We thank Ayumi Iizuka for operating the PESI-MS and Kazuko Sawa-nobori for her secretarial assistance. We thank Bronwen Gardner, Ph.D., from Edanz Group (www.edanzediting.com/ac) for editing a draft of this manuscript.

The institutional committee for animal care at the University of Yamanashi approved all the protocols and the use of experimental animals stated herein. Human sample usage was approved by the institutional ethics board at the University of Yamanashi.
1. Solid tissue preparation
NOTE: Samples must be kept on ice after their removal from the animal or human body to preserve the tissue freshness. If measurements do not immediately follow dissection, it is recommended to store tissue at -80 &#176;C. It is not advisable to place the tissue in any kind of buffer or saline, because they may extract certain contents from the tissue. Tissue that has been fixed with aldehydes or embedded in paraffin/wax or cryogel is not suitable for MS measurements.
<ol>
	<li>Cut the tissue specimen to approximately 2 x 2 x 2 mm using a scalpel or knife. Alternatively, punch out the sample with a trepan (a disposable biopsy punch, bore size 3 mm) used for the skin examination. In this case, trim the length of the column to 2 mm. 
	NOTE: Any tissue can be analyzed using this method. In this experiment, liver15 and kidney19, have been successfully analyzed to obtain mass spectra. Generally, parenchymal organs give good mass spectra, while those that have fibrous components do not.</li>
	<li>If the tissue is contaminated with blood, wash briefly with ice-cold phosphate-buffered saline. 
	NOTE: To minimize the postmortem tissue damage, complete this step, as soon as possible, at room temperature. If measurements are not made immediately, snap freeze the tissue in liquid nitrogen and store at -80 &#176;C.</li>
	<li>Place the cut or punched out sample (approximately 10 mg) into a plastic microtube and add 100 &#181;L of 50% ethanol. 
	NOTE: The exact weight of samples is not determined because the mass spectrometry used in this system does not provide quantitative data. Approximately 10 mg is optimal for the parenchymal tissue.</li>
	<li>Homogenize the sample using a micropestle.</li>
	<li>Place 10 &#181;L of the homogenate into the well of the cartridge (Figure 2).</li>
	<li>Place the cartridge in the ionization chamber of the mass spectrometer and install the stainless-steel needle probe that will be used for the sample ionization (Figure 2). 
	NOTE: Probe needles are supplied by the manufacturer. They are made of stainless steel and have a curvature radius of approximately 400 nm.</li>
	<li>Close the chamber lid firmly to automatically activate the safety device.</li>
	<li>Start the on-board computer by clicking the Start icon to analyze. Using the onscreen panels, apply a voltage of 2.3 kV to the needle to generate the electrospray and ensure that the frequency of needle is 3 Hz.</li>
	<li>Wait for 30 s for the measurement to be completed. 
	NOTE: The session automatically ceases when data acquisition is completed. The quality of the analysis is monitored by a total ion chromatogram (TIC). The measurement time is defined to obtain the representative mass spectra and can be shortened or extended.</li>
	<li>Dispose of the cartridge and needle in a biohazard disposer after measuring each sample. 
	NOTE: Only one sample can be measured at a time. It is not necessary to calibrate the machine before every measurement; calibration depends on the regular check-up by the supplier once every six months.</li>
	<li>Analyze the mass spectra and export the mass spectral text data using the software associated with the mass spectrometer (see Table of Materials) as stated in the steps below (Figure 3).
	<ol>
		<li>Click on the lcd file in the data file browser window of the software.</li>
		<li>Choose and click on a single peak on the mass spectrum window and to automatically depict an extracted ion chromatogram (EIC).</li>
		<li>Check the TIC and EIC and click on the average spectrum icon to select the range-of-time window for generating the mass spectrum. 
		NOTE: In this analysis, the target molecules appear in the mass-to-charge ratio (m/z) window (Figure 3). Furthermore, because the duration of the ionization per single stroke of needle movement is very short, all the mass spectra obtained are essentially averaged spectra over 10 s (300 scans).</li>
		<li>Generate a text file containing m/z and ion intensity by clicking on the Export tab for further analysis. This text file can be stored in any folder. 
