Name: an efficient sample preparation method to enhance carbohydrate ion signals in matrix-assisted laser desorption/ionization mass spectrometry
Uploaded: 2018-07-29T13:00:00
Description: Watch this Scientific Journal Video about An Efficient Sample Preparation Method to Enhance Carbohydrate Ion Signals in Matrix-assisted Laser Desorption/Ionization Mass Spectrometry at JoVE.com

The authors have no acknowledgements.

1. Sample Plate Preconditioning
<ol>
	<li>Cleaning of the sample plate
	<ol>
		<li>Wear nitrile gloves to avoid contamination of the sample plate during cleaning.</li>
		<li>Hand-wash the sample plate with 100.0 mL of detergent solution (1.0 mg/mL).</li>
		<li>Hand-wash the sample plate with distilled-deionized water (DDW).</li>
		<li>Rinse the sample plate surface with 30.0 mL of MeOH.</li>
		<li>Put the sample plate in a 600 mL beaker and fill with DDW until the sample plate is fully immersed in wate...

<ol>
	<li>Holme, D. J., Peck, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Analytical Biochemistry. , (1998).</li><li>Costello, C. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Time,+life+...+and+mass+spectrometry+-+New+techniques+to+address+biological+questions.">Time, life ... and mass spectrometry - New techniques to address biological questions.</a> Biophysical Chemistry. 68 (1-3), 173-188 (1997).</li><li>Caroff, M., Karibian, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+of+bacterial+lipopolysaccharides.">Structure of bacterial lipopolysaccharides.</a> Carbohydrate Research. 338 (23), 2431-2447 (2003).</li><li>Marvin, L. F., Roberts, M. A., Fay, L. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Matrix-assisted+laser+desorption/ionization+time-of-flight+mass+spectrometry+in+clinical+chemistry.">Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in clinical chemistry.</a> Clinica Chimica Acta. 337 (1), 11-21 (2003).</li><li>Harvey, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Matrix-assisted+laser+desorption/ionization+mass+spectrometry+of+carbohydrates.">Matrix-assisted laser desorption/ionization mass spectrometry of carbohydrates.</a> Mass Spectrometry Reviews. 18 (6), 349-450 (1999).</li><li>Ciucanu, I., Kerek, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+simple+and+rapid+method+for+the+permethylation+of+carbohydrates.">A simple and rapid method for the permethylation of carbohydrates.</a> Carbohydrate Research. 131 (2), 209-217 (1984).</li><li>Lamari, F. N., Kuhn, R., Karamanos, N. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Derivatization+of+carbohydrates+for+chromatographic,+electrophoretic+and+mass+spectrometric+structure+analysis.">Derivatization of carbohydrates for chromatographic, electrophoretic and mass spectrometric structure analysis.</a> Journal of Chromatography B. 793 (1), 15-36 (2003).</li><li>Nishikaze, T., Amano, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reverse+thin+layer+method+for+enhanced+ion+yield+of+oligosaccharides+in+matrix-assisted+laser+desorption/ionization.">Reverse thin layer method for enhanced ion yield of oligosaccharides in matrix-assisted laser desorption/ionization.</a> Rapid Communications in Mass Spectrometry. 23 (23), 3787-3794 (2009).</li><li>Williams, T. I., Saggese, D. A., Wilcox, R. J., Martin, J. D., Muddiman, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+matrix+crystal+structure+on+ion+abundance+of+carbohydrates+by+matrix-assisted+laser+desorption/ionization+Fourier+transform+ion+cyclotron+resonance+mass+spectrometry.">Effect of matrix crystal structure on ion abundance of carbohydrates by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.</a> Rapid Communications in Mass Spectrometry. 21 (5), 807-811 (2007).</li><li>Nicola, A. J., Gusev, A. I., Proctor, A., Jackson, E. K., Hercules, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Application+of+the+fast-evaporation+sample+preparation+method+for+improving+quantification+of+angiotensin+II+by+matrix-assisted+laser+desorption/ionization.">Application of the fast-evaporation sample preparation method for improving quantification of angiotensin II by matrix-assisted laser desorption/ionization.</a> Rapid Communications in Mass Spectrometry. 9 (12), 1164-1171 (1995).</li><li>Lai, Y. H., 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=Reducing+Spatial+Heterogeneity+of+MALDI+Samples+with+Marangoni+Flows+During+Sample+Preparation.">Reducing Spatial Heterogeneity of MALDI Samples with Marangoni Flows During Sample Preparation.</a> Journal of the American Society for Mass Spectrometry. 27 (8), 1314-1321 (2016).</li><li>Ou, Y. -. M., 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=Preparation+of+Homogeneous+MALDI+Samples+for+Quantitative+Applications.">Preparation of Homogeneous MALDI Samples for Quantitative Applications.</a> Journal of Visualized Experiments. (116), e54409 (2016).</li><li>Lee, H., 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=Enhancing+carbohydrate+ion+yield+by+controlling+crystalline+structures+in+matrix-assisted+laser+desorption/ionization+mass+spectrometry.">Enhancing carbohydrate ion yield by controlling crystalline structures in matrix-assisted laser desorption/ionization mass spectrometry.</a> Analytica Chimica Acta. , 49-55 (2017).</li><li>Allwood, D. A., Perera, I. K., Perkins, J., Dyer, P. E., Oldershaw, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparation+of+'near'+homogeneous+samples+for+the+analysis+of+matrix-assisted+laser+desorption/ionisation+processes.">Preparation of 'near' homogeneous samples for the analysis of matrix-assisted laser desorption/ionisation processes.</a> Applied Surface Science. 103 (3), 231-244 (1996).</li><li>Sadeghi, M., Vertes, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crystallite+size+dependence+of+volatilization+in+matrix-assisted+laser+desorption+ionization.">Crystallite size dependence of volatilization in matrix-assisted laser desorption ionization.</a> Applied Surface Science. 127 (Supplement C), 226-234 (1998).</li></ol>

