The authors would like to acknowledge Caitlin Kowalewski for aiding in the editing and formatting of this publication.

1. Schlieren Photography
<ol>
	<li>Establishment of the Test Region 
	Note: The test region exists directly in front of the mirror.
	<ol>
		<li>Clamp a spherical concave mirror (150 mm diameter, focal length 1,500 mm) in a ring stand clamp large enough to support the mirror. Attach the ring stand clamp with the mirror to a ring stand perpendicular to the floor. The current study used a 3 foot ring stand, but any height can be used as long as it is tall enough to be able to center the mirror in the viewing window of the source.</li>
		<li>Place the ring stand and mirror to the side of the mass spectrometer source. Make the face of the mirror parallel to, and at the same height, as the source.</li>
		<li>Position the mirror so its center is aligned with the center source region of the mass spectrometer. Some overlap of the instrument will occur.</li>
	</ol>
	</li>
	<li>Cutoff, Camera and Light Source
	<ol>
		<li>Cutoff
		<ol>
			<li>Attach a metal plate to the top of the tripod. The plate will serve as a platform to hold both the razor blade and the light source. The razor blade acts as what is known as the &#34;cutoff&#34; in schlieren photography.</li>
			<li>Attach the razor blade to the metal plate using a magnet so that the sharp edge is vertical.</li>
			<li>Place the tripod in line with the mirror at twice the focal length of the mirror, 3,000 mm. Align the razor blade orthogonal to the path of light reflected from the mirror.</li>
			<li>Manually adjust the height of the tripod so that the sharp edge of the razor blade is approximately aligned with the center of the mirror. 
			NOTE: Fine adjustment will happen later.</li>
		</ol>
		</li>
		<li>Camera
		<ol>
			<li>Mount a digital camera with 300 mm telephoto lens on a separate tripod.</li>
			<li>Position the camera so the lens (when at full zoom) is 4 cm directly behind and at the same height as the razor blade. Do not remove the lens cap at this time.</li>
		</ol>
		</li>
		<li>Optional Monitor
		<ol>
			<li>Connect the video output of the camera to a computer monitor or TV to easily view the schlieren phenomenon in real time. 
			NOTE: This is a recommended process. This procedure may vary depending on the type of camera used.</li>
		</ol>
		</li>
		<li>Pinhole Light Source
		<ol>
			<li>Drill a small hole (approximately 0.6 mm in diameter) into the center of a cover (in this case, a vial cap the same diameter of the flashlight was used) which can be attached/taped to the light source. Ensure that the cover has sufficient diameter to completely cover the flashlight lens.</li>
			<li>Attach the cover over a 200 lumen LED flashlight using foil tape. 
			NOTE: The flashlight will get warm and a high temperature tape is recommended.</li>
		</ol>
		</li>
		<li>Light Source Positioning
		<ol>
			<li>First use a laser pointer to align the light source with the mirror, razor blade, and camera, to ensure proper positioning of the light source.</li>
			<li>Place the laser pointer on the metal plate next to the razor blade.</li>
			<li>Manually move the laser pointer so the beam is hitting the center of the mirror. Adjust as necessary to ensure the reflected beam intersects orthogonally to the razor blade so that approximately half of the beam is blocked.</li>
			<li>Manually adjust the mirror&#39;s position to aim the beam of the laser pointer directly at the razor blade if the beam alignment was not achieved in 1.2.5.3. 
			CAUTION! Do not look directly into the laser pointer or the reflected beam.</li>
			<li>Ensure that the laser beam is centered on the lens while keeping the lens cap on the camera.</li>
			<li>Replace the laser pointer with the covered flashlight while everything is aligned. Ensure that the flashlight is in the same orientation as the laser pointer.</li>
			<li>Turn on the flashlight and, using a piece of white paper, observe the reflected light at the cutoff. Ensure that the beam is a small focused spot at the cutoff.</li>
			<li>Make any vertical adjustments necessary to block approximately half of the reflected light beam with the cutoff.</li>
			<li>Remove the lens cap on the camera and focus on the mirror. 
			NOTE: It is recommended that the camera/lens be used in manual focusing mode.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
2. Example Test Object: Mass Spectrometry Ionization Source
<ol>
	<li>Manually align the mass spectrometry ion source within the test region, with a distance of 10 mm between the end of the nozzle and the inlet of the mass spectrometer.</li>
	<li>Manually open the needle valve to the ambient source allowing nitrogen to flow through the source.</li>
	<li>Open the software used to control the mass spectrometer. For this study, the software used was &#34;SQ driver&#34;. Click on file -open- then select the appropriate tune file.</li>
	<li>Apply all voltages and temperatures to the ambient source once the manual tune is opened. Each mass spectrometer will have its own software for this step. For the current study, once the manual tune is open, click the button &#34;Source Voltage is off&#34; and the button &#34;All gas and heaters are off&#34; to perform this task.</li>
	<li>Observe the appearance of the flow exiting the nozzle with the schlieren apparatus on the view screen of the digital camera as the temperature increases. Observe the gas stream (see description in &#34;Results&#34; section) coming out of the end of nozzle. The gas stream can be viewed on the back of the camera, or it can be viewed directly on a LCD monitor.</li>
	<li>Collect the image by either recording a video from the camera, or taking a picture of the gas stream, once desired images are visualized live on the camera.</li>
	<li>Transfer the picture(s) collected to a computer with the camera memory card or USB connection and view the image with software of your choosing.</li>
</ol>
3. Determination of Spray Half Angle from a Collected Image
<ol>
	<li>Open the collected image using an image viewing software and print out the collected image(s).</li>
	<li>Draw a line on the printed image(s) defining the center axis of the gas stream parallel to the direction of flow using a ruler.</li>
	<li>Draw a line along the edge of the visualized gas stream on the printed image(s) using a ruler. This can be visualized better from a recorded video due to a shimmer that is present in video format; use this to help identify the edge in the printed images. Mark the outer edges of the gas streams to obtain a range for the spray half angle.</li>
	<li>Measure the angle produced between the center axis and the line drawn in 3.2 using a protractor.</li>
</ol>