		NOTE: Any RNA preservatives will affect the native spectral pattern of samples. In addition, it is advisable to handle and store tissue without any liquid (such as phosphate-buffered saline) to prevent the elution of molecular components from the tissue into the liquid during storage. Ideally, fresh or fresh frozen samples without any treatment are used.</li>
	</ol>
	</li>
</ol>
2. Body fluids (serum) preparation
NOTE: This whole procedure is almost identical to that used for solid tissue. The cartridge for the fluid sample is available from the manufacturer. Because the contamination by red blood cells (RBCs) can greatly diminish the efficiency of spectral acquisition of the intended component (plasma or serum), be sure to eliminate all RBCs by centrifuging before measurements.
<ol>
	<li>Take 10 &#181;L of the serum sample and put it into a 1.5 mL microtube. 
	NOTE: Both fresh and stored serum can be used.</li>
	<li>Add 190 &#181;L of 50% ethanol to the 1.5 mL tube, then vortex for 2 min at room temperature.</li>
	<li>Centrifuge the liquid at 15,000 x g for 1-5 min at 4 &#176;C.</li>
	<li>Transfer 10 &#181;L of supernatant into the well of the cartridge.</li>
	<li>Place the cartridge in the ionization chamber of the machine and install the stainless steel needle probe that will be used for sample ionization (Figure 2).</li>
	<li>Close the chamber lid firmly to automatically activate the safety device.</li>
	<li>Start the on-board computer by clicking the Start icon to ionize.</li>
	<li>Discard the sample cartridge and needle as described in 1.10 once measurements have been taken.</li>
	<li>Analyze the obtained sets of EIC as stated below (Figure 3).
	<ol>
		<li>Open the lcd file on the data browser.</li>
		<li>Click on a single peak to display the TIC and EIC.</li>
		<li>Select the range-of-time window for generating mass spectra using the average spectrum icon.</li>
		<li>Export the generated file containing both the m/z and ion intensity of a corresponding peak by clicking the export tab on the monitor. 
		NOTE: This procedure can be applied to saliva, urine, and other body fluids as well.</li>
	</ol>
	</li>
</ol>
3. Preparation for in vivo PESI-MS in living organism
NOTE: In this section, an application to monitor the metabolic profile of 5-Fluoro-2&#39;-deoxyuridine (5-FdU) in a living mouse model is introduced. Use aseptic conditions throughout.
<ol>
	<li>Infuse 100 &#181;L of 100 mM 5-FdU solution into the tail vein of a 2-month-old mouse (approximately 20 g weight). 
	NOTE: There is no preference for sex, age, or mouse strain. While this protocol was approved at the time that we carried out the experiment5, the feasibility of this experiment depends on the ethical restrictions of the country in which it will be performed.</li>
	<li>Anesthetize the mouse following your approved animal care protocol. Assess the depth of anesthesia by the lack of response to tail pinching. 
	NOTE: If the usage of sodium pentobarbital is not permitted by the ethical committee for animal experiments, alternative methods may be used, such as ketamine hydrochloride.</li>
	<li>Shave the abdominal cavity using an electric razor and apply vet ointment to the eyes.</li>
	<li>Put the anesthetized mouse in a supine position and fix the paws onto the plastic plate using mending tape. Scrub the surgical site with scrubs of 70% alcohol three times.</li>
	<li>Cut open the abdominal cavity using scissors. First, cut the skin laterally (10 mm) from just above the diaphragm. Laterally cut the muscle of the abdominal body wall and peritoneum (ca. 7 mm) and hold the wound open using stainless wire to expose the liver surface. 
	NOTE: There is no need to perfuse the surface of the liver.</li>
	<li>Apply the tip of the probe needle to the surface of the liver. Adjust the depth of the needle to approximately 0.5 mm deep to optimize ionization efficiency, checking the TIC and spectral pattern simultaneously. Set the high voltage to 2.3 kV and frequency to 3 Hz on the screen of the control panel.</li>
	<li>Remove the animal from the plastic plate.</li>
	<li>Suture the wound using a surgical gut suture and return the mouse to the cage. Do not leave the mouse unattended until it has regained consciousness to maintain sternal recumbency. Do not return the mouse to the company of other animals until it has fully recovered.</li>
	<li>Perform the time course of ion intensity in EIC and the procedure of EIC depiction as in 1.11.1 to 1.11.4.</li>
</ol>

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The corresponding author was funded by Shimadzu, a manufacturer and supplier of PESI-MS instrument.

