The authors thank Heedeok Hong's group at the Department of Chemistry, Michigan State University, for kindly providing the Escherichia coli cells for the experiments. The authors thank the support from the National Institute of General Medical Sciences, the National Institutes of Health (NIH) through Grant R01GM118470 (to X. Liu) and Grant R01GM125991 (to L. Sun and X. Liu).

1. Preparation of LPA Coating on the Inner Wall of the Separation Capillary
<ol>
	<li>Pretreatment of the capillary
	<ol>
		<li>Flush a fused silica capillary (120 cm in length, 50 &#181;m in inner diameter [i.d.], 360 &#181;m in outer diameter [o.d.]) successively with 500 &#181;L of 1 M sodium hydroxide, deionized water, 1 M hydrochloric acid, deionized water, and LC-MS grade methanol using a syringe pump.</li>
		<li>Dry the capillary with nitrogen gas (10 psi, &#8805; 12 h) and fill the capillary wi...

<ol>
	<li>Aebersold, R., 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=How+many+proteoforms+are+there.">How many proteoforms are there.</a> Nature Chemical Biology. 14 (3), 206-214 (2018).</li><li>Tran, J. C., 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=Mapping+intact+protein+isoforms+in+discovery+mode+using+top-down+proteomics.">Mapping intact protein isoforms in discovery mode using top-down proteomics.</a> Nature. 480 (7376), 254-258 (2011).</li><li>Catherman, A. 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Using Dynamic pH Junction Preconcentration and Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry.</a> Analytical Chemistry. 86 (13), 6331-6336 (2014).</li><li>Lubeckyj, R. A., McCool, E. N., Shen, X., Kou, Q., Liu, X., Sun, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-Shot+Top-Down+Proteomics+with+Capillary+Zone+Electrophoresis-Electrospray+Ionization-Tandem+Mass+Spectrometry+for+Identification+of+Nearly+600+Escherichia+coli+Proteoforms.">Single-Shot Top-Down Proteomics with Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry for Identification of Nearly 600 Escherichia coli Proteoforms.</a> Analytical Chemistry. 89 (22), 12059-12067 (2017).</li><li>Busnel, J. 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Here we provide a detailed protocol to use CZE-MS/MS forthe high-resolution characterization of proteoforms in simple protein samples and for the large-scale identification of proteoforms in complex proteome samples. A diagram of the CZE-ESI-MS/MS system is shown in Figure 1. There are four critical steps in the protocol. First, the preparation of high-quality LPA coating on the inner wall of the separation capillary is extremely important. An LPA-coated separation capillary can reduce the E...

