Alexandra E Stanback1, Lindsey R Conroy1,2, Lyndsay E A Young3, Tara R Hawkinson1, Kia H Markussen3, Harrison A Clarke1, Derek B Allison2,4, Ramon C Sun1,2. 1. Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY 40536-0298, USA. 2. Markey Cancer Center, Lexington, KY 40536-0298, USA. 3. Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536-0298, USA. 4. Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY 40536, USA.
Abstract
N-glycans and lipids are structural metabolites that play important roles in cellular processes. Both show unique regional distribution in tissues; therefore, spatial analyses of these metabolites are crucial to our understanding of cellular physiology. Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) is an innovative technique that enables in situ detection of analytes with spatial distribution. This workflow details a MALDI-MSI protocol for the spatial profiling of N-glycans and lipids from tissues following application of enzyme and MALDI matrix. For complete details on the use and execution of this protocol, please refer to Drake et al. (2018) and Andres et al. (2020).
N-glycans and lipids are structural metabolites that play important roles in cellular processes. Both show unique regional distribution in tissues; therefore, spatial analyses of these metabolites are crucial to our understanding of cellular physiology. Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) is an innovative technique that enables in situ detection of analytes with spatial distribution. This workflow details a MALDI-MSI protocol for the spatial profiling of N-glycans and lipids from tissues following application of enzyme and MALDI matrix. For complete details on the use and execution of this protocol, please refer to Drake et al. (2018) and Andres et al. (2020).
The workflow described in this protocol takes several days and requires careful preparation of reagents and access to specific equipment (see Materials and equipment). This protocol can be adapted to both formalin-fixed paraffin-embedded (FFPE) (N-glycans) and fresh frozen tissues (lipid species) for MALDI-MSI analyses. Here, we describe the step-by-step process using mouse brain tissues; however, it can be applied to a large range of tissues.
Tissue processing and slide preparation of formalin-fixed paraffin-embedded (FFPE) tissues
Timing: can be done up to 1 month in advanceProcess and embed tissue samples (Figure 1A)
Figure 1
Processing, embedding, and sectioning FFPE tissue samples
(A) Tissues are formalin fixed in a cassette, followed by embedding in paraffin wax.
(B) Paraffin blocks are sectioned at 4 μm onto positively charged slides.
Fix and process tissuePlace fresh tissue in formalinAfter 24 h, transfer tissue to 70% ethanolPlace tissue in a cassette and dehydrate with increasing concentrations of ethanol (70%–100%)70% ethanol for 40 min90% ethanol for 40 min95% ethanol for 40 min100% ethanol for 40 min, 3×Permeate the tissue with xylene to dissolve ethanol for 40 minDisplace the xylene with paraffin wax for 40 min, 3×Place tissue specimen into a mold of paraffin wax and solidify on a cold plate to create a paraffin-embedded tissue blockProcessing, embedding, and sectioning FFPE tissue samples(A) Tissues are formalin fixed in a cassette, followed by embedding in paraffin wax.(B) Paraffin blocks are sectioned at 4 μm onto positively charged slides.Tissue cutting (Figure 1B)Load tissue block onto a microtomeCut slices at 4 μm thickness and place tissue ribbon in a cooled water bathTransfer tissue slice to a positively charged glass slide
Tissue processing and slide preparation (fresh frozen tissues)
Timing: can be done up to 1 month in advanceTissue collection and sectioning (Figure 2A)
Figure 2
Freezing and sectioning fresh frozen tissue samples
(A and B) (A) Tissues are slow frozen in an isopentane bath and (B) sectioned at 4 μm onto positively charged slides using a cryostat.
(C) Example of fresh (left) and frozen (right) mouse brain tissue.