Although PESI is a derivative of ESI for mass spectrometry4, it is most advantageous for monitoring real-time metabolomics, as well as for analyzing biochemical reactions without performing any complex or time-consuming pretreatments5,14,15,17. It is an easy and instantaneous mass spectrometry technique that can be applied to the integrated state of living organisms. Sin...

Mass spectrometry (MS) is a technological realization of reductionism; it reduces the object of analysis to a unit that can be interpreted on the basis of molecular species or cascades. Therefore, it is a representative method of analytical chemistry. It is made up of four processes: ionization, analysis, detection, and spectral acquisition. Because ionization of the molecule is the first process in mass spectrometry, it generally restricts the form of the analytes to be processed. Most ionization procedures require the destruction of the structure, morphology, and real-time biological processes of organic samples. For example, electrospray ionization (ESI) MS requires that the samples be in a liquid state for efficient ionization1. Samples, therefore, must go through a complex biochemical preparation, which alters the composition of molecules. Alternatively, while matrix-assisted laser desorption ionization (MALDI) MS can reconstruct molecular maps of thin sectioned tissue2,3, its ionization efficiency is too low to detect all molecules in the samples, and it is particularly poor at analyzing fatty acids. Considering these limitations, probe electrospray ionization (PESI)4 can be used to observe the real-time changes in biological systems in situ without destroying the structural integrity5, while the biological organism being observed is technically in a living state. A very fine needle is used in this case that serves simultaneously as a sample picker and an ion emitter. This means that the complex sample pretreatment sequences can be bypassed to obtain mass spectra that reflect the molecular components of the living system in situ.
There are several other ionization methods that rival PESI-MS. One is rapid evaporative ionization mass spectrometry (REIMS)6. This technique works well during surgery because it is assembled with an electrical knife and collects the ion plume generated during incision. While REIMS is very useful for the surgery, it is essentially a destructive method that requires the electrical ablation of the tissue. Therefore, it is not useful for the detailed analysis of cells and tissues in a preparative sample or in laboratory analyses. Moreover, because it collects a large amount of plume containing tissue debris, it requires lengthy maintenance of the devices after each use, thus limiting the use of this machine to special surgical procedures. A similar method, called laser desorption ionization mass spectrometry (LDI-MS)7, is another technique that is noninvasive and useful for the surface analysis. Because this technique is good at scanning the surface of a specimen, it achieves comprehensive two-dimensional analysis like MALDI imaging mass spectrometry8,9. However, because LDI-MS is only applicable to the surface analysis, PESI-MS is advantageous for analyzing the samples e.g., within the tissue. Another technique, the MasSpec Pen10, was reported to achieve high specificity and sensitivity in diagnosing thyroid cancer, but the diameter of the probe is in the order of mm and it is specific for the surface analysis, meaning that it cannot detect small nodules of cancer or deeply localized lesions. Moreover, as this method uses a microcapillary flow canal embedded in the probe pen, cross-contamination must be taken into consideration, similar to LDI-MS. Other techniques exist that have been applied to clinical settings, such as the flow probe and ionization form swab11, but they are not widespread.
PESI is extreme miniaturization of ESI, wherein the capillary of the nano-electrospray converges on a solid needle with a tip curvature radius of several hundred nm. Ionization takes place in the extremely restricted area of the needle tip by forming a Taylor cone, on which samples remain until ionization of all the fluid on the tip is completed12. If the analyte stays on the tip of the metal needle, excess charge is continuously generated at the interface between the metal needle and the analytes. Therefore, sequential ionization of molecules occurs depending on their surface activity. This property makes the needle tip a kind of chromatogram, separating the analytes depending on their surface activity. More technically, molecules with the stronger surface activity come to the surface of the Taylor cone and are ionized earlier than those with weaker surface activity, which adhere to the surface of the needle until the end of the ionization process. Thus, complete ionization of all molecules picked up by the needle is achieved13. Moreover, because this technique does not involve the addition of superfluous solvent to the sample, several hundreds of femtoliters are sufficient to get mass spectra strong enough for further analysis14. These properties are advantageous for the analysis of intact biological samples. However, a major disadvantage of PESI-MS lies in the discontinuity in ionization because of the reciprocating movement of the needle along the vertical axis, similar to a sawing machine. Ionization only takes place when the tip of the probe reaches the highest point when the height of the ion orifice is aligned on the horizontal axis. Ionization ceases while the needle picks up samples, and so the stability of ionization is not equal to that in conventional ESI. Therefore, PESI-MS is not an ideal method for proteomics.
To date, PESI-MS has been applied chiefly to the analysis of biological systems, covering a broad range of fields from basic research to clinical settings. For example, the direct analysis of human tissue prepared during the surgery was able to reveal the accumulation of triacylglycerol in both renal cell carcinoma15 and pharyngeal squamous carcinoma16. This method can also measure liquid samples, such as blood, to focus on the lipid profile. For example, some molecules have been delineated during dietary changes in rabbits; it was reported that some of these molecules decreased at very early stages of the experiments, indicating the high sensitivity and usefulness of this system for clinical diagnosis17. Furthermore, direct application to a living animal allowed the detection of biochemical changes of the liver after just one night of fasting5. Zaitsu et al.18 revisited this experiment5 and analyzed the metabolic profiles of the liver in almost the same way, with results that reinforced the stability and reproducibility of our original method. Furthermore, we were able to discriminate the cancer tissue from surrounding non-cancerous liver in mice using this technique19. Therefore, this is a versatile mass spectrometry technique that is useful in various settings, both in vivo and in vitro. From another standpoint, the PESI module can be made to fit various mass spectrometers by adjusting the mounting attachment. In this short article, we introduce the basics and examples of applications (Figure 1), including applications with living animals5.
According to the regulations and laws in each country, parts of this protocol will need to be revised to meet the criteria of each institution. Application to the living organism is the most interesting and challenging because it can provide biochemical or metabolic changes in tissues or organs in living animals in situ. While this application was approved by the institutional committee for animal care at the University of Yamanashi, in 20135, another round of approval will now be necessary because of recent changes in regulations for the animal experiments. Several modifications in the experimental scheme are, therefore, advisable. Regarding the mass spectra obtained in experiments, taking the fluctuations of mass spectra between each measurement into account, there is no spectral information sharing system that is common to the nucleotide sequencing community. Care must be taken when the operator handles the needle to avoid needle-stick accidents, especially when removing the needle from the needle holder. A special device for detaching the needle is very useful for this purpose. Since the compartment of the PESI module is an airtight, closed chamber, leakage of the ion plume does not occur if the mass spectrometer is operated according to the instructions.