Sample heterogeneity is a crucial problem in MALDI-MS. DD is the most commonly used sample preparation method, but the resultant crystals are highly heterogeneous. Such samples show poor shot-to-shot and sample-to-sample signal reproducibility. Therefore, searching for &#34;sweet spots&#34; in sample areas during data acquisition is a common procedure in MALDI experiments. Such heterogeneous samples are unsuitable for quantification in routine analyses.
In the current study, MALDI sample morph...

Carbohydrate analysis is an important and challenging subject. Carbohydrates and their derivatives play important roles in living organisms1,2,3. These molecules have complicated structures and are prone to decompose. Many of them cannot be clearly characterized due to difficulties in separation and detection. Although matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) has been applied to analysis of a wide range of biomolecules, due to its sensitivity and comprehensible results4, analyzing carbohydrates using MALDI-MS continues to be a major challenge due to the low ionization efficiency of such molecules5. Chemical derivatization is a common way to improve ionization efficiency of carbohydrates6,7, but such procedures are time and sample consuming. Besides, the ionization efficiency of derivatized carbohydrates is still lower than that of proteins. Thus, the development of methods to improve carbohydrate signal in MALDI-MS without complicated procedures is necessary.
The application of MALDI-MS to quantitative analysis is another challenging subject. A major problem of MALDI-MS is that its sensitivity and data reproducibility relies critically on sample preparation protocols and experimental parameters. In many cases, quantitative analysis by MALDI-MS is unreliable due to heterogeneous sample morphologies and analyte distribution. A well-known example is samples prepared with a 2,5-dihydroxybenzoic acid (DHB) MALDI matrix. When DHB is crystallized slowly under ambient environment, the extent of analyte incorporation into matrix crystals is unpredictable, because resultant samples show irregular morphologies. Such samples normally consist of large needle-shaped and fine crystals. When DHB is prepared using a volatile solvent and/or a heated sample plate, a fast drying process results in more homogeneous fine crystals and better quantitative results8,9,10. This technique is known as &#34;recrystallization&#34; of MALDI samples. The improvement is attributed to better incorporation of analytes into fine matrix crystals during the fast crystallization process. We have also demonstrated that adjusting the sample preparation environment reduced the heterogeneity of carbohydrate signal and improved quantitative results11,12. The findings in these works suggest that sample morphology is a critical factor in determining carbohydrate signal quality. To develop a general strategy for daily analysis, an efficient sample reformation method providing improved carbohydrate sensitivity is required.
We have systematically examined the correlation between sample morphology and carbohydrate sensitivity in MALDI-MS in a recent report13. The results obtained using several important carbohydrates and matrixes show that the best signal enhancement is fulfilled by recrystallizing dried MALDI samples. The morphology of samples prepared using the conventional dried droplet (DD) method is reformed by fast recrystallization with methanol (MeOH). The detailed sample preparation protocols are demonstrated here. The protocol consists of three main steps, including sample plate preconditioning, sample deposition and recrystallization, and mass spectrometry analysis. The utilized carbohydrates include sialyl-lewis A (SLeA) and maltoheptaose (MH). DHB is used as a model matrix. The results show that carbohydrate signal intensity and spatial distribution improved markedly after recrystallization. Such a method can be applied to samples with other popular matrixes, including 2,4,6-trihydroxyacetophenone (THAP) and &#945;-cyano-4-hydroxycinnamic acid. This method serves as a general approach that can be easily integrated in the laboratory routine for carbohydrate analysis.

