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MALDI Guided SpatialOMx on the timsTOF fleX

MALDI-2: Bringing enhanced Sensitivity and Dimensionality

timsTOF fleX is now available with the innovative and powerful MALDI-2 technology option. This post-ionization technique leads to both a significant boost in ion yields and reduction in ion suppression effects, resulting in a signal increase of up to 1-3 orders of magnitude compared to traditional MALDI experiments. For a MALDI Imaging experiment, this increased efficiency translates to more than double the number of molecules detected per pixel resulting in much improved physiological context.

Figure 1: SchematicFigure 1: Schematic
Figure 1: Schematic

Increasing Sensitivity > 100x : Expanding Chemical Range

Ionizing a Wider Range of Compound Classes​ by Reducing Ion Suppression Effects

MALDI-2 Technology empowers your MALDI Imaging studies with unsurpassed sensitivity and the ability to map more compounds. Laser based post-ionization enhances the detection of numerous classes of biomolecules that aren’t typically ionized in the traditional MALDI experiment. MALDI-2 also increases sensitivity for targeted analytes in MALDI Imaging especially by enhancing ion yields and reducing ion suppression effects.

Figure 2: Upregulated compounds in brain tissue
Figure 2: Upregulated compounds in brain tissue

MALDI-2: Leading the Pharma Tissue Model Revolution

A major limiting factor in modern drug development is use of the “well-stirred model” which homogenizes organs and tissues prior to analysis and quantitation with LC-MS studies. This approach is well-suited to providing exact amounts of drugs and metabolites within a target organ, but not readily compatible with pathology methods that seek to describe physiological effects of drug compounds. MALDI imaging has made a significant impact towards the conversion of plasma to tissue models by pinpointing the exact location of drugs and metabolites in tissue. MALDI-2 enhances molecular imaging for pharma studies by increasing overall sensitivity enabling quantitation for a wider range of dosing levels. Additionally, the increased variety of molecular classes seen by MALDI-2 expands the applicability of imaging to many more pharma projects that involve both xenobiotics and endogenous molecules.

Figure 3: Drugs spotted in dilution series on liver homogenate
Figure 3: Drugs spotted in dilution series on liver homogenate
Figure 4: Drug imaging from dosed tissue (Chloroquine)
Figure 4: Drug imaging from dosed tissue (Chloroquine)

TIMS and MALDI-2: Deep Content Imaging for OMICS Context

OMICS studies involving small molecules desorbed from tissues sections such as lipidomics and Metabolomics typically involve biomolecules from a wide variety of chemical classes. These studies benefit from MALDI-2 as the technique provides access to many more compounds, providing unique insight into nature’s complexity.. The combination of TIMS and MALDI-2 is uniquely powerful as richer ion yields from the post-ionization process produce mass spectra with higher information content. TIMS provides fast orthogonal separation that efficiently unravels these complex spectra where each m/z can contain many overlapping features. The result is not only the ability to extract information from single isobars, but also exact masses that have different ion mobilities. Collisional Cross Section (CCS) values are recorded for each one of the spectral components for comparison to databases or LC/MS results.

Figure 5: MALDI-2 and TIMS
Figure 5: MALDI-2 and TIMS

Bruker provides the complete solution

Bruker supplies all elements needed for performing successful MALDI-2 experiments from the necessary matrix and IntelliSlides, to expert application support, and intuitive and user-friendly software solutions.


  • MALDI-2 enables access to chemical classes typically prone to ion suppression in MALDI
  • Sensitivity boost by up to 2-3 orders of magnitude compared to MALDI, depending on sample, matrix and analyte
  • No physical hardware changes needed, switch between MALDI and MALDI-2 with one click in the software
  • User friendly software solution, easy instrument calibration and application scientist tested methods to start measurements immediately
  • easy to use consumables available to provide complete solution

MALDI-2 on the timsTOF fleX

A tumor is more than meets the eye

The microenvironment of cancers contains a combination of healthy cells, tumor cells, connective tissue, blood vessels, and inflammation in different ratios at different time points. Each of these components will have their own unique-molecular signature of compounds. Researchers who study disease states rely heavily on interpreting tissue pathology and creating these maps within the context of biomolecules bridges the gap between traditional OMICS and understanding disease. 

Press release ASMS 2019

SpatialOMx – the key to biomarker discovery 

Cancer cells and other disease states have significant genetic and epigenetic modifications that influence the genomic expression cascade. Whether you’re looking at the proteome, lipidome or metabolome, the spatial distribution of compounds contains valuable Information for understanding your sample. If certain compounds are highly spatially concentrated or if molecules are co-distributed on specific structures, this vital information is missing when only examining homogenized samples. OMICS based biomarker discovery can be limited without the benefit of spatial information to add important contextual clues as tissue-level communications networks are integral to cancer growth. 