<table><tbody><tr><td>5-Fluoro-2&#039;-deoxyuridine (5-FdU)</td><td>Sigma-Aldrich</td><td>F8791-25MG</td><td>25mg</td></tr><tr><td>disposable biposy punch (Trepan)</td><td>kai Europa GmbH</td><td>BP-30F</td><td>bore size 3mm</td></tr><tr><td>ethanol</td><td>nacalai tesque</td><td>14710-25</td><td>extra pure reagent</td></tr><tr><td>LabSolutions</td><td>Shimadzu</td><td></td><td>ver. 5.96, Data analyzer</td></tr><tr><td>micropestle</td><td>United Scientific Supplies</td><td>S13091</td><td></td></tr><tr><td>microtube</td><td>Treff</td><td>982855</td><td>0.5 mL clear</td></tr><tr><td>PESI-MS (Direct Probe Ionization-MS)</td><td>Shimadzu</td><td>DPiMS-2020</td><td>Mass spectrometer equipped with PESI</td></tr><tr><td>PPGT solition</td><td>Shimadzu</td><td>ND</td><td>Attached to DPiMS-2020</td></tr></tbody></table>

sample preparation for probe electrospray ionization mass spectrometry

Mass spectrometry (MS) is a powerful tool in analytical chemistry because it provides very accurate information about molecules, such as mass-to-charge ratios (m/z), which are useful to deduce molecular weights and structures. While it is essentially a destructive analytical method, recent advancements in the ambient ionization technique have enabled us to acquire data while leaving tissue in a relatively intact state in terms of integrity. Probe electrospray ionization (PESI) is a so-called direct method because it does not require complex and time-consuming pretreatment of samples. A fine needle serves as a sample picker, as well as an ionization emitter. Based on the very sharp and fine property of the probe tip, destruction of the samples is minimal, allowing us to acquire the real-time molecular information from living things in situ. Herein, we introduce three applications of PESI-MS technique that will be useful for biomedical research and development. One involves the application to solid tissue, which is the basic application of this technique for the medical diagnosis. As this technique requires only 10 mg of the sample, it may be very useful in the routine clinical settings. The second application is for in vitro medical diagnostics where human blood serum is measured. The ability to measure fluid samples is also valuable in various biological experiments where a sufficient volume of sample for conventional analytical techniques cannot be provided. The third application leans toward the direct application of probe needles in living animals, where we can obtain real-time dynamics of metabolites or drugs in specific organs. In each application, we can infer the molecules that have been detected by MS or use artificial intelligence to obtain a medical diagnosis.