<ol>
	<li>Settles, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Schlieren and Shadowgraph Techniques: Visualization Phenomena in Transparent Media. , (2001).</li><li>Strawa, A. W., Chapman, G. T., Arnold, J. O., Canning, T. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ballistic+range+and+aerothermodynamic+testing.">Ballistic range and aerothermodynamic testing.</a> J. Aircraft. 28 (7), 443-449 (1991).</li><li>Settles, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+gas+leaks+by+using+schlieren+optics.">Imaging gas leaks by using schlieren optics.</a> Pipeline &amp; Gas Journal. 226 (9), 28-30 (1999).</li><li>Takagi, T., Kubota, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+application+of+schlieren+optics+for+detection+of+protein+bands+and+other+phenomena+in+polyacrylamide+gel+electrophoresis.">The application of schlieren optics for detection of protein bands and other phenomena in polyacrylamide gel electrophoresis.</a> Electrophoresis. 11 (5), 361-366 (1990).</li><li>Clark, I. G., Cruz, J. R., Huges, M. F., Ware, J. S., Madlangbayan, A., Braun, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aerodynamic+and+Aeroelastic+Characteristics+of+a+Tension+Cone+Inflatable+Aerodynamic+Decelerator.">Aerodynamic and Aeroelastic Characteristics of a Tension Cone Inflatable Aerodynamic Decelerator.</a> , (2009).</li><li>Froome, K. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Refractive+Indices+of+Water+Vapour,+Air,+Oxygen,+Nitrogen+and+Argon+at+72+kMc/s.">The Refractive Indices of Water Vapour, Air, Oxygen, Nitrogen and Argon at 72 kMc/s.</a> Proc. Phys. Soc. B. 68, 833-835 (1955).</li><li>Winter, G. T., Wilhide, J. A., LaCourse, W. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+a+Direct+Sample+Analysis+(DSA)+Ambient+Ionization.">Characterization of a Direct Sample Analysis (DSA) Ambient Ionization.</a> J. Am. Soc. Mass Spectrom. 26 (9), 1502-1507 (2015).</li><li>Pfeuffer, K. P., Schaper, J. N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Halo-Shaped+Flowing+Atmospheric+Pressure+Afterglow:+A+Heavenly+Design+for+Simplified+Sample+Introduction+and+Improved+Ionization+in+Ambient+Mass+Spectrometry.">Halo-Shaped Flowing Atmospheric Pressure Afterglow: A Heavenly Design for Simplified Sample Introduction and Improved Ionization in Ambient Mass Spectrometry.</a> Anal. Chem. , 7512-7518 (2013).</li><li>Pfeuffer, K. P., Shelley, J. T., Ray, S. J., Hieftje, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualization+of+Mass+Transport+and+Heat+Transfer+in+the+FAPA+Ambient+Ionization+Source.">Visualization of Mass Transport and Heat Transfer in the FAPA Ambient Ionization Source.</a> J. Anal. At. Spectrom. 28 (379-387), 379-387 (2013).</li><li>Pfeuffer, K. P., Ray, S. J., Hieftje, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+and+Visualization+of+Mass+Transport+for+the+Flowing+Atmospheric+Pressure+Afterglow+(FAPA)+Ambient+Mass-Spectrometry+Source.">Measurement and Visualization of Mass Transport for the Flowing Atmospheric Pressure Afterglow (FAPA) Ambient Mass-Spectrometry Source.</a> J. Am. Soc. Mass Spectrom. 25 (5), 800-808 (2014).</li><li>Keelor, J. D., Dwivedi, P., Fern&#225;ndez, F. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+Effective+Approach+for+Coupling+Direct+Analysis+in+Real+Time+with+Atmospheric+Pressure+Drift+Tube+Ion+Mobility+Spectrometry.">An Effective Approach for Coupling Direct Analysis in Real Time with Atmospheric Pressure Drift Tube Ion Mobility Spectrometry.</a> J. Am. Soc. Mass Spectrom. 25 (9), 1538-1548 (2014).</li></ol>

