The author thanks Prof. Lena Claesson-Welsh, Uppsala University, Sweden for her support for developing this project. Additionally, the author thanks Ross Smith and Lena Claesson-Welsh, Uppsala University for their critical reading and suggestions to improve the manuscript.

1. Cell Culture, Stimulation, and Lysis
Note: This method can be used with many cell types. To illustrate the method, an example using human umbilical vein endothelial cells (HUVECs) is described.
<ol>
	<li>Culture HUVECs on gelatin-coated, 10 cm Petri dishes in endothelial cell basal medium with appropriate supplementation (see Table of Materials), and also containing 5% FCS, epidermal growth factor (5 ng/mL), vascular endothelial growth factor (VEGF: 0.5 ng/mL), basic FGF (10 ng/mL), insulin-like growth factor (20 ng/mL), hydrocortisone (0.2 &#181;g/mL), and ascorbic acid (1 &#181;g/mL).</li>
	<li>Starve cells overnight with endothelial cell basal medium supplemented with 1% FCS and no growth factor supplement.</li>
	<li>Aspirate all medium, add 2 mL of endothelial cell culture medium without growth factors (starvation medium) in one dish (control), then add 50 ng/mL VEGF in 2 mL of starvation culture medium in a second dish for 7 min.</li>
	<li>Aspirate the medium and wash cells 2 times with 10 mL room temperature PBS.</li>
	<li>Ensure the Petri dishes are on ice and keep them there from this step onwards.</li>
	<li>Add 250-400 &#181;L of ice cold lysis buffer (Bicine/CHAPS; see Table of Materials) containing aqueous protease inhibitor mix and DMSO inhibitor mix (Phosphatase inhibitors; see Table of Materials) to each 10 cm plate. Swirl the plate to ensure proper coverage and keep it for 10 min on ice. 
	NOTE: The final concentration of protease and the DMSO inhibitor mix should be 1x.</li>
	<li>Scrape the cells from the dish with a cell scraper and transfer to a pre-chilled microfuge tube. Pipette up and down 5 times to lyse cells.</li>
	<li>Briefly sonicate the cells at 4 &#176;C. Set the sonicator as follows: number of cycles = 5, power = LOW, ON = 5 sec, OFF = 30 s. This step is included to break nucleic acids, and not to lyse cells. 
	NOTE: Sonication should be mild to prevent denaturation of proteins.</li>
	<li>Vortex the tube for 5 s (not continuously), 2 s at a time (3 times), and keep on ice.</li>
	<li>Clarify lysate by centrifugation at 14,000 x g for 15 min at 4 &#176;C, then immediately transfer the supernatant to a clean pre-chilled microfuge tube.</li>
	<li>Measure the protein concentration using a Bicinchoninic Acid (BCA) protein assay kit4.</li>
	<li>Make 10 &#181;L aliquots, snap freeze in dry ice or liquid nitrogen, and store at -80 &#176;C until use.</li>
</ol>
2. Sample Mix Preparation (Calculation for 150 &#181;L Sample Mix)
<ol>
	<li>First, prepare a sample diluent mix by adding 1 &#181;L of DMSO inhibitor mix (stock 50x) and 2 &#181;L of protease inhibitors (stock 25x) to 47 &#181;L of sample diluent (see Table of Materials), so that the final concentration of DMSO inhibitors and protease inhibitors becomes 1x. Next, dilute the protein lysates using the sample diluent mix to obtain the desired concentrations (see step 2.3).</li>
	<li>Prepare ampholyte/ladder/protease inhibitor/DMSO inhibitor mix by adding 3.325 &#181;L standard ladder (see Table of Materials; stock 60x), 6 &#181;L of protease inhibitor (25x), 3 &#181;L of DMSO (50x) inhibitor to 137.675 &#181;L ampholyte premix (see Table of Materials). Vortex the tube at least 15 s total, 5 s at a time (3-4 times), and keep on ice.</li>
	<li>Mix the solutions from steps 2.1 and 2.2 in a 1:3 ratio, so that the final concentrations of DMSO, protease inhibitors, and the pI standard ladder become 1X, and the proteins in the capillary reach the final desired concentrations (e.g., 50 &#181;g/mL was used for Figure 2). 
	NOTE: Protein concentration in the capillary and well are the same.</li>
	<li>Load 10 &#181;L of sample mix into the appropriate well, according to the 384-well plate assay template layout (see step 3 and Figure 1) and keep the plate on ice.</li>
	<li>Dilute the primary (pERK1/2, 1:50; ERK1/2, 1:100; HSP 70, 1:500) and secondary antibodies (1:300) with antibody diluent (see Table of Materials) and pipette 10 &#181;L of primary and 15 &#181;L of secondary antibodies into each well. 
	NOTE: In general, higher concentration of antibodies are required for cIEF assays as compared to conventional western blots.</li>
	<li>Mix Luminol and peroxide XDR (1:1 ratio; see Table of Materials) together and pipette 15 &#181;L into each well. 
	NOTE: Mix these solutions fresh every time before use and keep on ice.</li>
	<li>Once samples and all reagents are pipetted into the plate, centrifuge the plate at 2,500 x g for 10 min at 4 &#176;C to spin down the liquid and remove the bubbles. If bubbles still exist, remove them manually using a thin pipette tip. 
	NOTE: Do not load more than 20 &#181;L of sample or reagents per well; otherwise, the instrument pipette cannot be washed properly. Make sure to follow the instruction manual from the manufacturer to prepare all reagents.</li>
</ol>
3. Designing a New Assay Template with System Software (Figure 1)
<ol>
	<li>Open the system software and click &#34;new&#34; from the File menu.</li>
	<li>Go to the layout pane and assign locations for reagents and samples in a 384 well-plate. Use up to a maximum of 96 wells per 384-well plate.</li>