As depicted in Figure 3, the data obtained by PESI-MS technique are the mass spectra, whose m/z range from 10 to 1,200 in this system. While one can detect molecules up to m/z 2,000, there were few peaks obtained using this technique over the mass range of m/z 1,200. Therefore, we analyzed peaks from m/z 10 to 1,200. There were conspicuous groups of peaks around m/z 800 and 900; the former represents cell membrane ...

Watch this Scientific Journal Video about Sample Preparation for Probe Electrospray Ionization Mass Spectrometry at JoVE.com

Sample Preparation for Probe Electrospray Ionization Mass Spectrometry

This article introduces sample preparation methods for a unique real-time analytical method based on the ambient mass spectrometry. This method lets us perform real-time analysis of the biological molecules in vivo without any special pretreatments.

Mass spectrometry (MS) is a powerful tool in analytical chemistry because it provides very accurate information about molecules, such as mass-to-charge ...

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9.4K Views.  University of Yamanashi School of Medicine. This article introduces sample preparation methods for a unique real-time analytical method based on the ambient mass spectrometry. This method lets us perform real-time analysis of the biological molecules in vivo without any special pretreatments.

Video: Sample Preparation for Probe Electrospray Ionization Mass Spectrometry

A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample

Understanding of complex biological systems requires the measurement, analysis and integration of multiple compound classes of the living cell, usually determined by transcriptomic, proteomic, metabolomics and lipidomic measurements. In this protocol, we introduce a simple method for the reproducible extraction of metabolites, lipids and proteins from biological tissues using a single aliquot per sample. The extraction method is based on a methyl tert-butyl ether: methanol: water system for liquid: liquid partitioning of hydrophobic and polar metabolites into two immiscible phases along with the precipitation of proteins and other macromolecules as a solid pellet. This method, therefore, provides three different fractions of specific molecular composition, which are fully compatible with common high throughput 'omics' technologies such as liquid chromatography (LC) or gas chromatography (GC) coupled to mass spectrometers. Even though the method was initially developed for the analysis of different plant tissue samples, it has proved to be fully compatible for the extraction and analysis of biological samples from systems as diverse as algae, insects, and mammalian tissues and cell cultures.

A protocol for comprehensive extraction of lipids, metabolites and proteins from biological tissues using one sample is presented.

Understanding of complex biological systems requires the measurement, analysis and integration of multiple compound classes of the living cell, usually ...

An Efficient Sample Preparation Method to Enhance Carbohydrate Ion Signals in Matrix-assisted Laser Desorption/Ionization Mass Spectrometry

Sample preparation is a critical process in mass spectrometry (MS) analysis of carbohydrates. Although matrix-assisted laser desorption/ionization (MALDI) MS is the method of choice in carbohydrate analysis, poor ion signal and data reproducibility of carbohydrate samples continue to be severe problems. For quantitative analysis of carbohydrates, an effective analytical protocol providing superior data quality is necessary. This video demonstrates sample preparation protocols to improve signal intensity and minimize data variation of carbohydrates in MALDI-MS. After drying and crystallization of sample droplets, the crystal morphology is reformed by methanol before mass spectrometric analysis. The enhancement in carbohydrate signal is examined with MALDI imaging mass spectrometry (IMS). Experimental results show that crystal reformation adjusts crystalline structures and redistributes carbohydrate analytes. In comparison with the dried droplet preparation method in conventional MALDI-MS, reforming carbohydrate crystal morphologies with methanol shows significantly better signal intensity, ion image distribution, and data stability. Since the protocols demonstrated herein do not involve changes in sample composition, they are generally applicable to various carbohydrates and matrixes.

A protocol for enhancing carbohydrate ion signals in MALDI mass spectrometry by reforming crystalline structures during sample preparation processes is demonstrated.