Dissection and gradual freezing of the tissuePrepare a bath of isopentane over dry ice and wait for it to equilibrate to about −70°CPlace the dissected tissue in an aluminum covered weigh boat on the isopentane-dry ice bath for 7 min to freeze tissue. Larger samples may require additional time.Ensure complete freezing by checking the color or the tissue. Frozen tissue appears paler than raw tissue.Place tissue into foil packet and drop into liquid nitrogen for 1 minStore at −80°CSectioning the tissue (Figure 2B)Prepare cryostat by turning the internal temperature down to −23°CPlace a small amount of OCT (optimal cutting temperature compound) on the cryostat chuck and place the tissue on the OCTCRITICAL: Ensure that no OCT is on the tissue sections. OCT is ion suppressive and will interfere with lipid analysis.Allow the OCT and tissue to sit for 2 min inside the cryostat to ensure solidificationCut sections at 4–10 μm utilizing the plastic wedge to ensure even sectionsLift the wedge and touch slide to mount the freshly cut tissue section onto a positively charged slideStore slides at −80°CFresh frozen tissue slices do not require dewaxing, antigen retrieval, or enzyme application. As such, steps 4–6 of Before you begin may be skipped.Freezing and sectioning fresh frozen tissue samples(A and B) (A) Tissues are slow frozen in an isopentane bath and (B) sectioned at 4 μm onto positively charged slides using a cryostat.(C) Example of fresh (left) and frozen (right) mouse brain tissue.
Preparation of dewaxing solutions, humidity chamber, and antigen retrieval device
Timing: 0.5–1 hDewaxing solutions: fill 7 clean slide staining jars with each of the following solutionsXylenes (2×)100% ethanol95% ethanol70% ethanolDeionized water (2×)Fresh dewaxing solutions are critical for complete removal of paraffin wax and should be prepared fresh for every 10 slides processed.Prepare humidity chamber for PNGase F digestion (Figure 3A)
Figure 3
Preparation of humidity chamber for PNGase F digestion and water bath steamer for antigen retrieval
(A) Prepare humidity chamber in oven 1 h prior to PNGase F digestion.
(B) Prior to antigen retrieval, prepare water bath steamer (top). When ready, place mailer in top basket of steamer with slides facing inward (bottom).
Wet one paper towel and place in humidity chamberPlace humidity chamber in oven (38.5°C) at least 1 h prior to PNGase F digestionPreparation of humidity chamber for PNGase F digestion and water bath steamer for antigen retrieval(A) Prepare humidity chamber in oven 1 h prior to PNGase F digestion.(B) Prior to antigen retrieval, prepare water bath steamer (top). When ready, place mailer in top basket of steamer with slides facing inward (bottom).Prepare water bath steamer for antigen retrieval by filling with tap water to fill line and preheating for 5 min prior to antigen retrieval (Figure 3B)
Key resources table
Materials and equipment
Citraconic anhydride buffer: add 25 μL of Citraconic Anhydride and 2 μL of 12 M HCl to 50 mL of HPLC grade water in a 50 mL falcon tube. Vortex and confirm pH of 3.0 ± 0.5.PNGase F solution: Enzyme is supplied in lyophilized 100 μg aliquots. To prepare, quick spin to pellet enzyme and add 50 μL of HPLC water. Vortex for 10 s and add 950 μL of HPLC grade water. Prepare fresh on the same day.α-Cyano-4-hydroxycinnamic acid (CHCA) matrix (7 mg/mL): Weigh 40 mg of CHCA in a 15 mL falcon tube using a clean and dry spatula. Add 5.7 mL of 50% acetonitrile/0.1% TFA. Vortex and sonicate for 10 min at 89 s on, 30 s off. Prepare fresh on the same day.CRITICAL: It is important to clean the CHCA spatula with methanol, ethanol, or HPLC water only, do not use detergent. Detergent can significantly interfere with N-glycan and lipid ionization and detection, leading to poor signal.This protocol is optimized using the equipment specified above in the Key resources table, but they are not exclusive products to carry it out. If any materials or equipment are modified, further optimization is highly recommended as there is no guarantee that any change would not alter ionization efficiency and/or sensitivity of the mass spectrometer.
