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 border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>5-Fluoro-2&#39;-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 ...

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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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Mass Spectrometry Fragmentation Methods

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9.3K vues.  University of Yamanashi School of Medicine. Il s’agit donc d’une spectrométrie de masse ambiante unique, particulièrement adaptée à l’analyse d’échantillons biologiques, in vitro et in vivo. Comme cela ne nécessite pas régulièrement un prétraitement spécial des échantillons, comme le tri cellulaire, la fractionnement et la concentration, il peut analyser un échantillon avec une perte minimale de composants biologiques, en particulier ceux qui existent comme très petite quantité. Cette technique vous permet d’ana...

Vidéo: Sample Preparation for Probe Electrospray Ionization Mass Spectrometry

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. Hydrogen-Deuterium Exchange (HDX) measured at rapid time scales is uniquely suited to detect structures and hydrogen bonding networks that are briefly populated, allowing for the characterization of transient conformers in native ensembles. Coupling of HDX to mass spectrometry offers several key advantages, including high sensitivity, low sample consumption and no restriction on protein size. This technique has advanced greatly in the last several decades, including the ability to monitor HDX labeling times on the millisecond time scale. In addition, by incorporating the HDX workflow onto a microfluidic platform housing an acidic protease microreactor, we are able to localize dynamic properties at the peptide level. In this study, Time-Resolved ElectroSpray Ionization Mass Spectrometry (TRESI-MS) coupled to HDX was used to provide a detailed picture of residual structure in the tau protein, as well as the conformational shifts induced upon hyperphosphorylation.

Conformational flexibility plays a critical role in protein function. Herein, we describe the use of time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange for probing the rapid structural changes that drive function in ordered and disordered proteins.

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. ...

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological processes. Affinity purification coupled to mass spectrometry (AP-MS) has become the method of choice for identifying protein-protein interactions. However, conventional AP-MS studies provide information on protein interactions, but the organizational information is lost. To address this issue, we developed a strategy to unravel the distinct functional assemblies a protein might be involved in, by resolving affinity-purified protein complexes prior to their characterization by mass spectrometry. Protein complexes isolated through affinity purification of a bait protein using an epitope tag and competitive elution are separated through blue native electrophoresis. Comparison of protein migration profiles through correlation profiling using quantitative mass spectrometry allows assignment of interacting proteins to distinct molecular entities. This method is able to resolve protein complexes of close molecular weights that might not be resolved by traditional chromatographic techniques such as gel filtration. With little more work than conventional AP-geLC-MS/MS, we demonstrate this strategy may in many cases be adequate for obtaining protein complex topological information concomitantly to identifying protein interactions.

Here we present protocols for affinity purification of protein complexes and their separation by blue native PAGE, followed by protein correlation profiling using label free quantitative mass spectrometry. This method is useful to resolve interactomes into distinct protein complexes.

Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological ...

Lipid Droplet Isolation for Quantitative Mass Spectrometry Analysis

Lipid droplets are vital to the replication of a variety of different pathogens, most prominently the Hepatitis C Virus (HCV), as the putative site of virion morphogenesis. Quantitative lipid droplet proteome analysis can be used to identify proteins that localize to or are displaced from lipid droplets under conditions such as virus infections. Here, we describe a protocol that has been successfully used to characterize the changes in the lipid droplet proteome following infection with HCV. We use Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) and thus label the complete proteome of one population of cells with &#34;heavy&#34; amino acids to quantitate the proteins by mass spectrometry. For lipid droplet isolation, the two cell populations (i.e.&#160;HCV-infected/&#34;light&#34; amino acids and uninfected control/&#34;heavy&#34; amino acids) are mixed 1:1 and lysed mechanically in hypotonic buffer. After removing the nuclei and cell debris by low speed centrifugation, lipid droplet-associated proteins are enriched by two subsequent ultracentrifugation steps followed by three washing steps in isotonic buffer. The purity of the lipid droplet fractions is analyzed by western blotting with antibodies recognizing different subcellular compartments. Lipid droplet-associated proteins are then separated by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) followed by Coomassie staining. After tryptic digest, the peptides are quantified by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Using this method, we identified proteins recruited to lipid droplets upon HCV infection that might represent pro- or antiviral host factors. Our method can be applied to a variety of different cells and culture conditions, such as infection with pathogens, environmental stress, or drug treatment.

Lipid droplets are important organelles for the replication of several pathogens, including the Hepatitis C Virus (HCV). We describe a method to isolate lipid droplets for quantitative mass spectrometry of associated proteins; it can be used under a variety of conditions, such as virus infection, environmental stress, or drug treatment.

Lipid droplets are vital to the replication of a variety of different pathogens, most prominently the Hepatitis C Virus (HCV), as the putative site of ...

