TITLE: Pre-Extraction and Matrix Application via a HTX M5 Sprayer for Intact Proteoform MALDI Imaging
AUTHORS: Kevin J. Zemaitis, Dusan Velickovic, Ljiljana.PasaTolic

[DESCRIPTION]
Scope:

Using an HTX M5 sprayer this protocol outlines a pre-extraction step for increased sensitivity for intact proteoform analyses, this is an optional step within the MALDI-MSI pipeline for intact proteoform mapping using a Spectroglyph EP-MALDI-2 source coupled to a custom UHMR HF Orbitrap. This is followed by the coating and optional recrystallization of MALDI matrix on the sample, all steps have been completed on both human kidney and human pancreas. Other tissue types should go through validation.

Expected Outcomes:

A tissue section prepared for intact proteoform analyses.

[BEFORE_START]
Ensure that the MALDI matrix is prepared fresh according to the set protocol, and that the incubation chamber is equilibrated at the proper temperature based on the recrystallization steps. The status of the HTX M5 sprayer and other equipment including the incubation chamber, and UHMR HF Orbitrap should be checked prior to engaging in sample preparation protocols.

[STEPS]
SECTION: Preparing the HTX sprayer
1. The preparation of the HTX M5 sprayer employed is similar to other protocols, it has an external pump and 5 mL sample loop which must be purged prior to analyses.
 

SECTION: Preparing the HTX sprayer
2. House nitrogen gas flow is regulated to 10 PSI prior to turning on the pump power supply and initializing the HTX M5 sprayer once opening the application on the controlling laptop.
SECTION: Preparing the HTX sprayer
3. After initialization the pump line is purged while the sample valve is set to load similar to the aforementioned protocol, and allowed to spray through the nozzle.
SECTION: Tissue acidification
5. Once the HTX and matrix is prepared, the sample loop is then purged with 5% acetic acid (AA) in 50% ethanol, this is then run through the nozzle for several minutes at the set flow rate and the loop replenished if volume remaining is less than the volume to be sprayed.
SECTION: Tissue acidification
6. A slide is positioned on the sprayer bed, and secured with tape on the top and bottom edges (for use with Spectroglyph source) or on the sides (for use with Bruker sources).
SECTION: Tissue acidification
7. The method is loaded for tissue acidification, this includes the following parameters:

1250mm/min nozzle velocity
0.150 mL/min flow rate
30 °C nozzle temperature

3 mm track spacing
"CC" pattern

40 mm nozzle height
5 seconds drying time
SECTION: Tissue acidification
7.1. Note: This method and number of passes (4, 8, 12, etc.) should be evaluated on different tissue types and for different proteoforms, this pre-extraction was chosen as it demonstrated an improvement within histone intensity, however, for smaller proteoforms and on other instrumental platforms this may not be a necessary step.
SECTION: Tissue acidification
8. After the HTX method is loaded, the slide position is set and the method is started within the software. Nitrogen pressure is checked to ensure no fluctuation throughout the process, and solution is sprayed for several minutes and stability of pump pressure and spray is checked.
SECTION: Tissue acidification
8.1. Note: Pressure varies based upon flow rate, and the pump used, internal QC records are kept for various methods.
SECTION: Preparing the MALDI matrix
4. Prior to starting this protocol 2,5 dihydroxyacetophenone (DHA) should be prepared as outlined within the sub-steps below, matrix application was optimized within several minutes of tissue acidification.
SECTION: Application of MALDI matrix
12. After acidification is complete, the method is loaded for DHA deposition, this includes the following parameters:

1300 mm/min nozzle velocity
0.150 mL/min flow rate
30 °C nozzle temperature

2 mm track spacing
"CC" pattern

40 mm nozzle height
0 seconds drying time

4 passes for 277 μg/cm2 coverage
SECTION: Tissue acidification
10. Once the method is finished, switch the valve from spray to load, and the line and valve is purged with the solvent system of the matrix to be applied.
SECTION: Preparing the MALDI matrix
4.1. DHA is stored under roughly   in a vacuum desiccator, at temperatures per manufacturers recommendations.
SECTION: Preparing the MALDI matrix
4.2. 
Weigh out DHA into a scintillation vial which can hold at least 10 mL, the target concentration is 15 mg/mL and target between  7-10 mL of total matrix volume.

SECTION: Preparing the MALDI matrix
4.3. Calculate and add the specific volume of 90% acetonitrile to the scintillation vial and then vortex the solution for several minutes.
SECTION: Preparing the MALDI matrix
4.4. At this time the scintillation vial is placed into a ultrasonic sonicator for 15 min , after which the volume is split evenly into 2 mL Eppendorf tubes and then centrifuged for several minutes.