Step-by-step method details
Slide preparation and antigen retrieval (day 1)
Timing: 2–3 hIf analyzing lipids from fresh frozen tissue, remove slides from −80°C and bring to 20°C in a vacuum desiccator for 2 h. Proceed to step 9 for CHCA matrix application.Heat slidesHeat slides for 1 h in 60°C oven with small water bath, tissue side upAfter 1 h, remove slides and allow to cool to 20°C for 1 minDewax slidesPlace slides in slide holder and wash in dewaxing solutions for the following times:Xylenes for 3 min, 2×100% ethanol for 1 min, 2×95% ethanol for 1 min70% ethanol for 1 minDeionized water for 3 min, 2×Dry slides in vacuum desiccator for 8 minAntigen retrieval denatures and breaks protein crosslinks that were formed during fixation, allowing greater enzymatic access to proteins within the sample.Antigen retrievalEnsure that the water bath steamer is preheatedPlace no more than two slides in a 5-slide holder with side opening partially closedSlides should be placed with tissue facing inward in the first and last slide slot to ensure that tissue is not touching the inner walls of the holder.Fill holder with citraconic anhydride bufferIncubate in water bath steamer for 30 minApplication of positive control1 μL of positive control (horseradish peroxidase) can be spotted directly onto the slide adjacent to tissueControls can include a glycosylated protein or purified glycans.Dry slides for 15 min in vacuum desiccator
PNGase F application by HTX M5 sprayer
Timing: 3–4 h, done immediately following slide preparation and antigen retrievalPNGase F cleaves N-linked glycans from their carrier proteins. Use of the HTX M5 sprayer ensures even application of enzyme, allowing for consistency to improve rigor and reproducibility. This methodology preserves spatial localization for MALDI-MSI analysis of N-glycan distribution. Incubation in a humidity chamber allows for maximum cleavage of N-glycans by PNGase F (see Troubleshooting 1).Application of PNGase F (Figures 4A–4C)
Figure 4
Overview of HTX M5 sprayer setup
(A) HTX M5 sprayer connected to controlling computer, syringe pump, and Knauer pump with CHCA loading syringe shown.
(B) External sprayer connectors on the left of the HTX M5 sprayer.
(C) Internal sprayer connectors on the inside of the HTX M5 sprayer.
Turn on HTX M5 SprayerTurn on nitrogen gas and stabilize pressure to 10 psiAdjust pressure using dial on sprayerOpen HTX M5 software on controlling computer and confirm the following settings:Set point temperature: 45°CTray type: AmbientTurn off Knauer pump and disconnect from sprayerTurn on syringe pump and connect to sprayerIt is recommended to clean the syringe pump enzyme line before each application of PNGase F. Load 3 mL of HPLC water into a clean syringe and set the pump rate to 95 μL/min. Start the syringe pump, and let water flow through the sprayer for 5 min prior to loading PNGase F solution.Setting up samplesArrange slides on the sprayer stageOn controlling computer, change the XY parameters to define the spraying areaLoad PNGase F solutionUsing a clean syringe, draw up PNGase F and remove any bubblesAttach syringe to 6” enzyme line and connect line to the sprayerPlace syringe in the syringe pump and lock in placeCRITICAL: Bubbles in solution will interfere with even enzyme application. See Troubleshooting section.PNGase Application (Figure 4D)Set syringe pump flow rate to 25 μL/min and syringe diameter to 9.7 mmConfirm syringe diameter if not using Hsw Norm-Ject Sterile Luer-Lock Syringe (see Key resources table).Start the syringe pump and confirm even sprayer application on test slideOnce even spraying is confirmed, press start on the controlling computer to begin spraying across sample slidesMonitor spray to ensure even PNGase F application across sample slidesWhen the cycle has completed, press stop on the syringe pump and remove slides from the trayPlace slides tissue side up in basket of humidity chamber and cover with lidIncubate the samples for PNGase F digestion in preheated humidity chamber for 2 hDry slides in a vacuum desiccator for a minimum of 15 min, or up to 24 hIt is recommended to clean the HTX M5 sprayer after each application of PNGase F by lowering the set temperature to 35°C and flushing the enzyme line with HPLC water at a flow rate of 95 μL/min. After cleaning, the sprayer program, gas, and syringe sprayer can be turned off. Reattach the Knauer pump to the sprayer and set the Knauer pump to a flow rate of 100 μL/min.Overview of HTX M5 sprayer setup(A) HTX M5 sprayer connected to controlling computer, syringe pump, and Knauer pump with CHCA loading syringe shown.(B) External sprayer connectors on the left of the HTX M5 sprayer.(C) Internal sprayer connectors on the inside of the HTX M5 sprayer.(D) Syringe pump loaded with syringe locked in place. Label key: (1) controlling computer, (2) syringe pump, (3) Knauer pump, (4) CHCA loading syringe, (5) enzyme line, (6) Knauer line, (7) sprayer nozzle, and (8) stage.CRITICAL: Slides must lie flat in the humidity chamber and must be completely dried prior to CHCA matrix application. This ensures spatial localization of cleaved glycans is maintained.Pause point: After incubation, slides can remain in desiccator for up to 24 h. Matrix application can be done on day 2.
