Untargeted biomarker discovery

MALDI Imaging for untargeted biomarker discovery and classification

Molecular changes originate at the cellular level and solution-based techniques lack sensitivity to capture changes produced from small cell populations.

MALDI imaging of sample cohorts along with SCiLS Lab analytical software extracts unique spatial patterns of proteins, lipids or metabolites and correlates them with sample pathology to identify and map putative biomarker ions.

breast image
Image and segmentation analysis of a breast cancer biopsy. (l to r) delete unstained optical image; average profile spectra from 4 top-most segments; PCA analysis showing distribution of top four segments; segmentation map showing spatial distribution of top-four segments based on similarity of their molecular profiles.

Analyze large sample cohorts for biomarker discovery using molecular profiles and sample metadata to find relevant biomarkers that compliment histology. SCiLS lab is the leading biomarker discovery software for analyzing mass spectrometry imaging with 2D and 3D visualization, as well as sophisticated statistical analysis with just a few mouse clicks, including: automatic spatial segmentation, co-localization analysis,  classification model calculation, ROC and component analysis (PCA,pLSA etc). 

3D kidney
3D visualization with SCiLS lab, Oetjen et al., Journal of Proteomics, 2013
Brain sections
Segmentation analysis of five serial rat brain sections


Bruker’s SCiLS Lab analytical software can mine hundreds of thousands of pixels using a variety of statistical tools.

Biomarker discovery protocols can accommodate fresh-frozen or formalin-fixed and paraffin embedded (FFPE) tissues or tissue microarrays (TMAs). Many tissue banks routinely fix biological specimens for long-term storage. Fixation agents act by crosslinking proteins into an insoluble Network, creating an excellent preservation technique. FFPE protocols involve additional processing steps of antigen-retrieval and protein digestion. Numerous publications have demonstrated the utiilty of imaging tryptic peptides from tissue or liberated N-linked glycans.

Hear how Bruker’s MALDI imaging tools for biomarker discovery are helping Prof. Richard Drake of the Medical University of South Carolina, to gain new insight into the glycosylation pathways of cancer development.

timsTOF fleX for MALDI guided SpatialOMx

SpatialOMx on the timsTOF fleX rapidly provides a high definition, label-free overview that merges chemical information with vital morphological context.  Whether it’s proteomics, lipidomics, glycomics, or metabolomics, the timsTOF fleX is the ideal dual-source platform for MALDI guided SpatialOMx analyses. First, use the patented smartbeam™ 3D technology to conduct fast, label-free MALDI Imaging for mapping the distribution of molecules in your sample that identify molecularly unique regions of interest for microextraction and deeper X-Omic analyses. Then, apply timsTOF flex’s powerful LC-MS/MS with PASEF for the highest level of identifications and for greatest confidence in your results.  Regions of interest may be selected manually or use SCiLS Lab automated segmentation to know exactly where your microextraction will have the highest impact.

Literature MALDI Imaging

Increase lab output with MALDI Imaging

Bruker Daltonics IntelliSlides now support a brand new workflow which allows for fast, simple, and highly automated set-up of Imaging acquisitions using flexImaging 6.0 and COMPASS for flex 2.1.
Using the TissueScout to scan barcoded IntelliSlides allows for fast recognition of the correct sample image in flexImaging as well as alignment of the sample with instrument optics. The new workflow includes checks to confirm instrument performance, and automatic assignment of measurement regions using dedicated algorithms for whole tissue sections and Tissue microarrays (TMAs).

MALDI Imaging is made simple with Bruker Daltonics.

Additional information about the efficiency improvements with IntelliSlides and flexImaging 6.0 can be found in the video:


Brochure: Imaging made simple. Streamlined tools for MALDI Imaging experiment set up

App Note: Imaging venom peptides and proteins at high mass resolution, high lateral resolution and high speed using the timsTOF fleX

App Note: The Ease of Use workflow — A simple way to set up MALDI Imaging measurements

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