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			<td height="23" style="height:23px;width:332px;">Reagent</td>
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			<td height="23" style="height:23px;">2,5-dihydroxybenzoic acid (DHB)</td>
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			<td style="width:137px;">A11459</td>
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			<td style="width:157px;">Sigma-Aldrich</td>
			<td style="width:137px;">S1782</td>
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		</tr>
		<tr height="23">
			<td height="23" style="height:23px;">Maltoheptaose</td>
			<td style="width:157px;">Sigma-Aldrich</td>
			<td style="width:137px;">M7753</td>
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			<td height="23" style="height:23px;width:332px;">Temperature controllable drying chamber</td>
			<td style="width:157px;">This lab</td>
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			<td>Control software</td>
		</tr>
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			<td height="23" style="height:23px;width:332px;">Fleximaging Version 2.1</td>
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			<td>Imaging software</td>
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			<td height="23" style="height:23px;width:332px;">Flexanalysis Version 3.4</td>
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			<td>Analysis software</td>
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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.

Representative SEM images of SLeA mixed with DHB prepared using DD and recrystallization methods are shown in Figure 1. A typical DHB morphology as prepared by the DD method is large needle-shaped crystals at the rim and fine crystalline structures in the center of sample spots. The typical lengths of such needle-shaped crystals are ~100 &#181;m. After recrystallization by MeOH, the sample has a larger area covered evenly with fine flake-like cryst...

Watch this Scientific Journal Video about An Efficient Sample Preparation Method to Enhance Carbohydrate Ion Signals in Matrix-assisted Laser Desorption/Ionization Mass Spectrometry at JoVE.com

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

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) ...

