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Applied Imaging Mass Spectrometry - AIMS Core / Service Center

Overview of Services

Applied Imaging Mass Spectrometry (AIMS) Core / Service Center

The Johns Hopkins Applied Imaging Mass Spectrometry (AIMS) Core / Service Center, which is directed by Dr. Kristine Glunde, offers rapid matrix-assisted laser desorption/ionization (MALDI) imaging at high spatial resolution, which includes sample preparation, on-tissue digests and derivatizations, and data analysis. Spatially resolved MALDI imaging measurements are directly taken from a frozen or formalin-fixed paraffin-embedded (FFPE) tissue section without destroying it. MALDI imaging combines mass spectrometric analyses of biomolecules with simultaneous histological evaluation to analyze intact proteins, tryptic peptides (on-tissue tryptic digest), N-glycans (on-tissue PNGase digest), peptides, lipids, metabolites, drug molecules, and drug metabolites in a spatially resolved manner (see Figure below). This new Core is loated in the Cancer Research 2 building (CRBII) in the lower basement in rooms LB03D and LB03E.

Major Equipment

  • Bruker Rapiflex MALDI TOF/TOF instrument for high-throughput MALDI imaging
  • HTX M5 Sprayer for accurate robotic spraying of enzymes and matrices
  • Leica Cryostat for MALDI-imaging-compatible cryosectioning
  • Slide scanner for detecting histology and immunohistochemistry co-registered with MALDI imaging
  • Workstation with SCiLS lab for data analysis

Sample Preparation

The AIMS core facility is equipped with a variety of sample handling and automated sample preparation tools that allow the usage of controlled and reproducible protocols. Tissue samples are snap frozen at the site of collection or can be heat-treated to denature degradative enzymes. A Leica cryostat is available in the facility for cryo-sectioning of tissues at low temperatures without distorting molecular profiles. AIMS core staff closely collaborates with users to perform MALDI-imaging compatible cryo-sectioning in gelatin and other MALDI-compatible cryo-media in the facility. Protocols for MALDI imaging sample preparation of formalin-fixed, paraffin-embedded (FFPE) tissues are also well established, and are performed in the AIMS core facility.

Reproducible sample preparation is achieved by using the HTX M5 sprayer for accurate robotic spraying of enzymes for on-tissue digests, of derivatization agents for on-tissue derivatizations, and of matrices. Protocols for on-tissue digestions with trypsin and peptide N-glycosidase enzymes are available for proteomic and glycomic imaging investigations, respectively. Novel protocols for on-tissue derivatizations to detect amino acids and neurotransmitters are also available. AIMS core staff will perform all sample preparations as part of the MALDI imaging service provided. Customized development for novel sample preparation and MALDI imaging protocols is available in the AIMS core as well.

MALDI Imaging

MALDI is currently the most commonly employed approach for imaging mass spectrometry (IMS) of biological samples as the soft energies involved enable ionization of intact biological molecules. The AIMS core facility has realized an infrastructure dedicated to highly multiplexed high-throughput MALDI imaging with a Bruker Rapiflex MALDI TOF/TOF instrument. The Rapiflex instrument is currently one of the fastest available instruments for IMS, capable of imaging up to 50 pixels/second, offering high-throughput multiplexed MALDI imaging of up to 5,000 biomolecules at once at a spatial resolution of 20-micron pixel size or better. MALDI imaging covers an area of a regular microscopy slide of 75 mm by 25 mm.

The AIMS core offers targeted MALDI imaging of drugs, drug metabolites, imaging agents, contrast agents, or other agents, which is developed in close collaboration with the user to set up customized MALDI imaging protocols. We also offer discovery MALDI imaging of metabolites, lipids, peptides, intact proteins, tryptic peptides, and glycans. Tandem mass spectrometry (MS/MS) is also available in imaging or profiling mode, using collision induced dissociation (CID) for confirming molecular identifications through fragmentation directly from tissue sections.

Following MALDI imaging, the MALDI matrix can be washed off, and histology or immunohistochemistry (IHC) staining can be performed on the same slide. Technical staff in the AIMS core performs standard histology and IHC protocols in close collaboration with users, followed by slide scanning for co-registered overlay with MALDI imaging data.

Data Analysis

MALDI imaging generates big data of up to 10 gigabytes per dataset. The AIMS core offers several data analysis solutions, including segmentation analysis, pathology-guided analysis, and statistical analysis with the dedicated MALDI imaging analysis software package SCiLS Lab Pro. A workstation with the Bruker MALDI imaging software FlexImaging and SCiLS Lab Pro software packages is available in the AIMS core for self-guided or assisted data analysis. The SCiLS Lab Pro software package is available in the AIMS core with three licenses with nine floating hardlock USBs. This subscription package enables extended capabilities for statistical analysis for multiple MALDI imaging data sets of virtually unlimited size.


Dr. Kristine Glunde, AIMS Core Director


Location and hours of operation

Hours Location

Monday-Friday, 9am-5pm

1550 Orleans Street

Cancer Research Building II, Room LB03D/E

Baltimore, MD 21287

Links and Resources


Name Role Phone Email Location
Kristine Glunde, PhD
Traylor Building, Room 203
Caitlin Tressler, PhD
Assistant Director