There are no competing financial interests with this article.

There are several considerations which must be addressed prior to attempting this protocol. In addition to the space around the mass spectrometer for the source and mirror, enough open space must be available to accommodate the distance of twice the focal point of the mirror. Furthermore, the size of the mirror is ultimately decided by the size of the source that is under study. If the mirror is too small, the source will not be fully visualized. It is important to note that some, if not all, of the source covers must be...

Mass Spectrometry, an analytical tool available for molecular mass identification, has become one of the most powerful analytical techniques to date. Over the last decade a whole host of new ambient ionization sources have become available for mass spectrometry detection. For the data collected in this manuscript, the Direct Sample Analysis (DSA) source was utilized. Although these sources are extremely versatile, a more detailed knowledge of the physical ionization process is needed for its optimization and extension of purpose. The aim of this experiment is to gain a better understanding of the ionization process within the ambient sources through visualization of the nitrogen stream on the device using a technique called schlieren photography.
Scientific study often initiates through observation, which is difficult if the object of study is transparent to the naked eye. Schlieren photography is a technique that allows the invisible to become visible through relying on changes in the refractive index within transparent media1. The inhomogeneity of the refractive indices causes a distortion of the light allowing for visualization. The schlieren technique has been routinely used in a variety of specialty fields including ballistics modeling, aerospace engineering, general gas detection and flow monitoring, and at times to visualize protein bands in gel electrophoresis2-5.
Most ambient ionization sources use a stream of gas in order to facilitate the ionization. A wide range of conditions can exist for source options, however the parameters of this experiment must involve the utilization of a gas with a refractive index that differs from the surrounding lab air. This specific study utilizes hot nitrogen. It should be noted that only a small difference in refractive index is observed between pure nitrogen from the gas stream and air at RT6, mainly because air is composed mostly of nitrogen. This issue is overcome in this instance due to the high temperatures of the pure nitrogen in the gas stream which produces a significant enough change in refractive index for the gas to be observed.
Other mass spectrometry sources such as a Desorption Atmospheric Chemical Ionization (DAPCI)7, Flowing Atmospheric Pressure Afterglow (FAPA)8-10, and Direct Analysis in Real Time (DART)11 ionization sources have used schlieren photography. The intention of this protocol is to discuss how to study ambient ionization using a basic schlieren photography configuration. This technique, however, is applicable to any number of different analytical techniques that involve gaseous streams.