Top-down proteomics (TDP) aims for the large-scale characterization of proteoforms within a proteome. TDP relies on the effective liquid-phase separation of intact proteins before electrospray ionization-tandem mass spectrometry (ESI-MS/MS) analysis due to the high complexity and large concentration dynamic range of the proteome1,2,3,4,5. Capillary zone electrophoresis (CZE) is a powerful technique for the separation of biomolecules based on their size-to-charge ratios6. CZE is relatively simple, requiring only an open tubular-fused silica capillary, a background electrolyte (BGE), and a power supply. A sample of intact proteins can be loaded into the capillary using pressure or voltage, and separation is initiated by immersing both ends of the capillary in the BGE and applying a high voltage. CZE can approach ultra-high separation efficiency (&#62; one million theoretical plates) for the separation of biomolecules7. CZE-MS has a drastically higher sensitivity than widely used reversed-phase liquid chromatography (RPLC)-MS for the analysis of intact proteins8. Although CZE-MS has a great potential for large-scale top-down proteomics, its wide application in proteomics has been impeded by several issues, including a low sample-loading capacity and narrow separation window. The typical sample loading volume in CZE is about 1% of the total capillary volume, which usually corresponds to less than 100 nL9,10,11. The separation window of CZE is usually less than 30 min due to the strong electroosmotic flow (EOF)9,10. These issues limit the CZE-MS/MS for the identification of a large number of proteoforms and low abundant proteoforms from a complex proteome.
Much effort has been made to improve the sample loading volume of CZE via online sample concentration methods (e.g., solid-phase microextraction [SPME]12,13, field-enhanced sample stacking [FESS]9,11,14, and dynamic pH junction15,16,17,18). FESS and dynamic pH junction are simpler than SPME, only requiring a significant difference between the sample buffer and the BGE in conductivity and pH. FESS employs a sample buffer with much lower conductivity than the BGE, leading to a stacking of analytes on the boundary between the sample zone and the BGE zone in the capillary. Dynamic pH junction utilizes a basic sample plug (e.g., 50 mM ammonium bicarbonate, pH 8) and an acidic BGE (e.g., 5% [v/v] acetic acid, pH 2.4) on both sides of the sample plug. Upon application of a high positive voltage at the injection end of the capillary, titration of the basic sample plug occurs, focusing the analytes into a tight plug before undergoing a CZE separation. Recently, the Sun group systematically compared FESS and dynamic pH junction for the online stacking of intact proteins, demonstrating that dynamic pH junction could produce much better performance than FESS for the online concentration of intact proteins when the sample injection volume was 25% of the total capillary volume19.
Neutrally coated separation capillaries (e.g., linear polyacrylamide [LPA]) have been employed to reduce the EOF in the capillary, slowing down the CZE separation and widening the separation window20,21. Recently, the Dovichi group developed a simple procedure for the preparation of stable LPA coating on the inner wall of capillaries, utilizing ammonium persulfate (APS) as the initiator and temperature (50 &#176;C) for free radical production and polymerization22. Very recently, the Sun group employed the LPA-coated separation capillary and the dynamic pH junction method for the CZE separation of intact proteins, reaching a microliter-scale sample loading volume and a 90-min separation window19. This CZE system opens the door to using CZE-MS/MS for large-scale top-down proteomics.
CZE-MS requires a highly robust and sensitive interface to couple CZE to MS. Three CE-MS interfaces have been well developed and commercialized in the history of CE-MS, and they are the co-axial sheath-flow interface23, the sheathless interface using a porous tip as the ESI emitter24, and the electro-kinetically pumped sheath flow interface25,26. The electro-kinetically pumped sheath-flow-interface-based CZE-MS/MS has reached a low zeptomole peptide detection limit9, over 10,000 peptide identifications (IDs) from the HeLa cell proteome in a single run14, a fast characterization of intact proteins11, and highly stable and reproducible analyses of biomolecules26. Recently, the LPA-coated separation capillary, the dynamic pH junction method, and the electro-kinetically pumped sheath flow interface were used for large-scale top-down proteomics of an Escherichia coli (E. coli) proteome19,27. The CZE-MS/MS platform approached over 500 proteoform IDs in a single run19 and nearly 6,000 proteoform IDs via coupling with size-exclusion chromatography (SEC)-RPLC fractionation27. The results clearly show the capability of CZE-MS/MS for large-scale top-down proteomics.
Herein, a detailed procedure of using CZE-MS/MS for large-scale top-down proteomics is described. The CZE-MS/MS system employs the LPA-coated capillary to reduce the EOF in the capillary, the dynamic pH junction method for the online concentration of proteins, the electro-kinetically pumped sheath flow interface for coupling CZE to MS, an orbitrap mass spectrometer for the collection of MS and MS/MS spectra of proteins, and a TopPIC (TOP-Down Mass Spectrometry-Based Proteoform Identification and Characterization) software for proteoform ID via database search.