	<li>Make a reagent assignment by clicking a well anywhere in the block.Select a row block of 12 wells each. Wells, e.g., from 1-12 or 13-24, are assigned as a block by default.</li>
	<li>Go to the layout pane tool bar and insert either an empty row block or a sample, primary, secondary, or luminol row block. Each block is assigned a different color, so they are easy to differentiate. 
	NOTE: When clicking a well, a black border can be seen around the block where the new block will be inserted in the pane. A row block can also be deleted.</li>
	<li>Go to the protocol pane and select a reagent location in the plate. Then, click a cell in the sample column and select the reagent from the dropdown menu.</li>
	<li>In this same fashion, select the reagent locations for the primary, secondary, and luminol for each cycle.</li>
	<li>Click the cells, one at a time, in the primary or secondary antibody column, and change the incubation times, if necessary. 
	NOTE: Entry notes for each cycle can also be added.</li>
	<li>Add cycles by clicking the &#39;add&#39; button in the protocol section. 1 cycle, 4 cycles, or all cycles&#160;(a maximum of 8 cycles can be added to the protocol). 
	NOTE: It is possible to copy and paste cycle information in this step: select a cycle, go to edit, and copy and paste.</li>
	<li>Enter information pertaining to the sample, such as the identity of the primary and secondary antibodies, their catalog numbers and dilutions, etc., in the template pane. This is an optional step that is useful during the post-run analysis.</li>
	<li>Save the new assay file. Before clicking the &#39;start&#39; button, quickly check the layout to make sure that everything is correct.</li>
</ol>
4. Protocol for cIEF Instrument Setting
<ol>
	<li>Set capillary isoelectric focusing electrophoresis separation conditions. These should be 15,000 &#181;W and 40 min, and the UV immobilization time should be 80 s. However, the UV immobilization time can be set within the range of 80-140 s, and may need to be optimized for the protein of interest. 
	NOTE: A time point for UV immobilization can be set for each cycle, but not for each capillary.</li>
	<li>Set wash 1 to 2 washes, for 150 s each wash (default), and primary antibody incubation for 120 min.</li>
	<li>Set wash 2 to 2 washes, for 150 s each wash (default), and secondary antibody incubation for 60 min.</li>
	<li>Set wash 3, which should be 2 washes, for 150 s each wash (default).</li>
	<li>Set exposure times when chemiluminescence will be detected; these should be 30, 60, 120, 240, 490, and 960 s. All steps (1-8) will be carried out in a single capillary.</li>
</ol>
5. Running the Assay File
<ol>
	<li>Once everything is ready, click start to begin the run. The software will prompt you to remove the waste, to refill the water and the capillary box, to add anolyte and catholyte to the resource tray, to add wash buffer and finally to load the plate into the cooled sample tray. 
	NOTE: Remove the lid from the capillary box, but do not remove the lid from the assay plate. The lid from the plate can be removed automatically by the instrument when necessary. This helps to prevent reagent evaporation.</li>
	<li>A couple of minutes after the run has been started, an instrument status bar will be displayed on the computer screen. Status messages and progress bars can be seen corresponding to the instrument&#39;s current stage. 
	NOTE: Initially, the instrument will check if everything is correct before proceeding to pipette the anolyte and catholyte into the separation tray, picking the first block of 12 capillaries, removing the lid of the plate, and placing the samples from the sample plate into the capillaries, and then finally into the separation chamber for electrophoresis.</li>
	<li>Click on the run summary screen to see two panes: status and separation. Users can view the run progress, and movies of the separation (the 12 capillaries of each cycle) can be stored when the electrophoresis step of each cycle is completed. To observe the electrophoresis separation in a capillary, play the separation movie for that capillary by clicking the desired cycle and then the play button in the control panel.</li>
	<li>The run file can be stored automatically upon the completion of the run.</li>
</ol>
6. Analyze the Data (Figure S1)
<ol>
	<li>Open the run file and select the analysis screen tab. In Figure S1A, the data shown (peaks) in the sample graph is from the selected capillary (i.e., 4th capillary from cycle 1).</li>
	<li>Click edit and then analysis (Figure S1B). At this stage, users can change the pI range, apply the appropriate pI standard for a given experiment, add a peak fit, and add a peak name. 
	NOTE: When using a pH 5-8 ampholyte premix (as is the case here), the recommended standard ladder to use is one with fluorescently labeled peptides with pIs of 4.9, 6.0, 6.4, 7.0, and 7.3, and when using a pH 3-10 premix, the recommended ladder is one with pIs of 4.0, 4.9, 6.0, 6.4, and 7.3.2</li>
	<li>Results are displayed in the Peaks tab; the values displayed for the samples are Position, pI, peak Height and Area, % Area, peak Width, and signal to noise (S/N) (Figure S1C). Choose which data to use, and export the data for further analysis. 
	NOTE: Data can only be exported after labeling the peak (Figure S1C).</li>
</ol>