<table border="0" cellpadding="0" cellspacing="0" width="606">
	<tbody>
		<tr height="20">
			<td height="20" style="height:20px;width:303px;">Flashlight</td>
			<td style="width:109px;">EAGTAC</td>
			<td style="width:108px;">D25A Ti</td>
			<td style="width:87px;">or equvilent&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Spherical Concave Mirror</td>
			<td>Anchor Optics</td>
			<td>27633</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Rebel EOS T2i</td>
			<td>Canon</td>
			<td>4462B001</td>
			<td>or equvilent&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">300 mm telephoto lens</td>
			<td>Canon</td>
			<td>6473A003</td>
			<td>or equvilent&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Direct Sample Analysis (DSA) Ionization Source</td>
			<td>PerkinElmer</td>
			<td>MZ300560</td>
			<td>or equvilent&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Sq 300 MS with SQ Driver Software</td>
			<td>PerkinElmer</td>
			<td>N2910801</td>
			<td>or equvilent&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Ring Stand</td>
			<td>Fisher Scientific</td>
			<td>11-474-207</td>
			<td>or equvilent&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Laser Pointer</td>
			<td>Apollo</td>
			<td>MP1200</td>
			<td>or equvilent&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">razor blade</td>
			<td>Blue Hawk</td>
			<td>34112</td>
			<td>or equvilent&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">small drill bit #73</td>
			<td>CML Supply</td>
			<td>503-273</td>
			<td>or equvilent&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Protractor</td>
			<td>Sterling&#160;</td>
			<td>582</td>
			<td>or equvilent&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Hose Clamp</td>
			<td>Trident</td>
			<td>720-6000L</td>
			<td>or equvilent&#160;</td>
		</tr>
	</tbody>
</table>

visualization of ambient mass spectrometry with the use of schlieren photography

This manuscript outlines how to visualize mass spectrometry ambient ionization sources using schlieren photography. In order to properly optimize the mass spectrometer, it is necessary to characterize and understand the physical principles of the source. Most commercial ambient ionization sources utilize jets of nitrogen, helium, or atmospheric air to facilitate the ionization of the analyte. As a consequence, schlieren photography can be used to visualize the gas streams by exploiting the differences in refractive index between the streams and ambient air for visualization in real time. The basic setup requires a camera, mirror, flashlight, and razor blade. When properly configured, a real time image of the source is observed by watching its reflection. This allows for insight into the mechanism of action in the source, and pathways to its optimization can be elucidated. Light is shed on an otherwise invisible situation.

A schematic of the schlieren setup including the mass spectrometry ionization source can be found in Figure 1. When all schlieren components are properly aligned, gases within the test region can be seen as contrasting dark and light regions. Figure 2 illustrates how this contrast can be used to observe how the shape of the nitrogen jet flow from the mass spectrometry source changes as nozzle size decreases.
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Visualization of Ambient Mass Spectrometry with the Use of Schlieren Photography

This paper presents a protocol for the visualization of gaseous streams of an ambient ionization source using schlieren photography and mass spectrometry.