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Noncoding RNAs play important roles in several nuclear processes, including regulating gene expression, chromatin structure, and DNA repair. In most cases, the action of noncoding RNAs is mediated by proteins whose functions are in turn regulated by these interactions with noncoding RNAs. Consistent with this, a growing number of proteins involved in nuclear functions have been reported to bind RNA and in a few cases the RNA-binding regions of these proteins have been mapped, often through laborious, candidate-based methods.
Here, we report a detailed protocol to perform a high-throughput, proteome-wide unbiased identification of RNA-binding proteins and their RNA-binding regions. The methodology relies on the incorporation of a photoreactive uridine analog in the cellular RNA, followed by UV-mediated protein-RNA crosslinking, and mass spectrometry analyses to reveal RNA-crosslinked peptides within the proteome. Although we describe the procedure for mouse embryonic stem cells, the protocol should be easily adapted to a variety of cultured cells.

We describe a protocol to identify RNA-binding proteins and map their RNA-binding regions in live cells using UV-mediated photocrosslinking and mass spectrometry.

Noncoding RNAs play important roles in several nuclear processes, including regulating gene expression, chromatin structure, and DNA repair. In most ...

Optimal Preparation of Formalin Fixed Samples for Peptide Based Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Workflows

The use of matrix-assisted laser desorption/ionization, mass spectrometry imaging (MALDI MSI) has rapidly expanded, since this technique analyzes a host of biomolecules from drugs and lipids to N-glycans. Although various sample preparation techniques exist, detecting peptides from formaldehyde preserved tissues remains one of the most difficult challenges for this type of mass spectrometric analysis. For this reason, we have created and optimized a robust methodology that preserves the spatial information contained within the sample, while eliciting the greatest number of ionizable peptides. We have also aimed to achieve this in a cost effective and simple way, thereby eliminating potential bias or preparation error, which can occur when using automated instrumentation. The end result is a reproducible and inexpensive protocol.

This protocol describes a reproducible and reliable method for the sublimation-based preparation of formalin fixed tissue destined for imaging mass spectrometry.

The use of matrix-assisted laser desorption/ionization, mass spectrometry imaging (MALDI MSI) has rapidly expanded, since this technique analyzes a host ...

Leaf Spray Mass Spectrometry: A Rapid Ambient Ionization Technique to Directly Assess Metabolites from Plant Tissues

Plants produce thousands of small molecules that are diverse in their chemical properties. Mass spectrometry (MS) is a powerful technique for analyzing plant metabolites because it provides molecular weights with high sensitivity and specificity. Leaf spray MS is an ambient ionization technique where plant tissue is used for direct chemical analysis via electrospray, eliminating chromatography from the process. This approach to sampling metabolites allows for a wide range of chemical classes to be detected simultaneously from intact plant tissues, minimizing the amount of sample preparation needed. When used with a high-resolution, accurate mass MS, leaf spray MS facilitates the rapid detection of metabolites of interest. It is also possible to collect tandem mass fragmentation data with this technique to facilitate a compound identification. The combination of accurate mass measurements and fragmentation is beneficial in confirming compound identities. The leaf spray MS technique requires only minor modifications to a nanospray ionization source and is a useful tool to further expand the capabilities of a mass spectrometer. Here, fresh leaf tissue from Sceletium tortuosum (Aizoaceae), a traditional medicinal plant from South Africa, is analyzed; numerous mesembrine alkaloids are detected with leaf spray MS.

Leaf spray mass spectrometry is a direct chemical analysis technique that minimizes the sample preparation and eliminates chromatography, allowing for the rapid detection of small molecules from plant tissues.

Plants produce thousands of small molecules that are diverse in their chemical properties. Mass spectrometry (MS) is a powerful technique for analyzing ...

Nitropeptide Profiling and Identification Illustrated by Angiotensin II

Protein nitration is one of the most important post-translational modifications (PTM) on tyrosine residues and it can be induced by chemical actions of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in eukaryotic cells. Precise identification of nitration sites on proteins is crucial for understanding the physiological and pathological processes related to protein nitration, such as inflammation, aging, and cancer. Since the nitrated proteins are of low abundance in cells even under induced conditions, no universal and efficient methods have been developed for the profiling and identification of protein nitration sites. Here we describe a protocol for nitropeptide enrichment by using a chemical reduction reaction and biotin labeling, followed by high resolution mass spectrometry. In our method, nitropeptide derivatives can be identified with high accuracy. Our method exhibits two advantages compared to the previously reported methods. First, dimethyl labeling is used to block the primary amine on nitropeptides, which can be used to generate quantitative results. Second, a disulfide bond containing NHS-biotin reagent is used for the enrichment, which can be further reduced and alkylated to enhance the detection signal on a mass spectrometer. This protocol has been successfully applied to the model peptide Angiotensin II in the current paper.

Proteomic profiling of tyrosine-nitrated proteins has been a challenging technique due to the low abundance of the 3-nitrotyrosine modification. Here we describe a novel approach for nitropeptide enrichment and profiling by using Angiotensin II as the model. This method can be extended for other in vitro or in vivo systems.

Protein nitration is one of the most important post-translational modifications (PTM) on tyrosine residues and it can be induced by chemical actions of ...

