANT-PS we offer 2 viewpoints with one experiment and further improved cardio risk analysis is obtained.

An extract showing 1 page of the quantification report including the Aminoacid part of the quantification is displayed below. In case of doubt, an interactive plot can be obtained showing the real spectrum versus the fit.

All Metabolites have undergone wet spiking according to DIN-ISO norm.

Bruker IVDr Quantification in Plasma Serum B.I.QUANT PS Figure 1Bruker IVDr Quantification in Plasma Serum B.I.QUANT PS Figure 2

Level 3 – Bruker IVDr Quantification in Urine: B.I.QUANT-UR

Fully automated quantification in urine is available on the IVDr platform in 3 versions

  • B.I.QUANT-UR basic: 50 endogenous metabolites
  • B.I.QUANT-UR extended: 150 metabolites, thereof the 50 endogenous (contained in the basic version) and additionally 100 disease markers, age range from 6 month to adults
  • B.I.QUANT-UR neonate extended: 150 metabolites as in the extended version however selective for newborns, in addition a classification against a healthy normal model of newborns is included

B.I.QUANT-UR basic allows to investigate a multitude of diseases as listed below.

Bruker IVDr Quantification in Urine B.I.QUANT UR Figure 1Bruker IVDr Quantification in Urine B.I.QUANT UR Figure 2

Level 4 – Bruker IVDr Inborn Error of Metabolism Panel: B.I.IEM Panel

For the 2 extended versions, B.I.IEM-Panel new can be applied on the quantification list. If added as part of the analysis process, the quantification results are transferred automatically to the Bruker version of the Metagene knowledge base, which covers more than 1000 rare diseases and is constantly updated. The output of Metagene to the user consists of a ranked list of diseases, that can be explained by the metabolites identified in outlying concentration ranges. In addition to the disease, the markers and their expected concentrations as well as the clinical symptoms are listed.

Bruker IVDr Inborn Error of Metabolism Panel B.I.IEM Panel Figure 1
With this additional automatic step a new level of intelligent analysis is offered.
Bruker IVDr Inborn Error of Metabolism Panel B.I.IEM Panel Figure 2
With this additional automatic step a new level of intelligent analysis is offered.

Level 3 – Bruker IVDr BioBank Tool: B.I.BIOBANK-TOOL

NMR analysis is a sensitive and specific tool for biobank QC. As it is also completely standardized, it strongly supports the high need for standardization in biobanks. A biobank should only contain high quality specimens to justify the storage cost. It is vital to be able to have as much information on each aliquot as possible to avoid any wrong conclusions in biobank based clinical trials or research studies. The IVDr Biobank tool generates 36 parameters e.g. for urine QC, it checks for wrong labeling of samples, for unreported drug treatment, high protein content in the urine and  fasted or non-fasted state, just to mention a few.

In addition to the QC part, NMR can deliver added value for the biobanks. Whenever a QC test is done through the IVDr platform, a spectrum is available, that can also be transferred to the biobank metadata. Having spectra allows to run the quantification tools ( B.I.LISA and B.I.QUANT-PS 2.0 for plasma/serum and B.I.QUANT-UR for urine) and the results thereof can be added to the biobank as well. The potential of this can be imagined easily, when multiple biobanks work along the IVDr SOPs and store spectra and quantification results, as these data are completely standardized and can be exchanged with other biobanks worldwide.

An overview of IVDr based biobanking solutions is given below

Bruker IVDr BioBank Tool B.I.BIOBANK TOOL Figure 1Bruker IVDr BioBank Tool B.I.BIOBANK TOOL Figure 2

Quantification results are available as follows and can be ordered as package together with the B.I.Biobank-Tool

Plasma/serum:

  • B.I.LISA lipoprotein parameters including subclass information
  • B.I.QUANT-PS Small molecule quantification

Urine:

  • B.I.QUANT-UR basic 50 small molecule endogenous metabolites
  • B.I.QUANT-UR extended 150 small molecules endogenous + disease markers (children + adults)
  • B.I.QUANT-UR neonate extended 150 small molecules endogenous + disease markers (newborns) + non-targeted statistical classification result compared to healthy newborn model
Licenses and Packages of Layer 3 Enabling Tools on the IVDr platform

The following Licenses are available for all enabling tools through remote analysis:

  • 1 year license: Flatrate
  • 3 year license: Flatrate
  • Pay per use: price per report generated

Packages available:

  • B.I.QUANT-UR extended + B.I.IEM-TOOL 1y/3y/ppu (from Layer 3 and Layer 4)
  • B.I.QUANT-UR neoneate extended + B.I.IEM-TOOL 1y/3y/ppu (from Layer 3 and Layer 4)
  • All enabling tools except B.I.BIOBANK-TOOL in 1 package 1y/3y flat
  • B.I.BIOBANK complete: All enabling tools in 1 package 3y/7y flat

All analysis tools can run fully automatic, transfer the data to the analysis server and receive the results 24/7. Pay-per-use licenses are useful during the phase where you might want to evaluate the methods for your needs. Flatrates allow nearly unlimited usage of the tools, as the maximum number of analysis fits the typical maximum throughput of one IVDr system.

Your sales person can support you to identify the best package to fit your needs and/or budget. If you want to see demonstration examples on your samples, your sales person will also be there to arrange.

Conditions for sending demonstration examples:

  • Transport to the closest demonstration site needs to be deep frozen to prevent degradation of samples during transport
  • A statement needs to be filled, that only non-infectious samples are sent (standard form supplied by Bruker)

Any further questions you might have, will be handled by your sales person in coordination with clinical application development.