This manuscript outlines how to visualize mass spectrometry ambient ionization sources using schlieren photography. In order to properly optimize the mass ...

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8.2K Views.  University of Maryland, Baltimore County. This paper presents a protocol for the visualization of gaseous streams of an ambient ionization source using schlieren photography and mass spectrometry.

Video: Visualization of Ambient Mass Spectrometry with the Use of Schlieren Photography

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

All cellular processes depend on the functionality of proteins. Although the functionality of a given protein is the direct consequence of its unique amino acid sequence, it is only realized by the folding of the polypeptide chain into a single defined three-dimensional arrangement or more commonly into an ensemble of interconverting conformations. Investigating the connection between protein conformation and its function is therefore essential for a complete understanding of how proteins are able to fulfill their great variety of tasks. One possibility to study conformational changes a protein undergoes while progressing through its functional cycle is hydrogen-1H/2H-exchange in combination with high-resolution mass spectrometry (HX-MS). HX-MS is a versatile and robust method that adds a new dimension to structural information obtained by e.g. crystallography. It is used to study protein folding and unfolding, binding of small molecule ligands, protein-protein interactions, conformational changes linked to enzyme catalysis, and allostery. In addition, HX-MS is often used when the amount of protein is very limited or crystallization of the protein is not feasible. Here we provide a general protocol for studying protein dynamics with HX-MS and describe as an example how to reveal the interaction interface of two proteins in a complex. &#160;&#160;

Protein conformation and dynamics are key to understanding the relationship between protein structure and function. Hydrogen exchange coupled with high-resolution mass spectrometry is a versatile method to study the conformational dynamics of proteins as well as characterizing protein-ligand and protein-protein interactions, including contact interfaces and allosteric effects.

All cellular processes depend on the functionality of proteins. Although the functionality of a given protein is the direct consequence of its unique ...

A Study of the Complexation of Mercury(II) with Dicysteinyl Tetrapeptides by Electrospray Ionization Mass Spectrometry

In this study we evaluated a method for the characterization of complexes, formed in different relative ratios of mercury(II) to dicysteinyl tetrapeptide, by electrospray ionization orbitrap mass spectrometry. This strategy is based on previous successful characterization of mercury-dicysteinyl complexes involving tripeptides by utilizing mass spectrometry among other techniques. Mercury(II) chloride and a dicysteinyl tetrapeptide were incubated in a degassed buffered medium at varying stoichiometric ratios. The complexes formed were subsequently analyzed on an electrospray mass spectrometer consisting of a hybrid linear ion- and orbi- trap mass analyzer. The electrospray ionization mass spectrometry (ESI-MS) spectra were acquired in the positive mode and the observed peaks were then analyzed for distinct mercury isotopic distribution patterns and associated monoisotopic peak. This work demonstrates that an accurate stoichiometry of mercury and peptide in the complexes formed under specified electrospray ionization conditions can be determined by using high resolution ESI MS based on distinct mercury isotopic distribution patterns.

A Study of the Complexation of MercuryII with Dicysteinyl Tetrapeptides by Electrospray Ionization Mass Spectrometry

The characterization of complexes formed in different relative ratios of mercury(II) to dicysteinyl tetrapeptides by electrospray ionization orbitrap mass spectrometry is presented.

In this study we evaluated a method for the characterization of complexes, formed in different relative ratios of mercury(II) to dicysteinyl tetrapeptide, ...