Sample preparation is a critical process in mass spectrometry (MS) analysis of carbohydrates. Although matrix-assisted laser desorption/ionization (MALDI) ...

Chemistry

Preparation of Human Tissues Embedded in Optimal Cutting Temperature Compound for Mass Spectrometry Analysis

Sphingolipids are cellular components that have well-established roles in human metabolism and disease. Mass spectrometry can be used to determine whether sphingolipids are altered in a disease and investigate whether sphingolipids can be targeted clinically. However, properly powered prospective studies that acquire tissues directly from the surgical suite can be time consuming, and technically, logistically, and administratively challenging. In contrast, retrospective studies can take advantage of cryopreserved human specimens already available, usually in large numbers, at tissue biorepositories. Other advantages of procuring tissues from biorepositories include access to information associated with the tissue specimens including histology, pathology, and in some instances clinicopathological variables, all of which can be used to examine correlations with lipidomics data. However, technical limitations related to the incompatibility of optimal cutting temperature compound (OCT) used in the cryopreservation and mass spectrometry is a technical barrier for the analysis of lipids. However, we have previously shown that OCT can be easily removed from human biorepository specimens through cycles of washes and centrifugation without altering their sphingolipid content. We have also previously established that sphingolipids in human tissues cryopreserved in OCT are stable for up to 16 years. In this report, we outline the steps and workflow to analyze sphingolipids in human tissue specimens that are embedded in OCT, including washing tissues, weighing tissues for data normalization, the extraction of lipids, preparation of samples for analysis by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS), mass spectrometry data integration, data normalization, and data analysis.

Sphingolipids are bioactive metabolites with well-established roles in human disease. Characterizing alterations in tissues with mass-spectrometry can reveal roles in disease etiology or identify therapeutic targets. However, the OCT-compound used for cryopreservation in biorepositories interferes with mass-spectrometry. We outline methods to analyze sphingolipids in human tissues embedded in OCT with LC-ESI-MS/MS.

Sphingolipids are cellular components that have well-established roles in human metabolism and disease. Mass spectrometry can be used to determine whether ...

Cancer Research

Integrated Cell Manipulation Platform Coupled with the Single-probe for Mass Spectrometry Analysis of Drugs and Metabolites in Single Suspension Cells

Single cell mass spectrometry (SCMS) enables sensitive detection and accurate analysis of broad ranges of cellular species on the individual-cell level. The single-probe, a microscale sampling and ionization device, can be coupled with a mass spectrometer for on-line, rapid SCMS analysis of cellular constituents under ambient conditions. Previously, the single-probe SCMS technique was primarily used to measure cells immobilized onto a substrate, limiting the types of cells for studies. In the current study, the single-probe SCMS technology has been integrated with a cell manipulation system, typically used for in vitro fertilization. This integrated cell manipulation and analysis platform uses a cell-selection probe to capture identified individual floating cells and transfer the cells to the single-probe tip for microscale lysis, followed by immediate mass spectrometry analysis. This capture and transfer process removes the cells from the surrounding solution prior to analysis, minimizing the introduction of matrix molecules in the mass spectrometry analysis. This integrated setup is capable of SCMS analysis of targeted patient-isolated cells present in body fluids samples (e.g., urine, blood, saliva, etc.), allowing for potential applications of SCMS analysis to human medicine and disease biology.

An integrated cell manipulation platform is developed for use in conjunction with a single-probe mass spectrometry setup for the on-line analysis of individual suspension cells under ambient conditions.

Single cell mass spectrometry (SCMS) enables sensitive detection and accurate analysis of broad ranges of cellular species on the individual-cell level. ...

Digital Microfluidics for Automated Proteomic Processing

Clinical proteomics has emerged as an important new discipline, promising the discovery of biomarkers that will be useful for early diagnosis and prognosis of disease. While clinical proteomic methods vary widely, a common characteristic is the need for (i) extraction of proteins from extremely heterogeneous fluids (i.e. serum, whole blood, etc.) and (ii) extensive biochemical processing prior to analysis. Here, we report a new digital microfluidics (DMF) based method integrating several processing steps used in clinical proteomics. This includes protein extraction, resolubilization, reduction, alkylation and enzymatic digestion. Digital microfluidics is a microscale fluid-handling technique in which nanoliter-microliter sized droplets are manipulated on an open surface. Droplets are positioned on top of an array of electrodes that are coated by a dielectric layer - when an electrical potential is applied to the droplet, charges accumulate on either side of the dielectric. The charges serve as electrostatic handles that can be used to control droplet position, and by biasing a sequence of electrodes in series, droplets can be made to dispense, move, merge, mix, and split on the surface. Therefore, DMF is a natural fit for carrying rapid, sequential, multistep, miniaturized automated biochemical assays. This represents a significant advance over conventional methods (relying on manual pipetting or robots), and has the potential to be a useful new tool in clinical proteomics.
Mais J. Jebrail, Vivienne N. Luk, and Steve C. C. Shih contributed equally to this work.
Sergio L. S. Freire's current address is at the University of the Sciences in Philadelphia located at 600 South 43rd Street, Philadelphia, PA 19104.