<ol>
	<li>O'Neill, R. A., 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=Isoelectric+focusing+technology+quantifies+protein+signaling+in+25+cells.">Isoelectric focusing technology quantifies protein signaling in 25 cells.</a> Proc Natl Acad Sci U S A. 103 (44), 16153-16158 (2006).</li><li>Aspinall-O'Dea, 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=Antibody-based+detection+of+protein+phosphorylation+status+to+track+the+efficacy+of+novel+therapies+using+nanogram+protein+quantities+from+stem+cells+and+cell+lines.">Antibody-based detection of protein phosphorylation status to track the efficacy of novel therapies using nanogram protein quantities from stem cells and cell lines.</a> Nat Protoc. 10 (1), 149-168 (2015).</li><li>Fan, A. 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=Nanofluidic+proteomic+assay+for+serial+analysis+of+oncoprotein+activation+in+clinical+specimens.">Nanofluidic proteomic assay for serial analysis of oncoprotein activation in clinical specimens.</a> Nat Med. 15 (5), 566-571 (2009).</li><li>Padhan, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High+sensitivity+isoelectric+focusing+to+establish+a+signaling+biomarker+for+the+diagnosis+of+human+colorectal+cancer.">High sensitivity isoelectric focusing to establish a signaling biomarker for the diagnosis of human colorectal cancer.</a> BMC Cancer. 16 (1), 683 (2016).</li><li>Sun, Z., 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=VEGFR2+induces+c-Src+signaling+and+vascular+permeability+in+vivo+via+the+adaptor+protein+TSAd.">VEGFR2 induces c-Src signaling and vascular permeability in vivo via the adaptor protein TSAd.</a> J Exp Med. 209 (7), 1363-1377 (2012).</li><li>Iacovides, D. 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=Identification+and+quantification+of+AKT+isoforms+and+phosphoforms+in+breast+cancer+using+a+novel+nanofluidic+immunoassay.">Identification and quantification of AKT isoforms and phosphoforms in breast cancer using a novel nanofluidic immunoassay.</a> Mol Cell Proteomics. 12 (11), 3210-3220 (2013).</li><li>Price, F. D., 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=Inhibition+of+JAK-STAT+signaling+stimulates+adult+satellite+cell+function.">Inhibition of JAK-STAT signaling stimulates adult satellite cell function.</a> Nat Med. 20 (10), 1174-1181 (2014).</li><li>Unger, F. T., 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=Nanoproteomic+analysis+of+ischemia-dependent+changes+in+signaling+protein+phosphorylation+in+colorectal+normal+and+cancer+tissue.">Nanoproteomic analysis of ischemia-dependent changes in signaling protein phosphorylation in colorectal normal and cancer tissue.</a> J Transl Med. 14, 6 (2016).</li><li>Urasaki, Y., Pizzorno, G., Le, T. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chronic+uridine+administration+induces+fatty+liver+and+pre-diabetic+conditions+in+mice.">Chronic uridine administration induces fatty liver and pre-diabetic conditions in mice.</a> PLoS One. 11 (1), e0146994 (2016).</li><li>Schmidt, L., 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=Case-specific+potentiation+of+glioblastoma+drugs+by+pterostilbene.">Case-specific potentiation of glioblastoma drugs by pterostilbene.</a> Oncotarget. 7 (45), 73200-73215 (2016).</li></ol>

The author has no disclosures.

Sensitivity and resolution of proteins are crucial for proteomic research on biological samples. There is great value in being able to detect proteins which are present in minute quantities in cells. cIEF can offer improved sensitivity and resolution for the detection of proteins and their isoforms4.
This technology has been successfully used in many proteomic research reports5,6,7</...