A simple sample preparation procedure was developed to improve the conventional method in matrix-assisted laser desorption ionization mass spectrometry by reforming the simple morphology during the drying process. The advantage of this technique is that the signal intensity of carbohydrate samples prepared by this optimized method can be effectively enhanced. Generally, individuals new to this method will struggle because the methanol depressurization step is very crucial and it needs to be done in one go.Any hesitation will decrease the data quality. To begin, while wearing nitrile gloves, use 100 milliliters of detergent solution to hand wash the sample plate. Use distilled-deionized, or DD, water to hand wash the plate.Then, with 30 milliliters of methanol, rinse its surface. Insert the sample plate into a 600 milliliter beaker and fill it with DD water until the plate is fully immersed. Then place the beaker into an ultrasonic bath and sonicate the plate for 15 minutes.Remove the sample plate from the beaker and use pressurized nitrogen to blow off the water drops. Then deposit 0.2 microliters of methanol on the sample plate to check whether it spreads to other spots. If it does, repeat the wash, sonication and nitrogen treatment as just demonstrated.After preparing the drying chamber according to the text protocol, premix 0.25 microliters of 2, 5-Dihydroxybenzoic acid solution and 0.25 microliters of Sialyl-Lewis A, or maltoheptaose solution in the micro centrifuge tube. Then vortex the tube for three seconds. Spin down the mixed solution in the mini centrifuge at 2000 times G for two seconds.Then immediately pipette 0.1 microliter of the pre-mixed solution on to the sample plate. When the sample has dried, while working quickly to avoid evaporation, pipette 0.2 microliters of methanol directly on to the sample spot. The sample will redissolve and then immediately dry out.The methanol deposition step is the most difficult step that determines data quality and reproducibility. To ensure the best performance, we recommend that the user finish the deposition in three to five seconds to avoid significant evaporation loss of methanol. Wear nitrile gloves and carefully remove the sample plate from the drying chamber.Then, under a microscope, examine the sample. If the crystal morphologies are not as expected, repeat mixing the sample and spotting onto the sample plate. To ensure the sample crystals have the optimal morphology after recrystallization, always use a microscope to exam them.It is difficult to determine the quality of crystal morphology correctly with the naked eye. To analyze a one microliter sample, premix 2.5 microliters of 2, 5-Dihydroxybenzoic acid solution and 2.5 microliters of Sialyl-Lewis A or maltoheptaose solution in a micro centrifuge tube. Vortex the pre-mixed solution for five seconds.Spin down the mixed solution at 2000 times G for two seconds, then immediately pipette one microliter of the pre-mixed solution on to the sample plate. After the sample dries out, pipette 1.5 microliters of methanol directly on to the dried sample spot. The sample will redissolve and immediately dry out.Carefully remove the sample from the drying chamber. Examine the sample under a microscope. If the crystal morphologies are not as expected, repeat the solution preparation as just demonstrated.To carry out mass spectrometry, open the mass spectrometer control software and insert the sample plate into the machine. Select the pre-optimized data acquisition method in the software, then using the imaging software, register the whole sample region for imaging mass spectrometry. Start data acquisition in batch mode of the control software.When data acquisition is complete, use the imaging software to plot the ion images and analyze the data according to the text protocol. Representative SEM images of Sialyl-Lewis A mixed with 2, 5-Dihydroxybenzoic acid prepared using dried droplet and recrystallization methods are shown here. A typical 2, 5-Dihydroxybenzoic acid morphology is large, needle-shaped crystals at the rim and fine crystalline structures in the center of sample spots.After recrystallization by methanol, the sample has a larger area covered evenly with fine, flake-like crystals. This figure depicts imaging mass spectrometry results of Sialyl-Lewis A and maltoheptaose with and without methanol recrystallization. After recrystallization, the distribution of Sialyl-Lewis A and maltohepaose signals match well with the bright-field images of sample spots.The signal intensities of the recrystallized carbohydrate samples are also enhanced compared to conventional dry droplet samples. This graph compares the signal intensity of sodiated or positive ion mode and deprotonated or negative ion mode carbohydrates of recrystallized samples with respect to that of dried droplet samples. On average, recrystallization of Sialyl-Lewis A and maltoheptaose samples increased sodiated signals by factors of 3.9 and 3.3.Deprotonated Sialyl-Lewis A ion signals were enhanced by a factor of 4.7 after recrystallization. Once mastered, samples can be prepared in 10 minutes using this technique if it is performed properly. While attempting this procedure, it's important that the methanol droplet be immediately and precisely deposited on the sample spot.After watching this video, you should have a good understanding of how to effectively control crystal morphology of multi samples to obtain the best ion signals for routine analysis.