CHCA matrix application by HTX M5 sprayer (day 1 continued or day 2)
Timing: 0.5–1 hApplication of the CHCA matrix facilitates ionization of the cleaved N-glycans, ensuring sufficient signal intensity. Use of the HTX M5 sprayer ensures even application of CHCA matrix, allowing for consistent sample ionization across tissue regions (see Troubleshooting 1).Prepare the CHCA matrixPrepare matrix at 7 mg/mL in 50% acetonitrile/0.1% TFAFilter the CHCA solution using a 0.2 μm syringe filterCarefully filter the CHCA solution as undissolved CHCA can clog components of the HTX M5 sprayer.Application of CHCA matrix (Figures 4A–4C)Scan slides in slide holder with a scanner before application of matrixA scanned image of the slide in the slide holder is used to program tissue regions to be analyzed by MALDI-MSI. Scanning prior to CHCA matrix application yields a clearer image of tissue boundaries.Turn on the HTX M5 sprayerTurn on nitrogen gas and stabilize pressure to 10 psi and adjust pressure using dial on sprayerOpen HTX M5 software on controlling computer and confirm the following settings:Set point temperature: 79°CTray temperature: 50°CPump flow rate: 100 μL/minPrime the Knauer pumpUnscrew black cap on the front of pump and pull degassed 50% methanol through using the attached syringe. Return the black cap and discard the methanol.Clean the sprayer lineIn the “LOAD” position, remove the stopper syringe and flush the line with 5 mL of 50% acetonitrile. Immediately replace with stopper syringe. With drip catcher below the sprayer nozzle, switch to “SPRAY” position and flush the line for 5 min.Load the CHCA matrix solutionDraw up filtered CHCA into clean syringe and remove all bubbles.In the “LOAD” position, remove the stopper syringe and expel the CHCA into the sprayer line. Immediately replace the stopper syringe.Bubbles the sprayer line will interfere with even CHCA matrix application. See Troubleshooting section.Setting up samplesArrange slides on the sprayer stageOn controlling computer, change the XY parameters to define the spraying areaCHCA matrix applicationEnsure that drip catcher is below the sprayer nozzle and switch sprayer position from “LOAD” to “SPRAY.”Confirm that the temperature has reached 79°C and flow rate is 100 μL/min.Start the Knauer pump and confirm even sprayer application on test slideOnce even spraying is confirmed, press start on the controlling computer to begin spraying across sample slidesMonitor spray to ensure even CHCA matrix application across all slidesOnce the application is complete, switch sprayer back to “LOAD” positionRemove slides and lay flat to dry. Slides can be immediately analyzed by MALDI-MSI or stored in a vacuum desiccator at 20°C for up to 1 week.It is highly recommended to clean the HTX M5 sprayer after each CHCA matrix application. With the nitrogen gas still on, change the sprayer set point temperature and tray temperature to 30°C, and adjust the Knauer pump flow rate to 300 μL/min using the controlling computer. While the sprayer cools down, switch the sprayer to “load,” flush the line with 5 mL of 50% acetonitrile twice. Repeat line flush with 50% methanol twice. Switch sprayer to “spray” and allow 50% methanol to run through the line until the set point temperature and tray temperature reach 30°C, then switch the sprayer back to the “load” position. Adjust the Knauer pump flow rate back to 100 μL/min, return the drip catcher to below the sprayer nozzle, and turn off the nitrogen gas. Any residual CHCA matrix on the slide stage can be removed with 50% methanol.
Image acquisition by waters synapt G2-XS mass spectrometer
The parameters indicated in Tables 1, 2, and 3 are used for N-glycan and lipid analysis on a Waters Synapt G2-XS Mass Spectrometer and can be programmed in the HDI software.