Capillary isoelectric focusing (cIEF) is an automated, capillary-based immunoassay that resolves proteins on the basis of their charge1,2,3. It is highly reproducible and capable of resolving proteins and their post-translationally modified isoforms rapidly and quantitatively. It presents an alternative to conventional methods such as western blotting. While western blotting is very good for confirming the presence of abundant proteins in readily accessible samples; variability, time consumption, and accurate quantitation all present challenges, in particular when examining biological tissue samples. Indeed, variability is an inherent problem in western blotting, as there are numerous steps involved, such as loading and running of SDS-PAGE gels, transfer of proteins onto membrane, incubation with various reagents (e.g., primary and secondary antibodies, ECL), and development onto X-ray film4. Presently, the western blotting technique is improving with the implementation of digital recording of chemiluminescent signals (digital westerns). Recently, an automated western blotting system has been developed, namely the capillary western, which is a more hands-free and gel-free system. The entire assay is automated following the loading of a sample plate (samples with all necessary reagents) into the system3,4. The instrument will perform all the steps such as protein separation, immobilization of proteins onto capillary wall, antibody incubations, washes between different steps, and development and quantification of the chemiluminescent signals. Thus, the cIEF procedure presented here provides higher resolution and sensitivity.
This method is sensitive, as signals can be generated and quantified from picograms of proteins1. The high sensitivity with excellent reproducibility makes this technology very useful for the analysis of clinical samples. It can detect as well as distinguish post translational modification (e.g., different phosphorylated protein isoforms) of proteins. This technology has been successfully used to dissect different signaling pathways4,5 in clinical studies aiming to develop new therapeutics in cancer3, and it has great potential for protein biomarker and drug discovery.

<table border="0" cellpadding="0" cellspacing="0" width="920">
	<tbody>
		<tr height="40">
			<td height="40" style="height:40px;width:367px;">NanoPro 1000</td>
			<td style="width:107px;">ProteinSimple</td>
			<td style="width:301px;"></td>
			<td style="width:147px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Premix G2, pH 5&#8211;8 (nested) separation gradient, pH 2&#8211;4 plug</td>
			<td>ProteinSimple</td>
			<td>040-972</td>
			<td>Ampholyte premix</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">DMSO inhibitor mix</td>
			<td>ProteinSimple</td>
			<td>040-510</td>
			<td>Phosphatase inhibitors; for cIEF 1:50 dilution used</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Aqueous Inhibitor Mix</td>
			<td>ProteinSimple</td>
			<td>040-482</td>
			<td>Protease inhibitor; for cIEF 1:25 dilution used</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">pI standard ladder 3</td>
			<td>ProteinSimple</td>
			<td>040-646</td>
			<td>For cIEF 1:60 dilution used</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Sample diluent</td>
			<td>ProteinSimple</td>
			<td>040-649</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Antibody diluent&#160;</td>
			<td>ProteinSimple</td>
			<td>040-309</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Wash concentrate</td>
			<td>ProteinSimple</td>
			<td>041-108</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Anolyte Refill</td>
			<td>ProteinSimple</td>
			<td>040-337</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Catholyte Refill</td>
			<td>ProteinSimple</td>
			<td>040-338</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Peroxide XDR</td>
			<td>ProteinSimple</td>
			<td>041-084</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Luminol</td>
			<td>ProteinSimple</td>
			<td>040-652</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Bicine/CHAPS Lysis Buffer</td>
			<td>ProteinSimple</td>
			<td>040-764</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Capillaries-Charge Separation (1 pack) for&#160;</td>
			<td>ProteinSimple</td>
			<td>CBS700</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Assay Plate/Lid Kit</td>
			<td>ProteinSimple</td>
			<td>040-663</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Peroxidase-AffiniPure Donkey Anti-Rabbit IgG (H+L)&#160;</td>
			<td>Jackson ImmunoResearch&#160;</td>
			<td>711-035-152</td>
			<td>For cIEF used (1: 300)</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Peroxidase-AffiniPure Donkey Anti-Mouse IgG (H+L)&#160;</td>
			<td>Jackson ImmunoResearch&#160;</td>
			<td>715-035-150</td>
			<td>For cIEF used (1: 300)</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Phospho-Erk 1/2 Primary Antibody</td>
			<td>Cell Signaling</td>
			<td>9101</td>
			<td>For cIEF used (1: 50)</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Pan Erk Primary Antibody</td>
			<td>Cell Signaling</td>
			<td>9102</td>
			<td>For cIEF used (1: 100)</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Compass software</td>
			<td>ProteinSimple</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">HUVEC</td>
			<td>ATCC</td>
			<td>PCS-100-010</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">MV2 (EBM-2)</td>
			<td>PromoCell</td>
			<td>&#160;C-22221</td>
			<td>Endothelia cell basal medium</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Endothelial Cell Growth Medium MV2 SupplementPack</td>
			<td>PromoCell</td>
			<td>C-39221</td>
			<td>Supplementation to MV2 above</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">VEGFA</td>
			<td>PeproTech</td>
			<td>100-20</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Long R3 IGF</td>
			<td>Sigma-Aldrich</td>
			<td>85580C/I1146</td>
			<td>Insulin-like growth factor</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Bioruptor (Sonicator)</td>
			<td>Diagenode</td>
			<td>B01020001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">BCA Protein Assay kit&#160;</td>
			<td>Thermo Fischer Scientific</td>
			<td>23225</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NuPAGE 4-12% Bis-Tris Protein Gels</td>
			<td>Thermo Fischer Scientific</td>
			<td>NP0322BOX</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NuPAG MOPS SDS Running Buffer (20X)</td>
			<td>Thermo Fischer Scientific</td>
			<td>NP0001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NuPAGE Transfer Buffer (20X)</td>
			<td>Thermo Fischer Scientific</td>
			<td>NP0006</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Immobilon PVDF membrane</td>
			<td>Millipore</td>
			<td>IPVH00010</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Microfuge tube vortexer</td>
			<td></td>
			<td></td>
			<td style="width:147px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:367px;">Centrifuge</td>
			<td style="width:107px;"></td>
			<td style="width:301px;"></td>
			<td style="width:147px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:367px;">Microtiter plate adapter for centrifuge</td>
			<td style="width:107px;"></td>
			<td style="width:301px;"></td>
			<td style="width:147px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:367px;">Pipettors&#160;</td>
			<td style="width:107px;"></td>
			<td style="width:301px;"></td>
			<td style="width:147px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:367px;">Tips</td>
			<td style="width:107px;"></td>
			<td style="width:301px;"></td>
			<td style="width:147px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:367px;">Ice</td>
			<td style="width:107px;"></td>
			<td style="width:301px;"></td>
			<td style="width:147px;"></td>
		</tr>
	</tbody>
</table>