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Chemistry

Untargeted Metabolomics from Biological Sources Using Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry (UPLC-HRMS)

Here we present a workflow to analyze the metabolic profiles for biological samples of interest including; cells, serum, or tissue. The sample is first separated into polar and non-polar fractions by a liquid-liquid phase extraction, and partially purified to facilitate downstream analysis. Both aqueous (polar metabolites) and organic (non-polar metabolites) phases of the initial extraction are processed to survey a broad range of metabolites. Metabolites are separated by different liquid chromatography methods based upon their partition properties. In this method, we present microflow ultra-performance (UP)LC methods, but the protocol is scalable to higher flows and lower pressures. Introduction into the mass spectrometer can be through either general or compound optimized source conditions. Detection of a broad range of ions is carried out in full scan mode in both positive and negative mode over a broad m/z range using high resolution on a recently calibrated instrument. Label-free differential analysis is carried out on bioinformatics platforms. Applications of this approach include metabolic pathway screening, biomarker discovery, and drug development.

Untargeted Metabolomics from Biological Sources Using Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry UPLC-HRMS

Untargeted metabolomics provides a hypothesis generating snapshot of a metabolic profile. This protocol will demonstrate the extraction and analysis of metabolites from cells, serum, or tissue. A range of metabolites are surveyed using liquid-liquid phase extraction, microflow ultraperformance liquid chromatography/high-resolution mass spectrometry (UPLC-HRMS) coupled to differential analysis software.

Here we present a workflow to analyze the metabolic profiles for biological samples of interest including; cells, serum, or tissue. The sample is first ...

Matrix-assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) Mass Spectrometric Analysis of Intact Proteins Larger than 100 kDa

Effectively determining masses of proteins is critical to many biological studies (e.g. for structural biology investigations). Accurate mass determination allows one to evaluate the correctness of protein primary sequences, the presence of mutations and/or post-translational modifications, the possible protein degradation, the sample homogeneity, and the degree of isotope incorporation in case of labelling (e.g. 13C labelling).
Electrospray ionization (ESI) mass spectrometry (MS) is widely used for mass determination of denatured proteins, but its efficiency is affected by the composition of the sample buffer. In particular, the presence of salts, detergents, and contaminants severely undermines the effectiveness of protein analysis by ESI-MS. Matrix-assisted laser desorption/ionization (MALDI) MS is an attractive alternative, due to its salt tolerance and the simplicity of data acquisition and interpretation. Moreover, the mass determination of large heterogeneous proteins (bigger than 100 kDa) is easier by MALDI-MS due to the absence of overlapping high charge state distributions which are present in ESI spectra.
Here we present an accessible approach for analyzing proteins larger than 100 kDa by MALDI-time of flight (TOF). We illustrate the advantages of using a mixture of two matrices (i.e. 2,5-dihydroxybenzoic acid and &#945;-cyano-4-hydroxycinnamic acid) and the utility of the thin layer method as approach for sample deposition. We also discuss the critical role of the matrix and solvent purity, of the standards used for calibration, of the laser energy, and of the acquisition time. Overall, we provide information necessary to a novice for analyzing intact proteins larger than 100 kDa by MALDI-MS.

Matrix-assisted Laser Desorption/Ionization Time of Flight MALDI-TOF Mass Spectrometric Analysis of Intact Proteins Larger than 100 kDa

Accurate mass measurement represents an important step during the investigation of proteins. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) can be used for such determination and its key advantage is the tolerance to salts, detergents and contaminants. Here we illustrate an accessible approach for the analysis of proteins larger than 100 kDa by MALDI-MS.

Effectively determining masses of proteins is critical to many biological studies (e.g. for structural biology investigations). Accurate mass ...

Improved In-gel Reductive &#946;-Elimination for Comprehensive O-linked and Sulfo-glycomics by Mass Spectrometry