Rat brain lipid image acquired on the timsTOF fleX. Measured at 20 µm spatial resolution, this contains 312,095 spectra with acquisition time of five hours. Lower panel shows segmentation analysis generated from this dataset in SCiLS Lab. The spectra are clustered into regions corresponding to different brain regions.

Bring a spatial dimension to X-Omics analyses

The timsTOF fleX is a versatile instrument for probing the molecular content of your sample. Built on Bruker’s pioneering timsTOF Pro platform, the timsTOF fleX is a fully functional high speed, high sensitivity ESI instrument for all your X-Omics analyses, combined with a high spatial resolution MALDI source and stage specifically designed for resolving molecular distributions and bringing a spatial dimension to OMICS analyses. Transform proteomics analysis into spatial proteomics, lipidomics into spatial lipidomics, and metabolomics into spatial metabolomics. 

SpatialOMx Workflow
SpatialOMx Workflow (click to enlarge)

Create your own Atlases of Intricate Interactions

Mapping complex molecular networks exposes intricate systems of interacting molecules within intracellular networks. Using SpatialOMx to create insightful atlases of communication mechanisms means learning more about the way cells communicate with each other to support change:

  • how cells interact with the local microenvironment to formulate promotion and mediation processes
  • how molecular networks of specific cells interact to perform specific biological functions
  • what effect epigenetic modifications have within these networks.  

The timsTOF fleX – the flexibility to switch between spatial metabolomics, spatial lipidomics or spatial proteomics with ease.

Rick Drake

Prof. Richard R. Drake, Director, Proteomics Center, Medical University South Carolina, USA

“The timsTOF fleX is an innovative instrument that synergizes multiple analytical capabilities to allow development of novel omics workflows. For imaging MS, it may be potentially transformative, especially for tissue metabolomics and glycomic applications.”

Combining the world’s fastest proteomics instrument with over 25 years of MALDI experience

Match PASEF powered LC-MS/MS identification with label-free spatial localization to decode the molecular make up of your sample

Built on the standard for shotgun proteomics, the timsTOF fleX combines best in class 4D X-Omics with Bruker’s cutting edge MALDI Imaging technology, including SmartBeam 3D laser optics for fast measurement all in one platform. A dual source instrument ideal for SpatialOMx, timsTOF fleX conducts robust ESI measurements and spatially resolves a wide range of molecules directly from tissue using one platform. No single instrument has before provided access to both essential capabilities for the most advanced OMICS researchers. 

Schematic of the timsTOF fleX
Schematic of the timsTOF fleX

From 4D OMICS to molecular imaging without stopping, changing, modifying or compromises

SpatialOMx demands PASEF enabled LC-MS/MS for deep 4D OMICS combined with the ability to create molecular images of tissue sections with MALDI Imaging. To do this under one platform, Bruker engineers started with the award winning TIMS dual-stage ion funnel and incorporated target stage and laser elements from the rapifleX axial TOF instrument.  During operation, software activation of the SmartBeam 3D laser is the only change in the source region.  No complicated changeover means making zero compromises in productivity and the ability to move effortlessly from world class OMICS identification and quantification workflows to creating high definition molecular maps of tissue sections to see what matters most. 

Since ions produced by MALDI and ESI travel the same path to the detector from the source, MALDI workflows can take advantage of the most advanced features found in the timsTOF Pro, including TIMS ion mobility separation based on the collisional cross section of detected molecules and high-speed high-sensitivity PASEF fragmentation. Tuning and calibration can be performed in ESI mode and used for the MALDI experiment for additional ease of optimization.

Direct molecular profiling from tissue with MALDI Imaging

MALDI Imaging is a label-free tool for examining the distribution of molecules directly from thin tissue sections. Applicable for examining a wide range of analytes, including metabolites, lipids or glycans, and seamlessly compatible with microscopy workflows, MALDI Imaging can identify regionally specific compound distributions for SpatialOMx analyses. Use Bruker’s IntelliSlides for automated MALDI Imaging and SpatialOMx workflows on the timsTOF flex.

TIMS removes isobaric interferences in lipid imaging
TIMS removes isobaric interferences in lipid imaging.
Blue: m/z 762.6 +/-0.016; mob. 1.45 +/- 0.012
Yellow: m/z 762.6 +/-0.016; mob. 1.48 +/- 0.015

Zoom mode to see what really matters

Besides the ability to generate high definition “True Pixel” MALDI images, the SmartBeam 3D laser source provides rock solid laser guided targeting down to 10µm with Bruker’s new zoom mode technology. Users now have the flexibility to adjust their laser spot size and spacing to accommodate a wider range of granularity depending on biological features of interest.