Digital Microfluidics is a technique characterized by the manipulation of discrete droplets (~nL - mL) on an array of electrodes by the application of electrical fields. It is well-suited for carrying out rapid, sequential, miniaturized automated biochemical assays. Here, we report a platform capable of automating several proteomic processing steps.

Clinical proteomics has emerged as an important new discipline, promising the discovery of biomarkers that will be useful for early diagnosis and ...

Biology

Microsampling in Targeted Mass Spectrometry-Based Protein Analysis of Low-Abundance Proteins

This paper presents a protocol with detailed descriptions for efficient sample cleanup of low-abundance proteins from dried samples. This is performed using bead-based proteolysis prior to proteotypic peptide affinity-capture and liquid chromatography tandem mass spectrometry (LC-MS/MS) determination. The procedure can be applied to both conventional dried samples using paper cards (e.g., dried blood spots [DBSs] and dried serum spots [DSSs]), as well as samples collected with newer sampling methods such as volumetric absorptive microsampling (VAMS). In addition to describing this procedure, the preparation of both trypsin beads and antibody-coated beads is presented in a step-by-step manner in this work. The advantages of the presented procedure are time-efficient proteolysis using beads and selective robust cleanup using peptide affinity-capture. The current procedure describes the determination of the low-abundance small-cell lung cancer (SCLC) biomarker, progastrin-releasing peptide (ProGRP), in dried serum (both DSSs and VAMS). Detailed procedures for bead preparation make it easier to implement the workflow in new applications or other laboratories. It is demonstrated that the results may be dependent on the sampling material; for the present project, higher signal intensities were seen for samples collected using VAMS compared to DSSs.

A protocol is presented for the determination of low-abundance biomarkers from dried serum samples exemplified with the biomarker progastrin-releasing peptide (ProGRP). Antibody-coated magnetic beads are used for the selective cleanup and enrichment of a proteotypic ProGRP peptide. The captured peptide is subsequently analyzed by liquid chromatography-tandem mass spectrometry.

This paper presents a protocol with detailed descriptions for efficient sample cleanup of low-abundance proteins from dried samples. This is performed ...

Sample Preparation for Endopeptidomic Analysis in Human Cerebrospinal Fluid

This protocol describes a method developed to identify endogenous peptides in human cerebrospinal fluid (CSF). For this purpose, a previously developed method based on molecular weight cut-off (MWCO) filtration and mass spectrometric analysis was combined with an offline high-pH reverse phase HPLC pre-fractionation step.
Secretion into CSF is the main pathway for removal of molecules shed by cells of the central nervous system. Thus, many processes in the central nervous system are reflected in the CSF, rendering it a valuable diagnostic fluid. CSF has a complex composition, containing proteins that span a concentration range of 8 - 9 orders of magnitude. Besides proteins, previous studies have also demonstrated the presence of a large number of endogenous peptides. While less extensively studied than proteins, these may also hold potential interest as biomarkers.
Endogenous peptides were separated from the CSF protein content through MWCO filtration. By removing a majority of the protein content from the sample, it is possible to increase the sample volume studied and thereby also the total amount of the endogenous peptides. The complexity of the filtrated peptide mixture was addressed by including a reverse phase (RP) HPLC pre-fractionation step at alkaline pH prior to LC-MS analysis. The fractionation was combined with a simple concatenation scheme where 60 fractions were pooled into 12, analysis time consumption could thereby be reduced while still largely avoiding co-elution.
Automated peptide identification was performed by using three different peptide/protein identification software programs and subsequently combining the results. The different programs were complementary rather than comparable with less than 15% of the identifications overlapped between the three.