Separation of proteins by SDS-PAGE followed by in-gel proteolytic digestion of resolved protein bands has produced high-resolution proteomic analysis of biological samples. Similar approaches, that would allow in-depth analysis of the glycans carried by glycoproteins resolved by SDS-PAGE, require special considerations in order to maximize recovery and sensitivity when using mass spectrometry (MS) as the detection method. A major hurdle to be overcome in achieving high-quality data is the removal of gel-derived contaminants that interfere with MS analysis. The sample workflow presented here is robust, efficient, and eliminates the need for in-line HPLC clean-up prior to MS. Gel pieces containing target proteins are washed in acetonitrile, water, and ethyl acetate to remove contaminants, including polymeric acrylamide fragments. O-linked glycans are released from target proteins by in-gel reductive &#946;-elimination and recovered through robust, simple clean-up procedures. An advantage of this workflow is that it improves sensitivity for detecting and characterizing sulfated glycans. These procedures produce an efficient separation of sulfated permethylated glycans from non-sulfated (sialylated and neutral) permethylated glycans by a rapid phase-partition prior to MS analysis, and thereby enhance glycomic and sulfoglycomic analyses of glycoproteins resolved by SDS-PAGE.

In order to comprehensively explore the diversity of O-linked glycans, a new procedure for in-gel reductive &#946;-elimination, combined with permethylation and a rapid phase-partition method, is applied to the analysis of O-linked glycans directly released from glycoproteins resolved by SDS-PAGE and amenable to subsequent glycomic analysis by mass spectrometry.

Separation of proteins by SDS-PAGE followed by in-gel proteolytic digestion of resolved protein bands has produced high-resolution proteomic analysis of ...

Sequencing of Plant Wall Heteroxylans Using Enzymic, Chemical (Methylation) and Physical (Mass Spectrometry, Nuclear Magnetic Resonance) Techniques

This protocol describes the specific techniques used for the characterization of reducing end (RE) and internal region glycosyl sequence(s) of heteroxylans. De-starched wheat endosperm cell walls were isolated as an alcohol-insoluble residue (AIR)1 and sequentially extracted with water (W-sol Fr) and 1 M KOH containing 1% NaBH4 (KOH-sol Fr) as described by Ratnayake et al. (2014)2. Two different approaches (see summary in Figure 1) are adopted. In the first, intact W-sol AXs are treated with 2AB to tag the original RE backbone chain sugar residue and then treated with an endoxylanase to generate a mixture of 2AB-labelled RE and internal region reducing oligosaccharides, respectively. In a second approach, the KOH-sol Fr is hydrolyzed with endoxylanase to first generate a mixture of oligosaccharides which are subsequently labelled with 2AB. The enzymically released ((un)tagged) oligosaccharides from both W- and KOH-sol Frs are then methylated and the detailed structural analysis of both the native and methylated oligosaccharides is performed using a combination of MALDI-TOF-MS, RP-HPLC-ESI-QTOF-MS and ESI-MSn. Endoxylanase digested KOH-sol AXs are also characterized by nuclear magnetic resonance (NMR) that also provides information on the anomeric configuration. These techniques can be applied to other classes of polysaccharides using the appropriate endo-hydrolases.

Sequencing of Plant Wall Heteroxylans Using Enzymic, Chemical Methylation and Physical Mass Spectrometry, Nuclear Magnetic Resonance Techniques

This protocol describes the specific techniques used for the structural characterization of reducing end (RE) and internal region glycosyl sequence(s) of heteroxylans by tagging the RE with 2 aminobenzamide prior to enzymatic (endoxylanase) hydrolysis and then analysis of the resultant oligosaccharides using mass spectrometry (MS) and nuclear magnetic resonance (NMR).

This protocol describes the specific techniques used for the characterization of reducing end (RE) and internal region glycosyl sequence(s) of ...

An HS-MRM Assay for the Quantification of Host-cell Proteins in Protein Biopharmaceuticals by Liquid Chromatography Ion Mobility QTOF Mass Spectrometry