Fizzy Extraction of Volatile Organic Compounds Combined with Atmospheric Pressure Chemical Ionization Quadrupole Mass Spectrometry

Chemical analysis of volatile and semivolatile compounds dissolved in liquid samples can be challenging. The dissolved components need to be brought to the gas phase, and efficiently transferred to a detection system. Fizzy extraction takes advantage of the effervescence phenomenon. First, a carrier gas (here, carbon dioxide) is dissolved in the sample by applying overpressure and stirring the sample. Second, the sample chamber is decompressed abruptly. Decompression leads to the formation of numerous carrier gas bubbles in the sample liquid. These bubbles assist the release of the dissolved analyte species from the liquid to the gas phase. The released analytes are immediately transferred to the atmospheric pressure chemical ionization interface of a triple quadrupole mass spectrometer. The ionizable analyte species give rise to mass spectrometric signals in the time domain. Because the release of the analyte species occurs over short periods of time (a few seconds), the temporal signals have high amplitudes and high signal-to-noise ratios. The amplitudes and areas of the temporal peaks can then be correlated with concentrations of the analytes in the liquid samples subjected to fizzy extraction, which enables quantitative analysis. The advantages of fizzy extraction include: simplicity, speed, and limited use of chemicals (solvents).

Fizzy extraction is a new laboratory technique for analysis of volatile and semivolatile compounds. A carrier gas is dissolved in the liquid sample by applying overpressure and stirring the sample. The sample chamber is then decompressed. The analyte species are liberated to the gas phase due to effervescence.

Chemical analysis of volatile and semivolatile compounds dissolved in liquid samples can be challenging. The dissolved components need to be brought to ...

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have been thought of as a type of molecular information storage. Mass spectrometry analysis has been considered the method of choice for sequencing peptoids. Peptoids can be synthesized via solid phase chemistry using a repeating two-step reaction cycle. Here we present a method to manually synthesize oligo-peptoids and to analyze the sequence of the peptoids using tandem mass spectrometry (MS/MS) techniques. The sample peptoid is a nonamer consisting of alternating N-(2-methyloxyethyl)glycine (Nme) and N-(2-phenylethyl)glycine (Npe), as well as an N-(2-aminoethyl)glycine (Nae) at the N-terminus. The sequence formula of the peptoid is Ac-Nae-(Npe-Nme)4-NH2, where Ac is the acetyl group. The synthesis takes place in a commercially available solid-phase reaction vessel. The rink amide resin is used as the solid support to yield the peptoid with an amide group at the C-terminus. The resulting peptoid product is subjected to sequence analysis using a triple-quadrupole mass spectrometer coupled to an electrospray ionization source. The MS/MS measurement produces a spectrum of fragment ions resulting from the dissociation of charged peptoid. The fragment ions are sorted out based on the values of their mass-to-charge ratio (m/z). The m/z values of the fragment ions are compared against the nominal masses of theoretically predicted fragment ions, according to the scheme of peptoid fragmentation. The analysis generates a fragmentation pattern of the charged peptoid. The fragmentation pattern is correlated to the monomer sequence of the neutral peptoid. In this regard, MS analysis reads out the sequence information of the peptoids.

A protocol is described for the manual synthesis of oligo-peptoids followed by sequence analysis by mass spectrometry.

Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have ...

Imaging Corrosion at the Metal-Paint Interface Using Time-of-Flight Secondary Ion Mass Spectrometry

Corrosion developed at the paint and aluminum (Al) metal-paint interface of an aluminum alloy is analyzed using time-of-flight secondary ion mass spectrometry (ToF-SIMS), illustrating that SIMS is a suitable technique to study the chemical distribution at a metal-paint interface. The painted Al alloy coupons are immersed in a salt solution or exposed to air only. SIMS provides chemical mapping and 2D molecular imaging of the interface, allowing direct visualization of the morphology of the corrosion products formed at the metal-paint interface and mapping of the chemical after corrosion occurs. The experimental procedure of this method is presented to provide technical details to facilitate similar research and highlight pitfalls that may be encountered during such experiments.

Time-of-flight secondary ion mass spectrometry is applied to demonstrate the chemical mapping and corrosion morphology at the metal-paint interface of an aluminum alloy after being exposed to a salt solution compared with a specimen exposed to air.

Corrosion developed at the paint and aluminum (Al) metal-paint interface of an aluminum alloy is analyzed using time-of-flight secondary ion mass ...

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. ...