A method for mass spectrometric analysis of endogenous peptides in human cerebrospinal fluid (CSF) is presented. By employing molecular weight cut-off filtration, chromatographic pre-fractionation, mass spectrometric analysis and a subsequent combination of peptide identification strategies, it was possible to expand the known CSF peptidome nearly ten-fold compared to previous studies.

This protocol describes a method developed to identify endogenous peptides in human cerebrospinal fluid (CSF). For this purpose, a previously developed ...

Neuroscience

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Proteins interact with their ligands to form active and dynamic assemblies which carry out various cellular functions. Elucidating these interactions is therefore fundamental for the understanding of cellular processes. However, many protein complexes are dynamic assemblies and are not accessible by conventional structural techniques. Mass spectrometry contributes to the structural investigation of these assemblies, and particularly the combination of various mass spectrometric techniques delivers valuable insights into their structural arrangement.
In this article, we describe the application and combination of two complementary mass spectrometric techniques, namely chemical cross-linking coupled with mass spectrometry and native mass spectrometry. Chemical cross-linking involves the covalent linkage of amino acids in close proximity by using chemical reagents. After digestion with proteases, cross-linked di-peptides are identified by mass spectrometry and protein interactions sites are uncovered. Native mass spectrometry on the other hand is the analysis of intact protein assemblies in the gas phase of a mass spectrometer. It reveals protein stoichiometries as well as protein and ligand interactions. Both techniques therefore deliver complementary information on the structure of protein-ligand assemblies and their combination proved powerful in previous studies.

The architecture of protein complexes is essential for their function. Combining various mass spectrometric techniques proved powerful to study their assembly. We provide protocols for chemical cross-linking and native mass spectrometry and show how these complementary techniques help to elucidate the architecture of multi-subunit protein assemblies.

Proteins interact with their ligands to form active and dynamic assemblies which carry out various cellular functions. Elucidating these interactions is ...

Sample Preparation for Mass-spectrometry-based Proteomics Analysis of Ocular Microvessels

The use of isolated ocular blood vessels in vitro to decipher the pathophysiological state of the eye using advanced technological approaches has greatly expanded our understanding of certain diseases. Mass spectrometry (MS)-based proteomics has emerged as a powerful tool to unravel alterations in the molecular mechanisms and protein signaling pathways in the vascular beds in health and disease. However, sample preparation steps prior to MS analyses are crucial to obtain reproducible results and in-depth elucidation of the complex proteome. This is particularly important for preparation of ocular microvessels, where the amount of sample available for analyses is often limited and thus, poses a challenge for optimum protein extraction. This article endeavors to provide an efficient, rapid and robust protocol for sample preparation from an exemplary retrobulbar ocular vascular bed employing the porcine short posterior ciliary arteries. The present method focuses on protein extraction procedures from both the supernatant and pellet of the sample following homogenization, sample cleaning with centrifugal filter devices prior to one-dimensional gel electrophoresis and peptide purification steps for label-free quantification in a liquid chromatography-electrospray ionization-linear ion trap-Orbitrap MS system. Although this method has been developed specifically for proteomics analyses of ocular microvessels, we have also provided convincing evidence that it can also be readily employed for other tissue-based samples.

Proteome characterization of ocular microvascular beds is pivotal for in-depth understanding of many ocular pathologies in humans. This study demonstrates an effective, rapid, and robust method for protein extraction and sample preparation from small blood vessels employing the porcine short posterior ciliary arteries as model vessels for mass-spectrometry-based proteomics analyses.

The use of isolated ocular blood vessels in vitro to decipher the pathophysiological state of the eye using advanced technological approaches has greatly ...

Solid Phase Microextraction Sampling: A Probe-based Technique for Sample Extraction from Graft Tissues

Source: Stryjak, I. et al. <a href="https://www.jove.com/video/60946" target="_blank">Using a Chemical Biopsy for Graft Quality Assessment.</a> J. Vis. Exp. (2020)
In this video, we demonstrate SPME-probe-based extraction of metabolites from a pre-harvested donor kidney. The extracted metabolites can be used to perform metabolomic and lipidomic analysis in order to assess the organ quality for transplantation.

Source: Stryjak, I. et al. Using a Chemical Biopsy for Graft Quality Assessment. J. Vis. Exp. (2020)
In this video, we demonstrate SPME-probe-based ...