The analysis of low-level (1-100 ppm) protein impurities (e.g., host-cell proteins (HCPs)) in protein biotherapeutics is a challenging assay requiring high sensitivity and a wide dynamic range. Mass spectrometry-based quantification assays for proteins typically involve protein digestion followed by the selective reaction monitoring/multiple reaction monitoring (SRM/MRM) quantification of peptides using a low-resolution (Rs ~1,000) tandem quadrupole mass spectrometer. One of the limitations of this approach is the interference phenomenon observed when the peptide of interest has the "same" precursor and fragment mass (in terms of m/z values) as other co-eluting peptides present in the sample (within a 1-Da window). To avoid this phenomenon, we propose an alternative mass spectrometric approach, a high selectivity (HS) MRM assay that combines the ion mobility separation of peptide precursors with the high-resolution (Rs ~30,000) MS detection of peptide fragments. We explored the capabilities of this approach to quantify low-abundance peptide standards spiked in a monoclonal antibody (mAb) digest and demonstrated that it has the sensitivity and dynamic range (at least 3 orders of magnitude) typically achieved in HCP analysis. All six peptide standards were detected at concentrations as low as 0.1 nM (1 femtomole loaded on a 2.1-mm ID chromatographic column) in the presence of a high-abundance peptide background (2 &#181;g of a mAb digest loaded on-column). When considering the MW of rabbit phosphorylase (97.2 kDa), from which the spiked peptides were derived, the LOQ of this assay is lower than 50 ppm. Relative standard deviations (RSD) of peak areas (n = 4 replicates) were less than 15% across the entire concentration range investigated (0.1-100 nM or 1-1,000 ppm) in this study.

Here, we describe a chromatographic assay coupled with the ion mobility separation of peptide precursors followed by the high-resolution (~30,000) MS-detection of peptide fragments for the quantification of spiked peptide standards in a monoclonal antibody digest.

The analysis of low-level (1-100 ppm) protein impurities (e.g., host-cell proteins (HCPs)) in protein biotherapeutics is a challenging assay requiring ...

Characterization of Synthetic Polymers via Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) Mass Spectrometry

There are many techniques that can be employed in the characterization of synthetic homopolymers, but few provide as useful of information for end group analysis as matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). This tutorial demonstrates methods for optimization of the sample preparation, spectral acquisition, and data analysis of synthetic polymers using MALDI-TOF MS. Critical parameters during sample preparation include the selection of the matrix, identification of an appropriate cationization salt, and tuning the relative proportions of the matrix, cation, and analyte. The acquisition parameters, such as mode (linear or reflector), polarization (positive or negative), acceleration voltage, and delay time, are also important. Given some knowledge of the chemistry involved to synthesize the polymer and optimizing both the data acquisition parameters and the sample preparation conditions, spectra should be obtained with sufficient resolution and mass accuracy to enable the unambiguous determination of the end groups of most homopolymers (masses below 10,000) in addition to the repeat unit mass and the overall molecular weight distribution. Though demonstrated on a limited set of polymers, these general techniques are applicable to a much wider range of synthetic polymers for determining mass distributions, though end group determination is only possible for homopolymers with narrow dispersity.

Characterization of Synthetic Polymers via Matrix Assisted Laser Desorption Ionization Time of Flight MALDI-TOF Mass Spectrometry

A protocol for the matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) characterization of synthetic polymers is described including the optimization of sample preparation, spectral acquisition, and data analysis.

There are many techniques that can be employed in the characterization of synthetic homopolymers, but few provide as useful of information for end group ...

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 ...

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Electrospray ionization (ESI) can transfer an aqueous-phase peptide or peptide complex to the gas-phase while conserving its mass, overall charge, metal-binding interactions, and conformational shape. Coupling ESI with ion mobility-mass spectrometry (IM-MS) provides an instrumental technique that allows for simultaneous measurement of a peptide&#8217;s mass-to-charge (m/z) and collision cross section (CCS) that relate to its stoichiometry, protonation state, and conformational shape. The overall charge of a peptide complex is controlled by the protonation of 1) the peptide&#8217;s acidic and basic sites and 2) the oxidation state of the metal ion(s). Therefore, the overall charge state of a complex is a function of the pH of the solution that affects the peptides metal ion binding affinity. For ESI-IM-MS analyses, peptide and metal ions solutions are prepared from aqueous-only solutions, with the pH adjusted with dilute aqueous acetic acid or ammonium hydroxide. This allows for pH dependence and metal ion selectivity to be determined for a specific peptide. Furthermore, the m/z and CCS of a peptide complex can be used with B3LYP/LanL2DZ molecular modeling to discern binding sites of the metal ion coordination and tertiary structure of the complex. The results show how ESI-IM-MS can characterize the selective chelating performance of a set of alternative methanobactin peptides and compare them to the copper-binding peptide methanobactin.