<table border="0" cellpadding="0" cellspacing="0" style="width:905px;" width="903">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:287px;">Fused silica capillary</td>
			<td style="width:117px;">Polymicro Technologies</td>
			<td style="width:147px;">1068150017</td>
			<td style="width:355px;">50 &#181;m i.d. 360 &#181;m o.d.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:287px;">Sodium hydroxide pellets</td>
			<td style="width:117px;">Macron Fine Chemicals</td>
			<td style="width:147px;">7708-10</td>
			<td>Corrosive</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">LC-MS grade water</td>
			<td style="width:117px;">Fisher Scientific</td>
			<td>W6-1</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Hydrochloric acid</td>
			<td style="width:117px;">Fisher Scientific</td>
			<td style="width:147px;">SA48-1</td>
			<td>Corrosive</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Methanol</td>
			<td style="width:117px;">Fisher Scientific</td>
			<td style="width:147px;">A456-4</td>
			<td>Toxic, Health Hazard</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">3-(Trimethoxysilyl)propyl methacrylate</td>
			<td style="width:117px;">Sigma-Aldrich</td>
			<td style="width:147px;">M6514</td>
			<td>Moisture and heat sensitive</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Hydrofluoric acid</td>
			<td style="width:117px;">Acros Organics</td>
			<td style="width:147px;">423805000</td>
			<td>Highy toxic</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Acrylamide</td>
			<td style="width:117px;">Acros Organics</td>
			<td style="width:147px;">164855000</td>
			<td>Toxic, health hazard</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Ammonium persulfate</td>
			<td style="width:117px;">Sigma-Aldrich</td>
			<td style="width:147px;">A3678</td>
			<td>Health hazard, Oxidizer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">lysozyme</td>
			<td style="width:117px;">Sigma-Aldrich</td>
			<td style="width:147px;">L6876</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Cytochrome C</td>
			<td style="width:117px;">Sigma-Aldrich</td>
			<td style="width:147px;">C7752</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Myoglobin</td>
			<td style="width:117px;">Sigma-Aldrich</td>
			<td style="width:147px;">M1882</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">&#223;-casein</td>
			<td style="width:117px;">Sgma-Aldrich</td>
			<td style="width:147px;">C6905</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Carbonic anhydrase</td>
			<td style="width:117px;">Sigma-Aldrich</td>
			<td style="width:147px;">C3934</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Bovine serum albumin</td>
			<td style="width:117px;">Sigma-Aldrich</td>
			<td style="width:147px;">A2153</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Urea</td>
			<td style="width:117px;">Alfa Aesar</td>
			<td style="width:147px;">36428-36</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">DL-Dithiothreitol</td>
			<td style="width:117px;">Sigma-Aldrich</td>
			<td style="width:147px;">D0632</td>
			<td>Health Hazard</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Iodoacetamide</td>
			<td style="width:117px;">Fisher Scientific</td>
			<td style="width:147px;">AC122270250</td>
			<td>Health Hazard</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Formic Acid</td>
			<td style="width:117px;">Fisher Scientific</td>
			<td style="width:147px;">A117-50</td>
			<td>Corrosive, Health Hazard</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:287px;">C4 trap column</td>
			<td style="width:117px;">Sepax Technologies</td>
			<td style="width:147px;">110043-4001C</td>
			<td>3 &#181;m particles, 300 &#197; pores, 4.0 mm i.d. 10 mm long</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Acetonitrile</td>
			<td style="width:117px;">Fisher Scientific</td>
			<td style="width:147px;">A998SK-4</td>
			<td>Toxic, Oxidizer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Ammonium bicarbonate</td>
			<td style="width:117px;">Sigma-Aldrich</td>
			<td style="width:147px;">1066-33-7</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:287px;">Nalgene rapid-flow filters</td>
			<td style="width:117px;">Thermo Scientific</td>
			<td style="width:147px;">126-0020</td>
			<td>0.2 &#181;m CN membrane, and 50 mm diameter</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">E. coli cells</td>
			<td style="width:117px;"></td>
			<td style="width:147px;"></td>
			<td>K-12 MG1655</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Dulbecco&#39;s phosphate-buffered saline</td>
			<td style="width:117px;">Sigma-Aldrich</td>
			<td style="width:147px;">D8537</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:287px;">BCA assay</td>
			<td style="width:117px;">Thermo Scientific</td>
			<td style="width:147px;">23250</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Acetone</td>
			<td style="width:117px;">Fisher Scientific</td>
			<td style="width:147px;">A11-1</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">HPLC system for protein desalting</td>
			<td style="width:117px;">Agilient</td>
			<td style="width:147px;">1260 Infinity II</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Acetic Acid</td>
			<td style="width:117px;">Fisher Scientific</td>
			<td style="width:147px;">A38-212</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">CE autosampler</td>
			<td style="width:117px;">CMP Scientific</td>
			<td style="width:147px;">ECE-001</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:287px;">Electro-kinetically pumped sheath flow interface</td>
			<td style="width:117px;">CMP Scientific</td>
			<td style="width:147px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:287px;">Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer</td>
			<td style="width:117px;">Thermo Fisher Scientific</td>
			<td style="width:147px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:287px;">Sutter flaming/brown micropipette puller</td>
			<td style="width:117px;">Sutter Instruments</td>
			<td style="width:147px;">P-1000</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:287px;">Ultrasonic cell disruptor for cell lysis</td>
			<td style="width:117px;">Branson</td>
			<td align="right" style="width:147px;">101063196</td>
			<td>Model S-250A</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:287px;">Vaccum concentrator</td>
			<td style="width:117px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">SPD131DDA-115</td>
			<td></td>
		</tr>
	</tbody>
</table>

large-scale top-down proteomics using capillary zone electrophoresis tandem mass spectrometry

Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has been recognized as a useful tool for top-down proteomics that aims to characterize proteoforms in complex proteomes. However, the application of CZE-MS/MS for large-scale top-down proteomics has been impeded by the low sample-loading capacity and narrow separation window of CZE. Here, a protocol is described using CZE-MS/MS with a microliter-scale sample-loading volume and a 90-min separation window for large-scale top-down proteomics. The CZE-MS/MS platform is based on a linear polyacrylamide (LPA)-coated separation capillary with extremely low electroosmotic flow, a dynamic pH-junction-based online sample concentration method with a high efficiency for protein stacking, an electro-kinetically pumped sheath flow CE-MS interface with extremely high sensitivity, and an ion trap mass spectrometer with high mass resolution and scan speed. The platform can be used for the high-resolution characterization of simple intact protein samples and the large-scale characterization of proteoforms in various complex proteomes. As an example, a highly efficient separation of a standard protein mixture and a highly sensitive detection of many impurities using the platform is demonstrated. As another example, this platform can produce over 500 proteoform and 190 protein identifications from an Escherichia coli proteome in a single CZE-MS/MS run.

Figure 1&#160;shows a diagram of the dynamic pH-junction-based CZE-ESI-MS system used in the experiment. A long plug of the sample in a basic buffer is injected into an LPA-coated separation capillary filled with an acidic BGE. After applying high voltages I and II, the analytes in the sample zone will be concentrated via the dynamic pH junction method. To evaluate the performance of the CZE-MS system, a standard protein mixture (cytochrome c, lysozy...

Watch this Scientific Journal Video about Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry at JoVE.com

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

A detailed protocol is described for the separation, identification, and characterization of proteoforms in protein samples using capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS). The protocol can be used for the high-resolution characterization of proteoforms in simple protein samples and the large-scale identification of proteoforms in complex proteome samples.

Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has been recognized as a useful tool for top-down ...