Capillary Electrophoresis Mass Spectrometry Approaches for Characterization of the Protein and Metabolite Corona Acquired by Nanomaterials

The adsorption of biomolecules from surrounding biological matrices to the surface of nanomaterials (NMs) to form the corona has been of interest for the past decade. Interest in the bio-nano interface arises from the fact that the biomolecular corona confers a biological identity to NMs and thus causes the body to identify them as &#8220;self&#8221;. For example, previous studies have demonstrated that the proteins in the corona are capable of interacting with membrane receptors to influence cellular uptake and established that the corona is responsible for cellular trafficking of NMs and their eventual toxicity. To date, most research has focused upon the protein corona and overlooked the possible impacts of the metabolites included in the corona or synergistic effects between components in the complete biomolecular corona. As such, this work demonstrates methodologies to characterize both the protein and metabolite components of the biomolecular corona using bottom-up proteomics and metabolomics approaches in parallel. This includes an on-particle digest of the protein corona with a surfactant used to increase protein recovery, and a passive characterization of the metabolite corona by analyzing metabolite matrices before and after NM exposures. This work introduces capillary electrophoresis &#8211; mass spectrometry (CESI-MS) as a new technique for NM corona characterization. The protocols outlined here demonstrate how CESI-MS can be used for the reliable characterization of both the protein and metabolite corona acquired by NMs. The move to CESI-MS greatly decreases the volume of sample required (compared to traditional liquid chromatography &#8211; mass spectrometry (LC-MS) approaches) with multiple injections possible from as little as 5 &#181;L of sample, making it ideal for volume limited samples. Furthermore, the environmental consequences of analysis are reduced with respect to LC-MS due to the low flow rates (&#60;20 nL/min) in CESI-MS, and the use of aqueous electrolytes which eliminates the need for organic solvents.

Here we present a protocol to characterize the complete biomolecular corona, proteins, and metabolites, acquired by nanomaterials from biofluids using a capillary electrophoresis &#8211; mass spectrometry approach.

The adsorption of biomolecules from surrounding biological matrices to the surface of nanomaterials (NMs) to form the corona has been of interest for the ...

Gas Chromatography-Mass Spectrometry Paired with Total Vaporization Solid-Phase Microextraction as a Forensic Tool

Gas Chromatography &#8211; Mass Spectrometry (GC-MS) is a frequently used technique for the analysis of numerous analytes of forensic interest, including controlled substances, ignitable liquids, and explosives. GC-MS can be coupled with Solid-Phase Microextraction (SPME), in which a fiber with a sorptive coating is placed into the headspace above a sample or immersed in a liquid sample. Analytes are sorbed onto the fiber which is then placed inside the heated GC inlet for desorption. Total Vaporization Solid-Phase Microextraction (TV-SPME) utilizes the same technique as immersion SPME but immerses the fiber into a completely vaporized sample extract. This complete vaporization results in a partition between only the vapor phase and the SPME fiber without interference from a liquid phase or any insoluble materials. Depending upon the boiling point of the solvent used, TV-SPME allows for large sample volumes (e.g., up to hundreds of microliters). On-fiber derivatization may also be performed using TV-SPME. TV-SPME has been used to analyze drugs and their metabolites in hair, urine, and saliva. This simple technique has also been applied to street drugs, lipids, fuel samples, post-blast explosive residues, and pollutants in water. This paper highlights the use of TV-SPME to identify illegal adulterants in very small samples (microliter quantities) of alcoholic beverages. Both gamma-hydroxybutyrate (GHB) and gamma-butyrolactone (GBL) were identified at levels that would be found in spiked drinks. Derivatization by a trimethylsilyl agent allowed for conversion of the aqueous matrix and GHB into their TMS derivatives. Overall, TV-SPME is quick, easy, and requires no sample preparation aside from placing the sample into a headspace vial.