Ion mobility-mass spectrometry and molecular modeling techniques can characterize the selective metal chelating performance of designed metal-binding peptides and the copper-binding peptide methanobactin. Developing new classes of metal chelating peptides will help lead to therapeutics for diseases associated with metal ion misbalance.

Electrospray ionization (ESI) can transfer an aqueous-phase peptide or peptide complex to the gas-phase while conserving its mass, overall charge, ...

Analysis of Complex Molecules and Their Reactions on Surfaces by Means of Cluster-Induced Desorption/Ionization Mass Spectrometry

Desorption/Ionization Induced by Neutral SO2 Clusters (DINeC) is employed as a very soft and efficient desorption/ionization technique for mass spectrometry (MS) of complex molecules and their reactions on surfaces. DINeC is based on a beam of SO2 clusters impacting on the sample surface at low cluster energy. During cluster-surface impact, some of the surface molecules are desorbed and ionized via dissolvation in the impacting cluster; as a result of this dissolvation-mediated desorption mechanism, low cluster energy is sufficient and the desorption process is extremely soft. Both surface adsorbates and molecules of which the surface is composed of can be analyzed. Clear and fragmentation-free spectra from complex molecules such as peptides and proteins are obtained. DINeC does not require any special sample preparation, in particular no matrix has to be applied. The method yields quantitative information on the composition of the samples; molecules at a surface coverage as low as 0.1 % of a monolayer can be detected. Surface reactions such as H/D exchange or thermal decomposition can be observed in real-time and the kinetics of the reactions can be deduced. Using a pulsed nozzle for cluster beam generation, DINeC can be efficiently combined with ion trap mass spectrometry. The matrix-free and soft nature of the DINeC process in combination with the MSn capabilities of the ion trap allows for very detailed and unambiguous analysis of the chemical composition of complex organic samples and organic adsorbates on surfaces.

Neutral SO2 clusters of low kinetic energy (&#60; 0.8 eV/constituent) are used to desorb complex surface molecules such as peptides or lipids for further analysis by means of mass spectrometry using an ion trap mass spectrometer. No special sample preparation is required, and real-time observation of reactions is possible.

Desorption/Ionization Induced by Neutral SO2 Clusters (DINeC) is employed as a very soft and efficient desorption/ionization technique for mass ...

3D Depth Profile Reconstruction of Segregated Impurities Using Secondary Ion Mass Spectrometry

The presented protocol combines excellent detection limits (1 ppm to 1 ppb) using secondary ion mass spectrometry (SIMS) with reasonable spatial resolution (~1 &#181;m). Furthermore, it describes how to obtain realistic three-dimensional (3D) distributions of segregated impurities/dopants in solid state materials. Direct 3D depth profile reconstruction is often difficult to achieve due to SIMS-related measurement artifacts. Presented here is a method to identify and solve this challenge. Three major issues are discussed, including the i) nonuniformity of the detector being compensated by flat-field correction; ii) vacuum background contribution (parasitic oxygen counts from residual gases present in the analysis chamber) being estimated and subtracted; and iii)&#160;performance of all steps within a stable timespan of the primary ion source. Wet chemical etching is used to reveal the position and types of dislocation in a material, then the SIMS result is superimposed on images obtained via scanning electron microscopy (SEM). Thus, the position of agglomerated impurities can be related to the position of certain defects. The method is fast and does not require sophisticated sample preparation stage; however, it requires a high-quality, stable ion source, and the entire measurement must be performed quickly to avoid deterioration of the primary beam parameters.

The presented method describes how to identify and solve measurement artifacts related to secondary ion mass spectrometry as well as obtain realistic 3D distributions of impurities/dopants in solid state materials.