Mouse retina
Mouse retina measured for lipids at 10 µm in Zoom mode. Scale bar indicates 100 µm
(Image courtesy Jeffrey Spraggins, Ph.D., Mass Spectrometry Research Center, Vanderbilt University)

Combining X-Omics performance with high MALDI sensitivity

timsTOF fleX uniquely enables SpatialOMx

Whether it’s proteomics, lipidomics, glycomics, or metabolomics, the timsTOF fleX is the ideal platform for deep SpatialOMx analyses. Use patented SmartBeam™ 3D technology to conduct fast, label-free MALDI Imaging for mapping the distribution of molecules in your sample and identify regions of interest for more specific analyses. Apply PASEF powered LC-MS/MS for the highest level of identifications and for greatest confidence in your results.

Differences in organ functions are reflected in differences in their expressed proteins
Differences in organ functions are reflected in differences in their expressed proteins

High speed and high sensitivity for biomarker discovery

Combining the power of trapped ion mobility spectrometry (TIMS) and Parallel Accumulation Serial Fragmentation (PASEF), the timsTOF fleX can deliver quantitative information from smaller amounts of highly complex mixtures. Using less than 200 ng sample load and a 90 min gradient length, more than 5400 protein groups can be identified from a typical human cell line lysate. The high sensitivity reduces sample preparation costs and decreases time lost to maintenance.

MALDI Imaging for investigating compound distributions

With existing protocols for lipidomics, metabolomics or glycomics, MALDI Imaging spectra can be used as a molecular fingerprint for specific regions, or to investigate how compounds are localized across an entire sample for biomarker discovery. This can also be used for investigation of temporal changes, quantification, and correlation of compounds to tissue states. The timsTOF fleX allows for fast high mass resolution MALDI imaging – with the SmartBeam 3D and specialized MALDI source and stage, a high spatial resolution measurement of lipids from a rat brain section consisting of 370,000 pixels takes less than 5 hours.

MALDI guided SpatialOMx for laser precise efficiency

Traditional workflows that sample small tissue sections (<100 µM) provide deep molecular details for a variety of chemical classes including RNA/DNA, proteins, glycans, lipids and metabolites. However, processing times are long and tissue excise locations are determined with optical images that lack molecular signal information. SpatialOMx on the timsTOF fleX rapidly provides a high definition, label-free overview that merges chemical information with vital morphological context. Choose your regions of interest manually or use SCiLS enabled automated segmentation to know exactly where your extraction will have the highest impact.

Introducing an automated molecular annotation workflow for SpatialOMx

Using Bruker’s industry leading software, it is now possible to annotate target molecules directly from tissue. Simply load your data into SCiLS Lab, define regions of interest, and export the peak lists to MetaboScape. Annotate your peaks using databases or compound lists from LC-MS/MS analyses, then review and export your annotations back to SCiLS for visualization. From SCiLS you can then visualize results with pathways and familiar nomenclature rather than mass labels to reduce the time from data to results. 

Figure 1
Novel Mass Spectrometry Imaging Workflow: Automated annotation of metabolites and lipids from tissue.
*Lipid Maps and HMDB are not Bruker products.

IntelliSlides™ - Maximize information content per pixel with intelligence

Specifically designed to simplify MALDI Imaging workflows, IntelliSlides are the optimal tool for mapping molecules across your samples.  Your effortless time-to-result has never been faster.

Simplify MALDI Imaging experiments

IntelliSlides are the ideal sample target for MALDI Imaging. Potential sources of inefficiency are removed by having permanent inscriptions on the conductive surface. These inscriptions streamline the User experience by aiding sample tracking and indicating where to place the tissue sample. Always correctly labelled, always oriented properly, IntelliSlides simplify the way to your results.

Perfect for SpatialOMx

In SpatialOMx workflows on the timsTOF fleX, MALDI Imaging is used to map molecule distributions across tissue sections, thereby identifying regions of interest and focusing X-Omics analyses to specific cell populations. With IntelliSlides and specialized software, the image registration process on the timsTOF fleX is automated at the touch of a button. Quickly aligning the target sample with the timsTOF fleX laser optics, the workflow set up is brought down to three minutes with IntelliSlides, allowing you to more rapidly and accurately match the chemical information to every pixel. 

Compatible with histology

IntelliSlides have the same dimensions of standard microscopy slides and are compatible with common histology stains and procedures, such as hematoxylin and eosin. With the permanent inscriptions, there’s no more concern that registration marks (also known as ‘teach marks’) will dissolve in histology solvents, allowing for easier co-registration of post-measurement stained tissues with the corresponding MALDI dataset.

Features and Benefits of IntelliSlides 

  • Fulfills all requirements for reliable MALDI ionization
  • All inscriptions on conductive slide surface
  • Permanent registration marks (teach marks) indicate where to place the sample and are used for alignment within MALDI instrument
  • Unique serial number and barcode to simplify sample tracking
  • Automated image acquisition set up with fleXimaging 5.1 and above
  • Compatible with histology and microscopy techniques
  • IntelliSlides are a single-use consumable to avoid potential sources of contamination
Total time depends on teach mark appearance and individual
user experience/ability (5 to 30 mins)

For Research Use Only. Not for Use in Clinical Diagnostic Procedures.