highly sensitive and quantitative detection of proteins and their isoforms by capillary isoelectric focusing method

Immunoblotting has become a routine technique in many laboratories for protein characterization from biological samples. The following protocol provides an alternative strategy, capillary isoelectric focusing (cIEF), with many advantages compared to conventional immunoblotting. This is an antibody-based, automated, rapid, and quantitative method in which a complete western blotting procedure takes place inside an ultrathin capillary. This technique does not require a gel to transfer to a membrane, stripping of blots, or x-ray films, which are typically required for conventional immunoblotting. Here, proteins are separated according to their charge (isoelectric point; pI), using less than a microliter (400 nL) of total protein lysate. After electrophoresis, proteins are immobilized onto the capillary walls by ultraviolet light treatment, followed by primary and secondary (horseradish peroxidase (HRP) conjugated) antibody incubation, whose binding is detected through enhanced chemiluminescence (ECL), generating a light signal that can be captured and recorded by a charge-coupled device (CCD) camera. The digital image can be analyzed and quantified (peak area) using software. This high throughput procedure can handle 96 samples at a time; is highly sensitive, with protein detection in the picogram range; and produces highly reproducible results because of automation. All of these aspects are extremely valuable when the quantity of samples (e.g., tissue samples and biopsies) is a limiting factor. The technique has wider applications as well, including screening of drugs or antibodies, biomarker discovery, and diagnostic purposes.

Design of a new assay: An assay plate layout is shown in Figure 1A. Maximally, 96 wells can be used from the 384-well plate in blocks of 12 wells for each condition (antibody). Each block of 12 wells can start either from A1-A12 or A13-A24. Color coded rows allow one to distinguish samples or reagents from one another. In the assay template (Figure 1B), relevant information for that particular assay can be stored...

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Highly Sensitive and Quantitative Detection of Proteins and Their Isoforms by Capillary Isoelectric Focusing Method

Capillary isoelectric focusing is an antibody-based, ultrasensitive, high throughput technique, enabling detailed characterization of proteins and their isoforms from extremely small biological samples. The following describes a protocol for detection and quantification of specific proteins and their isoforms in an automated and robotized manner.

Immunoblotting has become a routine technique in many laboratories for protein characterization from biological samples. The following protocol provides ...

highly-sensitive-quantitative-detection-proteins-their-isoforms

Universidad de Cartagena UDEC

Research

JoVE Journal

Biochemistry

6.6K Views.  751 85, Uppsala, Sweden. Capillary isoelectric focusing is an antibody-based, ultrasensitive, high throughput technique, enabling detailed characterization of proteins and their isoforms from extremely small biological samples. The following describes a protocol for detection and quantification of specific proteins and their isoforms in an automated and robotized manner. 

Video: Highly Sensitive and Quantitative Detection of Proteins and Their Isoforms by Capillary Isoelectric Focusing Method

Highly Sensitive and Rapid Fluorescence Detection with a Portable FRET Analyzer

Recent improvements in F&#246;rster resonance energy transfer (FRET) sensors have enabled their use to detect various small molecules including ions and amino acids. However, the innate weak signal intensity of FRET sensors is a major challenge that prevents their application in various fields and makes the use of expensive, high-end fluorometers necessary. Previously, we built a cost-effective, high-performance FRET analyzer that can specifically measure the ratio of two emission wavelength bands (530 and 480 nm) to achieve high detection sensitivity. More recently, it was discovered that FRET sensors with bacterial periplasmic binding proteins detect ligands with maximum sensitivity in the critical temperature range of 50 - 55 &#176;C. This report describes a protocol for assessing sugar content in commercially-available beverage samples using our portable FRET analyzer with a temperature-specific FRET sensor. Our results showed that the additional preheating process of the FRET sensor significantly increases the FRET ratio signal, to enable more accurate measurement of sugar content. The custom-made FRET analyzer and sensor were successfully applied to quantify the sugar content in three types of commercial beverages. We anticipate that further size reduction and performance enhancement of the equipment will facilitate the use of hand-held analyzers in environments where high-end equipment is not available.

