MCU General Services

MCU provides Standardized Mass Cytometry on customer-provided samples using StandardBioTools AB panels & kits and Custom AB panels.

Default level of experimental onsite service.

SMC:

• Fully prepared samples only
• Fresh samples are counted and delivered in the pellet after the last washing step to the CyTOF lab
• We usually do not offer services such as isolation, processing, counting, staining and fixation of cells prior washing after the IR intercalation step.
• However, shipped frozen samples (-80˚C) will be processed by MCU
• Acquired are preprocessed (Randomization, Normalization, Debarcoding), and finally stored in "Microsoft SharePoint" for data-transfer to the customer

IMC:

• Acquisition/ablation of fully prepared tissue slides  (FFPE or Fresh/Frozen)
• We do not offer slide preparation service.
• Acquired data are finally stored in "Microsoft SharePoint" for data-transfer to the customer

"Wet" Services (Staff operated):

SMC:

• CyTOF machine startup, tuning and calibration
• Actual sample acquisition of fully prepared samples:
• Acquisition of samples stained with AB and Intercalator (IR), fixed and frozen at -80C.
• Acquisition of fresh samples stained with AB and Intercalator (IR),fixed, counted, pelleted after CAS wash, pelleted and ready for acquisition
• Note: No "user only" acquisition/operation" of the CyTOF (until further notice)
• but the user may monitor the acquisition
• Shutdown and daily cleaning/maintenance
• Data Preprocessing (.IMG, .FCS, Randomisation, Normalisation, Debarcoding)
• Data Organisation, Transfer and Storage
• Weekly/Monthly/Periodic equipment maintenance
• Standard Protocols

IMC:

• Hyperion/CyTOF machine startup, tuning and calibration
• Preparation of Panoramas and Region of Interest (ROI) – User assisted
• Acquisition of ROIs (unassisted)
• Shutdown and cleaning/maintenance
• Data organization, Transfer and Storage
• Standard protocols

IMC <-> SMC Mode switch:

• Mode switch is not “plug and play” and will take usually ½ to 1 day
• Therefore SMC and IMC services are performed in weekly to monthly “blocks” to minimize switching time.

MCU "Desktop" assistance:

• Experimental Design
• Panel Design
• Data analysis assistance (Note: No full analysis service)

Consumables:

Smaller quantities of consumables as listed below are usually in stock, but availibility is not guaranteed.

Ask for availability and way of distribution.

Barcoding kits:

• X8 Palladium cellular Barcoding Kit (for Pre-fixed cells)
• Human peripheral Blood MaxPar Direct Immune Assay kit lyophylised antibodies
  • 30 surface markers in one tube, fast automated data analysis using Pathsetter software possible
  • Panel can be extended with drop-in antibodies.
• Antibodies:
• Increasing number of pre-labeled antibodies in stock

StandardBioTools/Fluidigm Reagents (frozen aliquots):

• Cell-ID Intercalator IR aliquots
• Cell-ID Viability Dye Rho103 aliquots
• Cell-ID Cisplatin (Mixed isotopes 194-198) aliquots

StandardBioTools/Fluidigm Reagents (refrigiated):

• MaxPar Cell Acquisition Solution (CAS)
• MaxPar Cell Staining solution (CSB)
• MaxPar PBS (MP-PBS)
• MaxPar Fix & Perm Solution (1x)

Suspension Mass Cytometry (SMC)

Mixes the fundamentals of flow cytometry with suspension mass spectrometry (MS).

Cellular targets in liquid suspension are labeled with heavy metal isotope-tagged reagents including antibodies, nucleic acid intercalators and analogs, as well as other biochemical ligands.

Each reagent is detected and quantified with cytometry by time-of-flight mass spectrometry in the CyTOF system.

Key features are:

• Simultaneously analysis of > 45 parameters allowing in deep phenotyping combined with functional assays (intracellular cytokine determination, intercellular signaling state, cell viability discrimination, proliferation tracking, …)
• Minimal background noise from signal overlap or endogenous cellular components
• Traditional labeling techniques can be used –> minimal change to current protocols
• Multiplexing (= barcoding of individual samples) allows minimization of technical variations during the processing/staining process (eliminating batch effects)
• Sample stability allows storage, freezing and shipping of stained and frozen samples to the MCU for sample acquisition.
• Standard output format (flow cytometry standard .fcs) makes data analysis compatible with traditional flow cytometry software and with advanced bioinformatics tools.
• Antibody cocktails can be frozen/reserved in aliquots (at -80˚C) for weeks/month for e.g. avoiding batch effect during long-term studies. 

Imaging mass cytometry (IMC)

Combines the principles of flow cytometry and mass spectrometry (MS) with laser scanning spatial resolution and offers unique advantages for the analysis of tissue samples in unprecedented detail.
IMC uses isoptope-coupled antibodies that allow multiplex analysis of up to 40 markers in the same tissue section simultaneously.

Key advantages are:

• Subcellular Resolution: Imaging quality and 1µm² pixel resolution, equivalent to 10X optical microscopy for effective cell segmentation
• Simultaneously analysis of up to 35 parameters allowing in deep phenotyping combined structural information and functional assays (intracellular cytokine determination, intercellular signaling state, cell viability discrimination, proliferation tracking, …)
• No Autofluorescence: Using non-naturally-occurring metals for tagging antibodies limits potential pitfalls that can impact reproducibility and/or data quality.
• Rapid Labeling and Turnaround: Unlike fluorescent multiplexing, all of the labels can be used simultaneously which reduces the need for multiple rounds of labeling and tedious processing.
• Traditional established labeling techniques (for IHC) can be used –> minimal change to current protocols
• Antibody cocktails can be frozen/reserved in aliquots (at -80˚C) for weeks/month for e.g. avoiding batch effect during long-term studies.