Table 1
MALDI laser settings for analysis of N-glycans and lipids
N-Glycans
Lipids
Laser energy
250 μJ
200 μJ
Laser firing rate
1,000 Hz
1,000 Hz
Raster size
50–200 μm
50–200 μm
Time per pixel
0.5 s
0.5 s
Table 2
Mass spectrometer settings for analysis of N-glycans and lipids
N-Glycans
Lipids
Trap collision energy
4 V
4 V
Transfer cell collision energy
2 V
2 V
Scan rate
0.5 s
0.5 s
Polarity
Positive
Negative
Analyzer mode
Sensitive
Sensitive
Mass range m/z
500–3,500
50–2,500
Table 3
Ion mobility settings for analysis of N-glycans and lipids
N-Glycans
Lipids
Trap
Entrance 2 V; bias 85 V, trap DC 0 V; exist 0 V
Entrance 2 V; bias 75 V, trap DC 0 V; exist 0 V
Wave velocity
Trap 9.6 m/s; IMS 4.6 m/s; transfer 17.4 m/s
Trap 9.6 m/s; IMS 4.6 m/s; transfer 17.4 m/s
Wave height
Trap 4 V; IMS 42.7 V; transfer 4 V
Trap 4 V; IMS 42.7 V; transfer 4 V
Variable wave Velocity mode
Ramp down; 1,400 m/s (start)-300 m/s (end)
Ramp down; 1,400 m/s (start)-300 m/s (end)
Proper laser firing is essential for sufficient ionization of the CHCA matrix, as well as N-glycans and lipids. As laser energy can decrease with time, it is recommended to confirm the laser is performing properly. We recommend testing laser firing on a slide coated with CHCA matrix only and confirming the signal intensity of CHCA matrix peaks. For these analyses, the laser used in this manuscript was approximately 6 months old.MALDI laser settings for analysis of N-glycans and lipidsMass spectrometer settings for analysis of N-glycans and lipidsIon mobility settings for analysis of N-glycans and lipids
Expected outcomes
In our experimental protocol, we describe a detailed method for visualization of N-glycans and lipids from FFPE and fresh frozen tissue, respectively, by MALDI-MSI. Typically, for most mammalian tissues, the Waters Synapt G2 mass spectrometer detects over 120 N-glycan and 200 lipid peaks, depending on the complexity and quality of the tissue. Here, we illustrate an example of the protocol to visualize N-glycans (Figure 5) and lipids (Figure 6) from a wild-type mouse brain using the HDI imaging software. Glycan and lipids were assigned based on previously established reports (Colsch and Woods, 2010; Powers et al., 2014; Zhang et al., 2016; Drake et al., 2017, Drake et al., 2018). In both cases, ion mobility improved N-glycan/lipid detection by separating their peaks from ionization matrix based on differential collision cross section (see Troubleshooting 2).
Figure 5
PNGase F digestion and MALDI-MSI analysis of N-glycans in mouse brain tissue
(Top) 2D plot of monoisotopic mass versus drift time in the ion mobility cell for N-glycans and the MALDI matrix. (Bottom) Extracted ion chromatogram of released N-glycans and matrix ions based on ion mobility separation for (A) both, (B) N-glycans, and (C) matrix. (D) Representative HDI images of 1809 m/z, 1581 m/z, 1905 m/z, and overlay image of 1809 m/z (red), 1581 m/z (green), and 1905 m/z (blue). Scale bar, 1.5 mm.
Figure 6
MALDI-MSI analysis of lipids in mouse brain tissue
(Top) 2D plot of monoisotopic mass versus drift time in the ion mobility cell for lipids and the MALDI matrix. (Bottom) Extracted ion chromatogram of lipids and matrix ions based on ion mobility separation for (A) both, (B) lipids, and (C) matrix. (D) Representative HDI images of 1,573.2 m/z, 888.6 m/z, 885.7 m/z, and overlay image of 885.7 m/z (red), 1,573.2 m/z (green), and 888.6 m/z (blue). Scale bar, 1.5 mm. Gangliosides (GM1) (20:1/18:0), 3-o-sulfogalactosylceramide (SM4) (d18:1-C24:1), Phosphatidylinositol (PI) 38:4.