This protocol describes the rapid and highly sensitive quantification of F&#246;rster resonance energy transfer (FRET) sensor data using a custom-made portable FRET analyzer. The device was used to detect maltose within a critical temperature range that maximizes detection sensitivity, enabling practical and efficient assessment of sugar content.

Recent improvements in F&#246;rster resonance energy transfer (FRET) sensors have enabled their use to detect various small molecules including ions and ...

An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Plant seeds accumulate large amounts of storage reserves comprising biodegradable organic matter. Humans rely on seed storage reserves for food and as industrial materials. Gene expression profiles are powerful tools for investigating metabolic regulation in plant cells. Therefore, detailed, accurate gene expression profiles during seed development are required for crop breeding. Acquiring highly purified RNA is essential for producing these profiles. Efficient methods are needed to isolate highly purified RNA from seeds. Here, we describe a method for isolating RNA from seeds containing large amounts of oils, proteins, and polyphenols, which have inhibitory effects on high-purity RNA isolation. Our method enables highly purified RNA to be obtained from seeds without the use of phenol, chloroform, or additional processes for RNA purification. This method is applicable to Arabidopsis, rapeseed, and soybean seeds. Our method will be useful for monitoring the expression patterns of low level transcripts in developing and mature seeds.

We have succeeded in establishing a method for RNA isolation from plant seeds containing large amounts of oils, proteins, and polyphenols, which have inhibitory effects on high-purity RNA isolation. Our method is suitable for monitoring the expression of genes with low level transcripts in seeds.

Plant seeds accumulate large amounts of storage reserves comprising biodegradable organic matter. Humans rely on seed storage reserves for food and as ...

Capillary Electrophoresis Separation of Monoclonal Antibody Isoforms Using a Neutral Capillary

Biotherapeutic proteins, such as monoclonal antibodies (mAbs), are feasible alternatives for the treatment of chronic-degenerative diseases. The biological activity of these proteins depends on their physicochemical properties. The use of high-performance techniques like chromatography and capillary electrophoresis has been described for the analysis of physicochemical heterogeneity of mAbs. Nowadays, capillary zone electrophoresis (CZE) technique constitutes one of the most resolutive and sensitive assays for the analysis of biomolecules. Besides, the electro-driven separation in CZE is governed by extensive properties of matter and offers the advantage of analyzing proteins close to their native state. However, the successful implementation of this technique for routine analysis depends on the skills of the analyst at the critical steps during sample and system preparation. The purpose of this tutorial is to detail the steps to succeed in the CZE analysis of mAbs. Further, this protocol can be used for the development and improvement of skills of the personnel involved in protein analytical chemistry laboratories.

Here, we present a comprehensive capillary zone electrophoresis protocol for the assessment of intrinsic physicochemical heterogeneity of monoclonal antibodies as a quality attribute.

Biotherapeutic proteins, such as monoclonal antibodies (mAbs), are feasible alternatives for the treatment of chronic-degenerative diseases. The ...

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

Monotopic proteins exert their function when attached to a membrane surface, and such interactions depend on the specific lipid composition and on the availability of enough area to perform the function. Nanodiscs are used to provide a membrane surface of controlled size and lipid content. In the absence of bound extrinsic proteins, sodium phosphotungstate-stained nanodiscs appear as stacks of coins when viewed from the side by transmission electron microscopy (TEM). This protocol is therefore designed to intentionally promote stacking; consequently, the prevention of stacking can be interpreted as the binding of the membrane-binding protein to the nanodisc. In a further step, the TEM images of the protein-nanodisc complexes can be processed with standard single-particle methods to yield low-resolution structures as a basis for higher resolution cryoEM work. Furthermore, the nanodiscs provide samples suitable for either TEM or non-denaturing gel electrophoresis. To illustrate the method, Ca2+-induced binding of 5-lipoxygenase on nanodiscs is presented.

Many proteins perform their function when attached to membrane surfaces. The binding of extrinsic proteins on nanodisc membranes can be indirectly imaged by transmission electron microscopy. We show that the characteristic stacking (rouleau) of nanodiscs induced by the negative stain sodium phosphotungstate is prevented by the binding of extrinsic protein.

Monotopic proteins exert their function when attached to a membrane surface, and such interactions depend on the specific lipid composition and on the ...

Formation of Covalent DNA Adducts by Enzymatically Activated Carcinogens and Drugs In Vitro and Their Determination by 32P-postlabeling

Covalent DNA adducts formed by chemicals or drugs with carcinogenic potency are judged as one of the most important factors in the initiation phase of carcinogenic processes. This covalent binding, which is considered the cause of tumorigenesis, is now evaluated as a central dogma of chemical carcinogenesis. Here, methods are described employing the reactions catalyzed by cytochrome P450 and additional biotransformation enzymes to investigate the potency of chemicals or drugs for their activation to metabolites forming these DNA adducts. Procedures are presented describing the isolation of cellular fractions possessing biotransformation enzymes (microsomal and cytosolic samples with cytochromes P450 or other biotransformation enzymes, i.e., peroxidases, NADPH:cytochrome P450 oxidoreductase, NAD(P)H:quinone oxidoreductase, or xanthine oxidase). Furthermore, methods are described that can be used for the metabolic activation of analyzed chemicals by these enzymes as well as those for isolation of DNA. Further, the appropriate methods capable of detecting and quantifying chemical/drug-derived DNA adducts, i.e., different modifications of the 32P-postlabeling technique and employment of radioactive-labeled analyzed chemicals, are shown in detail.