SECTION: Preparing the MALDI matrix
4.5. A black precipitant is formed, and the solution will no longer be opaque. Decant the solution into a clean scintillation vial. The matrix is now prepared for spraying within the HTX M5 sprayer.
SECTION: Application of MALDI matrix
13. Following loading the matrix into the loop with the injection valve on load, the pump is turned on and the valve set to spray.
SECTION: Application of MALDI matrix
14. Nitrogen pressure is checked to ensure no fluctuation throughout the process, and matrix is sprayed for several minutes and stability of pump pressure and spray is checked.
SECTION: Application of MALDI matrix
15. The same application region is used as within the tissue acidification step and the method is started. The sprayer is monitored throughout the process to ensure viable matrix application.
SECTION: Recrystallization of matrix
18. Directly following the matrix application an optional recrystallization step can be achieved using various parameters. Prepare an apparatus similar to that described.
 

SECTION: Application of MALDI matrix
15.1. As 2,5-DHA is slightly volatile and will sublime off within extended exposure to elevated pressure experienced within the MALDI source sample preparation should be minimized to samples being analyzed that day. Storage of matrix coated slides at room temperature, or within reduced temperatures from 4 °C  down to -80 °C is not advisable.

SECTION: Recrystallization of matrix
18.1. This apparatus uses an aluminum plate attached to the top of a petri-dish with double sided copper tape, the sample is mounted onto this plate. Within the bottom of the petri dish a Kimwipe is placed and 1 mL of the solution is pipetted evenly within to saturate the Kimwipe. Do not pipette the solution until directly prior to use.
SECTION: Recrystallization of matrix
19. The sample mounted onto the top plate is placed within the incubation chamber at 38.5 °C for 2 min 

SECTION: Recrystallization of matrix
20. 1 mL of 5% acetic acid in nanopure water is then pipetted directly before the timer expires, and the sample is placed on top of this bottom layer containing the kimwipe. This is allowed to incubate for 210 s 

SECTION: Recrystallization of matrix
21. After the time has elapsed the bottom plate is removed, and the sample is placed back within the incubation chamber to dry. After drying the sample is removed from the incubator, and removed the sample from the top plate.
SECTION: Recrystallization of matrix
22. Final tissue QC is completed as previously mentioned, this step in various forms is prone to causing loss of tissue adherence to the conductive slide. This can dramatically effect results and expected outcomes of proteoform informed MALDI-MSI.
SECTION: Recrystallization of matrix
22.1. We evaluate the integrity, lack of cracks, folds, detachment and tears in the tissue section after this step by visual inspection and/or bright-field (BF) microscopy images. Cracks, folds, detachments and tears should be < 10% of the section surface to pass tissue QC.

If tissue does not pass tissue QC at this stage, the run is aborted.
SECTION: Tissue acidification
11.1. We evaluate the integrity, lack of cracks, folds, detachment and tears in the tissue section after this step by visual inspection and/or bright-field (BF) microscopy images. Cracks, folds, detachments and tears should be < 10% of the section surface to pass tissue QC.

If tissue does not pass tissue QC at this stage, the run is aborted.
SECTION: Recrystallization of matrix
23. If tissue is intact, the samples are immediately taken to the UHMR HF Orbitrap for intact proteoform mapping outlined within a separate protocol.
 

SECTION: Preparing the HTX sprayer
3.1. After purging the sample line, switch the valve to spray. Pump flow rate is changed to 0.3 mL/min, and allowed to purge for roughly 10 min , then sprayer is now ready for use.

SECTION: Application of MALDI matrix
17. The sample loop is then flushed in the same manner as within earlier steps to prepare the HTX M5 sprayer. Power for the pump and the sprayer is then turned off, and the nitrogen flow is stopped.
SECTION: Tissue acidification
11. The sample integrity is monitored visually at this time.
SECTION: Application of MALDI matrix
14.1. Note: Pressure varies based upon flow rate, and the pump used, internal QC records are kept for various methods.
SECTION: Tissue acidification
9. The method is then started, the sprayer is monitored throughout the process to ensure viable acidification.
SECTION: Application of MALDI matrix
16. The sample integrity is monitored visually at this time.
SECTION: Application of MALDI matrix
16.1. We evaluate the integrity, lack of cracks, folds, detachment and tears in the tissue section after this step by visual inspection and/or bright-field (BF) microscopy images. Cracks, folds, detachments and tears should be < 10% of the section surface to pass tissue QC.

If tissue does not pass tissue QC at this stage, the run is aborted.