PNGase F digestion and MALDI-MSI analysis of N-glycans in mouse brain tissue(Top) 2D plot of monoisotopic mass versus drift time in the ion mobility cell for N-glycans and the MALDI matrix. (Bottom) Extracted ion chromatogram of released N-glycans and matrix ions based on ion mobility separation for (A) both, (B) N-glycans, and (C) matrix. (D) Representative HDI images of 1809 m/z, 1581 m/z, 1905 m/z, and overlay image of 1809 m/z (red), 1581 m/z (green), and 1905 m/z (blue). Scale bar, 1.5 mm.MALDI-MSI analysis of lipids in mouse brain tissue(Top) 2D plot of monoisotopic mass versus drift time in the ion mobility cell for lipids and the MALDI matrix. (Bottom) Extracted ion chromatogram of lipids and matrix ions based on ion mobility separation for (A) both, (B) lipids, and (C) matrix. (D) Representative HDI images of 1,573.2 m/z, 888.6 m/z, 885.7 m/z, and overlay image of 885.7 m/z (red), 1,573.2 m/z (green), and 888.6 m/z (blue). Scale bar, 1.5 mm. Gangliosides (GM1) (20:1/18:0), 3-o-sulfogalactosylceramide (SM4) (d18:1-C24:1), Phosphatidylinositol (PI) 38:4.
Quantification and statistical analysis
Imaging
For the qualitative comparison of N-glycan and lipid species between two or more groups, N-glycan and lipid masses should be normalized to total ion chromatograph (TIC) within each pixel. This will correct for small batch variations introduced by CHCA concentration and laser power reduction over time.
Regional analysis
For the qualitative analysis of regional abundance of N-glycans and lipids, first N-glycan and lipid masses should be normalized to TIC within each pixel. Then regions of interest (ROI) should be defined by the user. The number of pixels must be consistent between ROIs of two or more groups before exportation of mass spectrometry data. The appropriate statistical analysis for comparison between two more groups should be determined by the user. These include but are not limited to: student's T-test, ANOVA, clustering heat analysis, and principal component analysis.
Limitations
This protocol requires high quality tissue samples to be properly prepared prior to MALDI-MSI analysis. Tissues not fixed or frozen in a timely manner risk degradation, and tissue sections that are cut higher than the recommended thickness can result in poor quality images. It is also recommended to use recently sectioned tissue, as tissue that has been cut less than 30 days prior yields better sample ionization and signal.Use of this protocol for N-glycan profiling requires consistency in PNGase F enzymatic activity across sample preparations to ensure reproducible results. Maintaining proper oven temperature and humidity during PNGase F digestion, and the use of a positive control are key to confirming enzymatic activity. It is recommended to use PNGase F from the same vendor and lot number to ensure consistent N-glycan cleavage (see also Troubleshooting 3). PNGase F should be stored in single use aliquots in a −80°C freezer. Further, certain commercially available PNGase F frequently contains additives such as glycerol and high salt concentrations that will interfere with the ionization and detection of N-glycans. Such additives will require removal by dialysis.
Troubleshooting
Problem 1
Uneven PNGase F or CHCA matrix application.
Potential solution
Bubbles in the enzyme or matrix solution can interfere with even sprayer application and maintaining pressure in both the syringe and Knauer pumps. When loading solution into the syringe, make sure to pull the plunger up slowly to reduce the number of bubbles. Once the solution is in the syringe, gently tap it against a hard surface to push bubbles to the top and expel the air. Further, residual CHCA matrix in the sprayer nozzle can crystallize and lead to the sprayer nozzle sputtering. Allowing degassed 50% methanol to flow through the sprayer at 100 μL/min following cleaning, even when the sprayer is not in use, prevents crystallization of any residual matrix in the sprayer line. If the pressure in the Knauer pump fluctuates, this will cause the matrix spray to be uneven as well. This could be caused by an air bubble in the front of the pump, so prime the pump again and pull about 10 mL of methanol through the pump to get rid of the bubble.
Problem 2
Low signal across tissue.For N-glycans, PNGase F activity can be checked by use of a positive control. Following antigen retrieval, addition of a small amount of a protein such as horseradish peroxidase (known to be glycosylated) onto the slide away from the tissue can be used to assess PNGase F activity. If N-glycan signal is within range on the control protein, but not on the tissue sample, the dewaxing, or antigen retrieval steps may need to be investigated, as insufficient dewaxing or antigen retrieval can block enzymatic access to the N-glycans. If no signal was detected on the positive control, check PNGase F solution for integrity or sprayer may be blocked.For lipids, make sure tissue is 4–10 μm thickness. Tissue thicker than 10 μm decreases laser ionization efficiency; 4 μm provides better ionization for gangliosides. Make sure CHCA is prepared fresh daily and properly stored. Repeat freeze thawing cycle of CHCA will compromise ionization efficiency.