Formation of Covalent DNA Adducts by Enzymatically Activated Carcinogens and Drugs In Vitro and Their Determination by 32P-postlabeling

Evaluating the potency of environmental chemicals and drugs, to be enzymatically bioactivated to intermediates generating covalent DNA adducts, is an important field in the development of cancer and its treatment. Methods are described for compound activation to form DNA adducts, as well as techniques for their detection and quantification.

Covalent DNA adducts formed by chemicals or drugs with carcinogenic potency are judged as one of the most important factors in the initiation phase of ...

Detection of Detergent-sensitive Interactions Between Membrane Proteins

Our ability to explore protein-protein interactions is the key to understanding regulatory connections in the cell. However, detection of protein-protein interactions in many cases is associated with significant experimental challenges. In particular, sorting receptors interact with their protein cargo in the lumen of the membrane compartments often in a detergent-sensitive fashion, making co-immunoprecipitation of these proteins unusable. Binding of the sorting receptor sortilin to glucose transporter GLUT4 may serve as an example of weak luminal interactions between membrane proteins. Here, we describe a fast, simple, and inexpensive assay to validate the interaction between sortilin and GLUT4. For that, we have designed and chemically synthesized the myc-tagged peptide corresponding to the potential sortilin-binding epitope in the luminal part of GLUT4. Sortilin tagged with six histidines was expressed in mammalian cells, and isolated from cell lysates using Cobalt beads. Sortilin immobilized on the beads was incubated with the peptide solution at different pH values, and the eluted material was analyzed by Western blotting. This assay can be easily adapted to study other detergent-sensitive protein-protein interactions.

We describe a protocol for detection of detergent-sensitive interactions between membrane proteins using binding of the sorting receptor, sortilin, to the first luminal loop of the glucose transporter protein, GLUT4, as an example.

Our ability to explore protein-protein interactions is the key to understanding regulatory connections in the cell. However, detection of protein-protein ...

Quantitative and Qualitative Method for Sphingomyelin by LC-MS Using Two Stable Isotopically Labeled Sphingomyelin Species

We present a method of analyzing sphingomyelin (SM) qualitatively and quantitatively by liquid chromatography-electrospray Ionization-tandem mass spectrometry (LC-ESI-MS/MS). SM is a common sphingolipid composed of a phosphorylcholine and a ceramide as the hydrophilic and hydrophobic component, respectively. A number of SM species are present in mammalian cells due to a variety in the sphingoid long chain base (LCB) and an N-acyl moiety in the ceramide. In this report, we show a method of estimating the number of carbon and double bonds in a LCB and an N-acyl moiety based on their corresponding product ions in MS/MS/MS (MS3) experiments. In addition, we present a quantitative analysis method for SM using two stable isotopically labeled SM species, which facilitates determining the range used in SM quantitation. The present method will be useful in characterizing a variety of SM species in biological samples and industrial products such as cosmetics.

Here, we present a protocol to quantify and qualify each sphingomyelin species using multiple reaction monitoring and MS/MS/MS mode, respectively.

We present a method of analyzing sphingomyelin (SM) qualitatively and quantitatively by liquid chromatography-electrospray Ionization-tandem mass ...

Analysis of AtHIRD11 Intrinsic Disorder and Binding Towards Metal Ions by Capillary Gel Electrophoresis and Affinity Capillary Electrophoresis

Plants are strongly dependent on their environment. In order to adjust to stressful changes (e.g., drought and high salinity), higher plants evolve classes of intrinsically disordered proteins (IDPs) to reduce oxidative and osmotic stress. This article uses a combination of capillary gel electrophoresis (CGE) and mobility shift affinity electrophoresis (ACE) in order to describe the binding behavior of different conformers of the IDP AtHIRD11 from Arabidopsis thaliana. CGE is used to confirm the purity of AtHIRD11 and to exclude fragments, posttranslational modifications, and other impurities as reasons for complex peak patterns. In this part of the experiment, the different sample components are separated by a viscous gel inside a capillary by their different masses and detected with a diode array detector. Afterward, the binding behavior of the sample towards various metal ions is investigated by ACE. In this case, the ligand is added to the buffer solution and the shift in migration time is measured in order to determine whether a binding event has occurred or not. One of the advantages of using the combination of CGE and ACE to determine the binding behavior of an IDP is the possibility to automate the gel electrophoresis and the binding assay. Furthermore, CGE shows a lower limit of detection than the classical gel electrophoresis and ACE is able to determine the manner of binding a ligand in a fast manner. In addition, ACE can also be applied to other charged species than metal ions. However, the use of this method for binding experiments is limited in its ability to determine the number of binding sites. Nevertheless, the combination of CGE and ACE can be adapted for characterizing the binding behavior of any protein sample towards numerous charged ligands.