This method can help improve large scale and high resolution characterization of protein isoforms and protein post-translational modifications in cells. The main advantage of this technique is that capillary zone electrophoresis mass spectrometry offers highly efficient separation and highly sensitive detection of intact proteins. To pre-treat the capillary, dry it with nitrogen gas at 10 psi for at least 12 hours.Then, fill the capillary with 50%volume-by-volume 3-propyl methacrylate in methanol using a syringe pump. Seal both ends of the capillary with silica rubber. After incubating at room temperature for at least 24 hours, continue with a linear polyacrylamide coating on the inner wall of the separation capillary, as described in the text protocol.Burn a portion of the capillary using a gentle flame to remove the polyamide outer coating around four centimeters away from one end of the capillary. Gently clean the burnt portion of the capillary by wiping to remove the polyamide coating completely. Drill a small hole at the end of a 200 microliter tube around the same size as the capillary outer diameter to sufficiently hold the capillary in place once it is threaded through this hole.Thread the end of the capillary that is close to the burnt portion through the hole until the burnt portion is in the tube. Then, add approximately 150 microliters of HF to the 200 microliter tube so that the HF solution is about halfway up the burnt portion on the capillary. Incubate the capillary in the HF solution at room temperature for 90 to 100 minutes.Prepare the standard protein mixture and the E.coli sample as described in the text protocol. To set up the capillary zone electrophoresis, or CZE system, load the sample, the background electrolyte, and the separation capillary into CZE auto-sampler. Select sample load in the manual control page of the CZE auto-sampler.Load the background electrolyte vial into the buffer tray of the auto-sampler, noting its position in the buffer tray. Then, load the sample vial into the sample tray of the auto-sampler, noting its position in the sample tray. Put the auto-sampler to the alignment position using manual control.Now, load the separation capillary into CZE auto-sampler using the non-etched end of the capillary. Adjust the height of the injection end of the capillary if the sample volume is lower than 50 microliters. Switch the auto-sampler to standby using manual control.Type the sample position in the system and move the capillary to the sample. Push the injection end of the capillary further down to reach the bottom of the sample vial. Continuing to use the manual control, flush the capillary with the background electrolyte for 20 minutes using a pressure of 20 psi.Now, mount a commercial electrokinetically pumped sheath flow interface to the front of the mass spectrometer. Fill the sheath buffer reservoir with a buffer containing 10%volume-volume methanol and 0.2%volume-volume formic acid in LCMS-grade water. Flush the T in the interface with the sheath buffer via applying pressure manually with a syringe.Thread the one millimeter outer diameter end of an electrospray emitter through a sleeve tubing and connect the emitter with one port of the T via a fitting. Simply flush the T manually again with a syringe to fill the emitter with the sheath buffer. Adjust the distance between the orifice of the emitter and the entrance of the mass spectrometer to approximately two millimeters with the help of the camera that came with the interface.Apply a two to 2.2 kilovolt voltage at the sheath buffer vial for electrospray. Then, adjust the spray voltage to reach a stable electrospray. Apply a low pressure at the injection end of the capillary during this process to make sure there are no bubbles in the capillary.Turn off the spray voltage and gently thread the etched end of the separation capillary through the T into the emitter until it cannot be pushed further. After stopping the low pressure at the injection end of the capillary, flush the emitter a little bit with sheath buffer. Again, apply two to 2.2 kilovolts of spray voltage to test the spray.Select new method under the file dropdown menu on the main instrument screen. There, select inlet as starting sample vial, ending sample vial, tray as sample, pressure as five psi, kilovolts as zero, and duration as 95 seconds for a sample injection. Then, set inlet as inlet vial, tray as buffer, pressure as zero psi, kilovolts as 30, and duration as 4, 200 seconds for the separation of the standard protein mixture sample.For the separation of the E.coli proteome sample, set inlet as inlet vial, tray as buffer, pressure as zero psi, kilovolts as 20, and duration as 6, 600 seconds. Finally, select inlet as inlet vial, tray as buffer, pressure as 10 psi, kilovolts as 30, and duration as 600 seconds for capillary flushing. Now, setup the MS and MS/MS parameters for intact protein analysis using a quadruple ion trap mask spectrometer.To adjust the tune file settings, turn on intact protein mode and use a trapping pressure of 0.2. Set the ion transfer capillary temperature to 320 degrees Celsius and the S-lens RF level to 55. To perform the CZE MS/MS experiment, start the data acquisition method on the mass spectrometer computer, first by selecting run sequence.Then, start the capillary electrophoresis sequence on the capillary electrophoresis auto-sampler computer. Perform a database search with TopPIC in the TopPIC suite and in the TopPIC graphical user interface. Click on database file and select an appropriate database for searching.Click on spectrum file and select the generated ms2. msalign file generated as the input. Select the MS1 feature file and choose the generated feature file.Set cysteine carbamidomethyl C57 as a fixed modification due to the iodoacetamide treatment. Select the decoy database feature and under cutoff settings, select false discovery rate in the dropdown menu next to spectrum level. Set the false discovery rate to 0.01 at the spectrum level.Leave generating function unselected and set the error tolerance to 15 parts per million. Set the false discovery rate to 0.05 at the proteoform level. Under advanced parameters, select two for the maximum number of mass shifts in the dropdown menu.Set the maximum mass shift of unknown modifications to 500 daltons. Leave all other parameters at their default values and click the start button at the bottom right of the graphical user interface. The representative electropherogram for the standard protein mixture is shown.The standard protein mixture is typically run at least in duplicate to evaluate the separation efficiency and the reproducibility of the system. The separation efficiency can be evaluated with the number of theoretical plates of some proteins. The reproducibility can be evaluated by the relative standard deviations of protein intensity and migration time.The CZE MS/MS platform can be used for large-scale characterization of proteoforms in various complex proteomes, identifying over 500 proteoforms and 190 proteins from an E.coli proteome in a single run with high confidence. Here, a zoomed in view of the electropherogram can be used to assess the separation window of the system. The very low E-value and spectral FDR suggests the high confidence of the proteoform ID.The high number of matched fragment ions further indicates the high confidence of the ID.While attempting this procedure, it's important to remember to thread the etched separation capillary into the electrospray emitter slowly and gently.Stable isotope labeling or label-free methods can be incorporated into the CZE MS procedure to determine how proteoform abundance changes in cells across various conditions. After its development, this technique paved the way for researchers in the field of top-down proteomics to explore the roles of proteoforms in regulating various biological processes in cells. Don't forget that working with hydrofluoric acid can be extremely hazardous and precautions such as proper personal protective equipment and having emergency procedures in place should always be taken when performing this procedure.