Total Vaporization Solid Phase Microextraction (TV-SPME) completely vaporizes a liquid sample whilst analytes are sorbed onto a SPME fiber. This allows for partitioning of the analyte between only the solvent vapor and the SPME fiber coating.

Gas Chromatography &#8211; Mass Spectrometry (GC-MS) is a frequently used technique for the analysis of numerous analytes of forensic interest, including ...

Covalent Labeling with Diethylpyrocarbonate for Studying Protein Higher-Order Structure by Mass Spectrometry

Characterizing a protein&#39;s higher-order structure is essential for understanding its function. Mass spectrometry (MS) has emerged as a powerful tool for this purpose, especially for protein systems that are difficult to study by traditional methods. To study a protein&#39;s structure by MS, specific chemical reactions are performed in solution that encode a protein&#39;s structural information into its mass. One particularly effective approach is to use reagents that covalently modify solvent accessible amino acid side chains. These reactions lead to mass increases that can be localized with residue-level resolution when combined with proteolytic digestion and tandem mass spectrometry. Here, we describe the protocols associated with use of diethylpyrocarbonate (DEPC) as a covalent labeling reagent together with MS detection. DEPC is a highly electrophilic molecule capable of labeling up to 30% of the residues in the average protein, thereby providing excellent structural resolution. DEPC has been successfully used together with MS to obtain structural information for small single-domain proteins, such as &#946;2-microglobulin, to large multi-domain proteins, such as monoclonal antibodies.

The experimental procedures for performing diethylpyrocarbonate-based covalent labeling with mass spectrometric detection are described. Diethylpyrocarbonate is simply mixed with the protein or protein complex of interest, leading to the modification of solvent accessible amino acid residues. The modified residues can be identified after proteolytic digestion and liquid chromatography/mass spectrometry analysis.

Characterizing a protein&#39;s higher-order structure is essential for understanding its function. Mass spectrometry (MS) has emerged as a powerful tool ...

Capillary Electrophoresis-based Hydrogen/Deuterium Exchange for Conformational Characterization of Proteins with Top-down Mass Spectrometry

Resolving conformational heterogeneity of multiple protein states that coexist in solution remains one of the main obstacles in the characterization of protein therapeutics and the determination of the conformational transition pathways critical for biological functions, ranging from molecular recognition to enzymatic catalysis. Hydrogen/deuterium exchange (HDX) reaction coupled with top-down mass spectrometric (MS) analysis provides a means to characterize protein higher-order structures and dynamics in a conformer-specific manner. The conformational resolving power of this technique is highly dependent on the efficiencies of separating protein states at the intact protein level and minimizing the residual non-deuterated protic content during the HDX reactions. 
Here we describe a capillary electrophoresis (CE)-based variant of the HDX MS approach that aims to improve the conformational resolution. In this approach, proteins undergo HDX reactions while migrating through a deuterated background electrolyte solution (BGE) during the capillary electrophoretic separation. Different protein states or proteoforms that coexist in solution can be efficiently separated based on their differing charge-to-size ratios. The difference in electrophoretic mobility between proteins and protic solvent molecules minimizes the residual non-deuterated solvent, resulting in a nearly complete deuterating environment during the HDX process. The flow-through microvial CE-MS interface allows efficient electrospray ionization of the eluted protein species following a rapid mixing with the quenching and denaturing modifier solution at the outlet of the sprayer. The online top-down MS analysis measures the global deuteration level of the eluted intact protein species, and subsequently, the deuteration of their gas-phase fragments. This paper demonstrates this approach in differential HDX for systems, including the natural protein variants coexisting in milk.

Presented here is a protocol for a capillary electrophoresis-based hydrogen/deuterium exchange (HDX) approach coupled with top-down mass spectrometry. This approach characterizes the difference in higher-order structures between different protein species, including proteins in different states and different proteoforms, by conducting concurrent differential HDX and electrophoretic separation.

Resolving conformational heterogeneity of multiple protein states that coexist in solution remains one of the main obstacles in the characterization of ...