Problem 3
Inconsistent N-glycan cleavage across the sample or poor detection of regional N-glycans.This protocol requires that the tissue analyzed is sectioned evenly and of a specific thickness. Uneven tissue samples produce inconsistent and variable results. Further, problems during PNGase F incubation period can cause inconsistent enzymatic cleavage. Slides must remain flat in the humidity chamber during incubation, as well as proper temperature and humidity must be maintained. Ensure that the paper towel in the chamber remains wet during incubation.
Resource availability
Lead contact
Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Dr. Ramon C. Sun (ramon.sun@uky.edu).
Materials availability
This study did not generate new unique reagents.
Data and code availability
The published article includes all datasets generated or analyzed during this study.
REAGENT or RESOURCE
SOURCE
IDENTIFIER
Chemicals, peptides, and recombinant proteins
Xylene
Spectrum
CAS#: 1330-20-7
Ethanol
Decon Labs
CAS#: 64-17-5
HPLC water
Sigma-Aldrich
CAS#: 7732-18-5
Hydrochloric acid
LabChem
CAS#: 7647-01-0
Citraconic anhydride
Thermo Scientific
CAS#: 616-02-4
Horseradish Peroxidase
Sigma-Aldrich
CAS#: 9003-99-0
PNGase F
N-Zyme Scientifics
Lot: NZL-2020-0194
α-Cyano-4-hydroxycinnamic acid
Cayman Chemical
CAS#: 28166-41-8
Trifluoroacetic acid
Sigma-Aldrich
CAS#: 76-05-1
Acetonitrile
Sigma-Aldrich
CAS#: 75-05-8
Methanol
Sigma-Aldrich
CAS#: 67-56-1
Software and algorithms
High Definition Imaging (HDI) Software
Waters
Catalog #: 720005652EN
Other
INCU-Line IL 10 digital incubator
VWR
Catalog #: VWRI390-0384
Hsw Norm-Ject Sterile Luer-Lock syringe, 3 mL
VWR
Catalog #: 53548-017
SGE syringe, gas tight plunger, 5 mL
VWR
Catalog #: 60361-204
Millipore Sigma non-sterile syringe filter, 13 mm, 0.20 μm
Authors: Thomas W Powers; Benjamin A Neely; Yuan Shao; Huiyuan Tang; Dean A Troyer; Anand S Mehta; Brian B Haab; Richard R Drake Journal: PLoS One Date: 2014-09-03 Impact factor: 3.240
Authors: Lindsey R Conroy; Josephine E Chang; Qi Sun; Harrison A Clarke; Michael D Buoncristiani; Lyndsay E A Young; Robert J McDonald; Jinze Liu; Matthew S Gentry; Derek B Allison; Ramon C Sun Journal: Adv Cancer Res Date: 2022-03-18 Impact factor: 5.767
Authors: Ramon C Sun; Lyndsay E A Young; Ronald C Bruntz; Kia H Markussen; Zhengqiu Zhou; Lindsey R Conroy; Tara R Hawkinson; Harrison A Clarke; Alexandra E Stanback; Jessica K A Macedo; Shane Emanuelle; M Kathryn Brewer; Alberto L Rondon; Annette Mestas; William C Sanders; Krishna K Mahalingan; Buyun Tang; Vimbai M Chikwana; Dyann M Segvich; Christopher J Contreras; Elizabeth J Allenger; Christine F Brainson; Lance A Johnson; Richard E Taylor; Dustin D Armstrong; Robert Shaffer; Charles J Waechter; Craig W Vander Kooi; Anna A DePaoli-Roach; Peter J Roach; Thomas D Hurley; Richard R Drake; Matthew S Gentry Journal: Cell Metab Date: 2021-05-26 Impact factor: 31.373
Authors: Lindsey R Conroy; Alexandra E Stanback; Lyndsay E A Young; Harrison A Clarke; Grant L Austin; Jinze Liu; Derek B Allison; Ramon C Sun Journal: Mol Cancer Res Date: 2021-06-15 Impact factor: 6.333