large-scale-top-down-proteomics-using-capillary-zone-electrophoresis

Research

JoVE Journal

Chemistry

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)

Non-targeted metabolite profiling by ultra performance liquid chromatography coupled with mass spectrometry (UPLC-MS) is a powerful technique to investigate metabolism. The approach offers an unbiased and in-depth analysis that can enable the development of diagnostic tests, novel therapies, and further our understanding of disease processes. The inherent chemical diversity of the metabolome creates significant analytical challenges and there is no single experimental approach that can detect all metabolites. Additionally, the biological variation in individual metabolism and the dependence of metabolism on environmental factors necessitates large sample numbers to achieve the appropriate statistical power required for meaningful biological interpretation. To address these challenges, this tutorial outlines an analytical workflow for large scale non-targeted metabolite profiling of serum by UPLC-MS. The procedure includes guidelines for sample organization and preparation, data acquisition, quality control, and metabolite identification and will enable reliable acquisition of data for large experiments and provide a starting point for laboratories new to non-targeted metabolite profiling by UPLC-MS.

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS

Non-targeted metabolite profiling by ultra performance liquid chromatography coupled with mass spectrometry (UPLC-MS) is a powerful technique to investigate metabolism. This article outlines a typical workflow utilized for non-targeted metabolite profiling of serum including sample organization and preparation, data acquisition, data analysis, quality control, and metabolite identification.

Non-targeted metabolite profiling by ultra performance liquid chromatography coupled with mass spectrometry (UPLC-MS) is a powerful technique to ...

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 ...

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

Carboxylic acids are organic acids containing one or more terminal carboxyl (COOH) functional groups. Short chain carboxylic acids (SCCAs; carboxylic acids containing three to six carbons), such as malate and citrate, are critical to the proper functioning of many biological systems, where they function in cellular respiration and can serve as indicators of cell health. In foods, organic acid content can have significant impact on taste, with increased SCCA levels resulting in a sour or &#34;acid&#34; taste. Because of this, methods for the rapid analysis of organic acid levels are of particular interest to the food and beverage industries. Unfortunately, however, most methods used for SCCA quantification are dependent on time-consuming protocols requiring the derivatization of samples with hazardous reagents, followed by costly chromatographic and/or mass spectrometric analyses. This method details an alternate method for the detection and quantification of organic acids from plant material and food samples using free zonal capillary electrophoresis (CZE), sometimes simply referred to as capillary electrophoresis (CE). CZE provides a cost-effective method for measuring SCCAs with a low limit of detection (0.005 mg/ml). This article details the extraction and quantification of SCCAs from plant samples. While the method provided focuses on measurement of SCCAs from coffee beans, the method provided can be applied to multiple plant-based food materials.

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

This article presents a method for the detection and quantification of organic acids from plant material using free zonal capillary electrophoresis. An example of the potential application of this method, determining the effects of a secondary fermentation on organic acid levels in coffee seeds, is provided.

Carboxylic acids are organic acids containing one or more terminal carboxyl (COOH) functional groups. Short chain carboxylic acids (SCCAs; carboxylic ...

Microprobe Capillary Electrophoresis Mass Spectrometry for Single-cell Metabolomics in Live Frog (Xenopus laevis) Embryos

The quantification of small molecules in single cells raises new potentials for better understanding the basic processes that underlie embryonic development. To enable single-cell investigations directly in live embryos, new analytical approaches are needed, particularly those that are sensitive, selective, quantitative, robust, and scalable to different cell sizes. Here, we present a protocol that enables the in situ analysis of metabolism in single cells in freely developing embryos of the South African clawed frog (Xenopus laevis), a powerful model in cell and developmental biology. This approach uses a capillary microprobe to aspirate a defined portion from single identified cells in the embryo, leaving neighboring cells intact for subsequent analysis. The collected cell content is analyzed by a microscale capillary electrophoresis electrospray ionization (CE-ESI) interface coupled to a high-resolution tandem mass spectrometer. This approach is scalable to various cell sizes and compatible with the complex three-dimensional structure of the developing embryo. As an example, we demonstrate that microprobe single-cell CE-ESI-MS enables the elucidation of metabolic cell heterogeneity that unfolds as a progenitor cell gives rise to descendants during development of the embryo. Besides cell and developmental biology, the single-cell analysis protocols described here are amenable to other cell sizes, cell types, or animal models.