This protocol combines the characterization of a protein sample by capillary gel electrophoresis and a fast-binding screening for charged ligands by affinity capillary electrophoresis. It is recommended for proteins with a flexible structure, such as intrinsically disordered proteins, to determine any differences in binding for different conformers.

Plants are strongly dependent on their environment. In order to adjust to stressful changes (e.g., drought and high salinity), higher plants evolve ...

Detection of Heterodimerization of Protein Isoforms Using an in Situ Proximity Ligation Assay

Regulated protein-protein interactions are a guiding principle for many signaling events, and the detection of such events is an important element in understanding how such pathways are organized and how they function. There are many methods to detect protein-protein interactions in cells, but relatively few can be used to detect interactions between endogenous proteins. One such method, the proximity ligation assay (PLA), has several advantages to recommend its use. Compared to other common methods of protein-protein interaction analysis, PLA has relatively high sensitivity and specificity, can be performed with minimal cell manipulation, and, in the protocol described herein, requires only two target-specific antibodies derived from different species (e.g., from mouse and rabbit) and one specialized reagent: a set of secondary antibodies that are covalently linked to specific oligonucleotides that, when brought in close proximity of one another, create an amplifiable platform for in situ PCR or rolling circle amplification. In this presentation, we show how to apply the PLA technique to visualize changes in MST1 and MST2 proximity in fixed cells. The technique described in this manuscript is particularly applicable for the analysis of cell signaling studies.

Detection of Heterodimerization of Protein Isoforms Using an in Situ Proximity Ligation Assay

Here, we show how to use a Proximity Ligation Assay (PLA) to visualize MST1/MST2 heterodimerization in fixed cells with high sensitivity.

Regulated protein-protein interactions are a guiding principle for many signaling events, and the detection of such events is an important element in ...

Use of Recombinant Fusion Proteins in a Fluorescent Protease Assay Platform and Their In-gel Renaturation

Proteases are intensively studied enzymes due to their essential roles in several biological pathways of living organisms and in pathogenesis; therefore, they are important drug targets. We have developed a magnetic-agarose-bead-based assay platform for the investigation of proteolytic activity, which is based on the use of recombinant fusion protein substrates. In order to demonstrate the use of this assay system, a protocol is presented on the example of human immunodeficiency virus type 1 (HIV-1) protease. The introduced assay platform can be utilized efficiently in the biochemical characterization of proteases, including enzyme activity measurements in mutagenesis, kinetic, inhibition, or specificity studies, and it may be suitable for high-throughput substrate screening or may be adapted to other proteolytic enzymes.
In this assay system, the applied substrates contain N-terminal hexahistidine (His6) and maltose-binding protein (MBP) tags, cleavage sites for tobacco etch virus (TEV) and HIV-1 proteases, and a C-terminal fluorescent protein. The substrates can be efficiently produced in Escherichia coli cells and easily purified using nickel (Ni)-chelate-coated beads. During the assay, the proteolytic cleavage of bead-attached substrates leads to the release of fluorescent cleavage fragments, which can be measured by fluorimetry. Additionally, cleavage reactions can be analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). A protocol for the in-gel renaturation of assay components is also described, as partial renaturation of fluorescent proteins enables their detection based on molecular weight and fluorescence.

Here, we present the detailed procedure of a recently developed protease assay platform utilizing N-terminal hexahistidine/maltose-binding protein and fluorescent protein-fused recombinant substrates attached to the surface of nickel-nitrilotriacetic acid magnetic agarose beads. A subsequent in-gel analysis of the assay samples separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis is also presented.

Proteases are intensively studied enzymes due to their essential roles in several biological pathways of living organisms and in pathogenesis; therefore, ...

Highly Sensitive and Quantitative Detection of Proteins and Their Isoforms by Capillary Isoelectric Focusing Method

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Chapters in this video

Highly Sensitive and Rapid Fluorescence Detection with a Portable FRET Analyzer

An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Capillary Electrophoresis Separation of Monoclonal Antibody Isoforms Using a Neutral Capillary

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

Formation of Covalent DNA Adducts by Enzymatically Activated Carcinogens and Drugs In Vitro and Their Determination by ³²P-postlabeling

Detection of Detergent-sensitive Interactions Between Membrane Proteins

Quantitative and Qualitative Method for Sphingomyelin by LC-MS Using Two Stable Isotopically Labeled Sphingomyelin Species

Analysis of AtHIRD11 Intrinsic Disorder and Binding Towards Metal Ions by Capillary Gel Electrophoresis and Affinity Capillary Electrophoresis

Detection of Heterodimerization of Protein Isoforms Using an in Situ Proximity Ligation Assay

Use of Recombinant Fusion Proteins in a Fluorescent Protease Assay Platform and Their In-gel Renaturation