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation

Sample preparation for mass spectrometry analysis in proteomics requires enzymatic cleavage of proteins into a peptide mixture. This process involves numerous incubation and liquid transfer steps in order to achieve denaturation, reduction, alkylation, and cleavage. Adapting this workflow onto an automated workstation can increase efficiency and reduce coefficients of variance, thereby providing more reliable data for statistical comparisons between sample types. We previously described an automated proteomic sample preparation workflow1. Here, we report the development of a more efficient and better controlled workflow with the following advantages: 1) The number of liquid transfer steps is reduced from nine to six by combining reagents; 2) Pipetting time is reduced by selective tip pipetting using a 96-position pipetting head with multiple channels; 3) Potential throughput is increased by the availability of up to 45 deck positions; 4) Complete enclosure of the system provides improved temperature and environmental control and reduces the potential for contamination of samples or reagents; and 5) The addition of stable isotope labeled peptides, as well as &#946;-galactosidase protein, to each sample makes monitoring and quality control possible throughout the entire process. These hardware and process improvements provide good reproducibility and improve intra-assay and inter-assay precision (CV of less than 20%) for LC-MS based protein and peptide quantification. The entire workflow for digesting 96 samples in a 96-well plate can be completed in approximately 5 hours.

Here, we present an automated plasma protein digestion method for mass spectrometry-based quantitative proteomic analysis. In this protocol, the liquid transferring and incubation steps for protein denaturation, reduction, alkylation, and trypsin digestion reactions are streamlined and automated. It takes approximately five hours to prepare a 96-well plate with desired precision.

Sample preparation for mass spectrometry analysis in proteomics requires enzymatic cleavage of proteins into a peptide mixture. This process involves ...

Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

Lipids are structurally diverse amphipathic molecules that are insoluble in water. Lipids are essential contributors to the organization and function of biological membranes, energy storage and production, cellular signaling, vesicular transport of proteins, organelle biogenesis, and regulated cell death. Because the budding yeast Saccharomyces cerevisiae is a unicellular eukaryote amenable to thorough molecular analyses, its use as a model organism helped uncover mechanisms linking lipid metabolism and intracellular transport to complex biological processes within eukaryotic cells. The availability of a versatile analytical method for the robust, sensitive, and accurate quantitative assessment of major classes of lipids within a yeast cell is crucial for getting deep insights into these mechanisms. Here we present a protocol to use liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) for the quantitative analysis of major cellular lipids of S. cerevisiae. The LC-MS/MS method described is versatile and robust. It enables the identification and quantification of numerous species (including different isobaric or isomeric forms) within each of the 10 lipid classes. This method is sensitive and allows identification and quantitation of some lipid species at concentrations as low as 0.2 pmol/&#181;L. The method has been successfully applied to assessing lipidomes of whole yeast cells and their purified organelles. The use of alternative mobile phase additives for electrospray ionization mass spectrometry in this method can increase the efficiency of ionization for some lipid species and can be therefore used to improve their identification and quantitation.

Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

We present a protocol using liquid chromatography coupled with tandem mass spectrometry to identify and quantify major cellular lipids in Saccharomyces cerevisiae. The described method for a quantitative assessment of major lipid classes within a yeast cell is versatile, robust, and sensitive.

Lipids are structurally diverse amphipathic molecules that are insoluble in water. Lipids are essential contributors to the organization and function of ...

Untargeted Liquid Chromatography-Mass Spectrometry-Based Metabolomics Analysis of Wheat Grain

Understanding the interactions between genes, the environment and management in agricultural practice could allow more accurate prediction and management of product yield and quality. Metabolomics data provides a read-out of these interactions at a given moment in time and is informative of an organism&#39;s biochemical status. Further, individual metabolites or panels of metabolites can be used as precise biomarkers for yield and quality prediction and management. The plant metabolome is predicted to contain thousands of small molecules with varied physicochemical properties that provide an opportunity for a biochemical insight into physiological traits and biomarker discovery. To exploit this, a key aim for metabolomics researchers is to capture as much of the physicochemical diversity as possible within a single analysis. Here we present a liquid chromatography-mass spectrometry-based untargeted metabolomics method for the analysis of field-grown wheat grain. The method uses the liquid chromatograph quaternary solvent manager to introduce a third mobile phase and combines a traditional reversed-phase gradient with a lipid-amenable gradient. Grain preparation, metabolite extraction, instrumental analysis and data processing workflows are described in detail. Good mass accuracy and signal reproducibility were observed, and the method yielded approximately 500 biologically relevant features per ionization mode. Further, significantly different metabolite and lipid feature signals between wheat varieties were determined.

A method for the untargeted analysis of wheat grain metabolites and lipids is presented. The protocol includes an acetonitrile metabolite extraction method and reversed phase liquid chromatography-mass spectrometry methodology, with acquisition in positive and negative electrospray ionization modes.

Understanding the interactions between genes, the environment and management in agricultural practice could allow more accurate prediction and management ...