Microprobe Capillary Electrophoresis Mass Spectrometry for Single-cell Metabolomics in Live Frog Xenopus laevis Embryos

We describe steps that enable fast in situ sampling of a small portion of an individual cell with high precision and minimal invasion using capillary-based micro-sampling, to facilitate chemical characterization of a snapshot of metabolic activity in live embryos using a custom-built single cell capillary electrophoresis and mass spectrometry platform.

The quantification of small molecules in single cells raises new potentials for better understanding the basic processes that underlie embryonic ...

High-throughput and Comprehensive Drug Surveillance Using Multisegment Injection-Capillary Electrophoresis-Mass Spectrometry

New analytical methods are urgently needed to enable high-throughput, yet comprehensive drug screening, given an alarming opioid and prescription drug crisis in public health. Conventional urine drug testing based on a two-tier immunoassay screen followed by a gas chromatography-tandem mass spectrometry (GC-MS/MS) or liquid chromatography-tandem mass spectrometry (LC-MS/MS) method are expensive and prone to bias while being limited to targeted panels of known drugs of abuse (DoA). Herein, we outline an improved method for drug surveillance that allows for the resolution and detection of an expanded panel of DoA and their metabolites when using multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS). Multiplexed separations of ten urine samples with a quality control by CE (&lt; 3 min/sample) in conjunction with full-scan data acquisition using a time-of-flight mass spectrometer (TOF-MS) under positive ion mode detection allows for the identification and quantification of DoA above recommended cut-off levels. An excellent resolution of drug isomers and isobars, including background interferences, are achieved when using MSI-CE-MS with an electrokinetic spacer between sample segments, where accurate mass/molecular formula together with the comigration of a matching deuterated internal standard and the detection of one or more bio-transformed metabolites facilitate DoA identification over a wider detection window. Additionally, urine samples can be analyzed directly without enzyme deconjugation for the rapid screening without complicated sample workup. MSI-CE-MS enables the surveillance of a broad spectrum of DoA that is required for the treatment monitoring of high-risk patients, including confirming prescribed drug adherence, revealing illicit drug use/substitution, and evaluating optimal dosage regimes as required for new advances in precision medicine.

Here we describe a high-throughput method for comprehensive drug surveillance that allows for the improved resolution and detection of large panels of drugs of abuse and their metabolites, with quality control based on multisegment injection-capillary electrophoresis-mass spectrometry.

New analytical methods are urgently needed to enable high-throughput, yet comprehensive drug screening, given an alarming opioid and prescription drug ...

Setup of Capillary Electrophoresis-Inductively Coupled Plasma Mass Spectrometry (CE-ICP-MS) for Quantification of Iron Redox Species (Fe(II), Fe(III))

Dyshomeostasis of iron metabolism is accounted in the pathophysiological framework of numerous diseases, including cancer and several neurodegenerative conditions. Excessive iron results in free redox-active Fe(II) and can cause devastating effects within the cell like oxidative stress (OS) and death by lipid peroxidation known as ferroptosis (FPT). Therefore, quantitative measurements of ferrous (Fe(II)) and ferric (Fe(III)) iron rather than total Fe-determination is the key for closer insight into these detrimental processes. Since Fe(II)/(III) determinations can be hampered by fast redox-state shifts and low concentrations in relevant samples, like cerebrospinal fluid (CSF), methods should be available that analyze quickly and provide low limits of quantification (LOQ). Capillary electrophoresis (CE) offers the advantage of fast Fe(II)/Fe(III) separation and works without a stationary phase, which could interfere with the redox balance or cause analyte sticking. CE combined with inductively coupled plasma mass spectrometry (ICP-MS) as a detector offers further improvement of detection sensitivity and selectivity. The presented method uses 20 mM HCl as a background electrolyte and a voltage of +25 kV. Peak shapes and concentration detection limits are improved by conductivity-pH-stacking. For reduction of 56[ArO]+, ICP-MS was operated in the dynamic reaction cell (DRC) mode with NH3 as a reaction gas. The method achieves a limit of detection (LOD) of 3 &#181;g/L. Due to stacking, higher injection volumes were possible without hampering separation but improving LOD. Calibrations related to peak area were linear up to 150 &#181;g/L. Measurement precision was 2.2% (Fe(III)) to 3.5% (Fe(II)). Migration time precision was &#60;3% for both species, determined in 1:2 diluted lysates of human neuroblastoma (SH-SY5Y) cells. Recovery experiments with standard addition revealed accuracy of 97% Fe(III) and 105 % Fe(II). In real-life bio-samples like CSF, migration time can vary according to varying conductivity (i.e., salinity). Thus, peak identification is confirmed by standard addition.

Setup of Capillary Electrophoresis-Inductively Coupled Plasma Mass Spectrometry CE-ICP-MS for Quantification of Iron Redox Species FeII, FeIII

This iron redox speciation method is based on capillary electrophoresis-inductively coupled plasma mass spectrometry with sample stacking combined with short analysis in one run. The method quickly analyzes and provides low limits of quantification for iron redox species across a diverse range of tissues and biofluid samples.

Dyshomeostasis of iron metabolism is accounted in the pathophysiological framework of numerous diseases, including cancer and several neurodegenerative ...

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 ...

Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis

This protocol identifies the immunity proteins of the bactericidal enzymes: colicin E3 and bacteriocin, produced by a pathogenic Escherichia coli strain using antibiotic induction, and identified by MALDI-TOF-TOF tandem mass spectrometry and top-down proteomic analysis with software developed in-house. The immunity protein of colicin E3 (Im3) and the immunity protein of bacteriocin (Im-Bac) were identified from prominent b- and/or y-type fragment ions generated by the polypeptide backbone cleavage (PBC) on the C-terminal side of aspartic acid, glutamic acid, and asparagine residues by the aspartic acid effect fragmentation mechanism. The software rapidly scans in silico protein sequences derived from the whole genome sequencing of the bacterial strain. The software also iteratively removes amino acid residues of a protein sequence in the event that the mature protein sequence is truncated. A single protein sequence possessed mass and fragment ions consistent with those detected for each immunity protein. The candidate sequence was then manually inspected to confirm that all detected fragment ions could be assigned. The N-terminal methionine of Im3 was post-translationally removed, whereas Im-Bac had the complete sequence. In addition, we found that only two or three non-complementary fragment ions formed by PBC are necessary to identify the correct protein sequence. Finally, a promoter (SOS box) was identified upstream of the antibacterial and immunity genes in a plasmid genome of the bacterial strain.

Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis

Here we present a protocol for the rapid identification of proteins produced by genomically sequenced pathogenic bacteria using MALDI-TOF-TOF tandem mass spectrometry and top-down proteomic analysis with software developed in-house. Metastable protein ions fragment because of the aspartic acid effect and this specificity is exploited for protein identification.

This protocol identifies the immunity proteins of the bactericidal enzymes: colicin E3 and bacteriocin, produced by a pathogenic Escherichia coli strain ...

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 ...

Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing (Frog) Embryo

Characterization of molecular events as cells give rise to tissues and organs raises a potential to better understand normal development and design efficient remedies for diseases. Technologies enabling accurate identification and quantification of diverse types and large numbers of proteins would provide still missing information on molecular mechanisms orchestrating tissue and organism development in space and time. Here, we present a mass spectrometry-based protocol that enables the measurement of thousands of proteins in identified cell lineages in Xenopus laevis (frog) embryos. The approach builds on reproducible cell-fate maps and established methods to identify, fluorescently label, track, and sample cells and their progeny (clones) from this model of vertebrate development. After collecting cellular contents using microsampling or isolating cells by dissection or fluorescence-activated cell sorting, proteins are extracted and processed for bottom-up proteomic analysis. Liquid chromatography and capillary electrophoresis are used to provide scalable separation for protein detection and quantification with high-resolution mass spectrometry (HRMS). Representative examples are provided for the proteomic characterization of neural-tissue fated cells. Cell-lineage-guided HRMS proteomics is adaptable to different tissues and organisms. It is sufficiently sensitive, specific, and quantitative to peer into the spatio-temporal dynamics of the proteome during vertebrate development.

Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing Frog Embryo

Here we describe a mass spectrometry-based proteomic characterization of cell lineages with known tissue fates in the vertebrate Xenopus laevis embryo.

Characterization of molecular events as cells give rise to tissues and organs raises a potential to better understand normal development and design ...