We are very grateful to Dr. Brigitte Sturm for her support with the ECLIA instrument.

Approval for skin biopsy procurement for research purposes was obtained from the Human Research Ethics Committee of the Children&#8217;s Hospital at Westmead, Australia. Consent for animal experiments was obtained from the Austrian Federal Ministry of Science, Research and Economy, which were performed in accordance with local animal welfare regulations (GZ: 66.009/0218-II/3b/2015).
NOTE: The principle of the ECLIA system is depicted in Figure 1.
1. Antibody selection
<ol>
	<li>Evaluate the signal-to-noise ratio for a range of various MeCP2 antibodies and identify the best signal strength and highest specificity within the combination of a primary mouse monoclonal MeCP2 antibody (clone Mec-168) and rabbit polyclonal MeCP2 detection antibody (custom made). For the secondary antibody, use a system-specific antibody (Table of Materials), which was also experimentally verified. 
	NOTE: Table 1 gives an overview of all verified antibodies during MeCP2-ECLIA development and their tested dilution ranges.</li>
</ol>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Function</td>
			<td>Name</td>
			<td>Clone</td>
			<td>Dilution</td>
		</tr>
		<tr>
			<td>Primary</td>
			<td>Mouse, anti-MeCP2</td>
			<td>Mec-168</td>
			<td>1:500&#8722;1:10,000</td>
		</tr>
		<tr>
			<td>Primary</td>
			<td>Mouse, anti-MeCP2</td>
			<td>4B6</td>
			<td>1:250&#8722;1:4,000</td>
		</tr>
		<tr>
			<td>Primary</td>
			<td>Mouse, anti-MeCP2</td>
			<td>Men-8</td>
			<td>1:500&#8722;1:4,000</td>
		</tr>
		<tr>
			<td>Primary</td>
			<td>Mouse, anti-MeCP2</td>
			<td>1B11</td>
			<td>1:500&#8722;1:4,000</td>
		</tr>
		<tr>
			<td>Primary</td>
			<td>Rabbit, anti-MeCP2</td>
			<td>D4F3</td>
			<td>1:500&#8722;1:4,000</td>
		</tr>
		<tr>
			<td>Secondary</td>
			<td>Rabbit, anti-MeCP2</td>
			<td>polyclonal</td>
			<td>1:2,000&#8722;1:20,000</td>
		</tr>
		<tr>
			<td>Secondary</td>
			<td>Rabbit, anti-MeCP2</td>
			<td>polyclonal</td>
			<td>1:2,000&#8722;1:20,000</td>
		</tr>
		<tr>
			<td>Detection</td>
			<td>SULFO-TAG labeled anti-rabbit</td>
			<td>polyclonal</td>
			<td>1:500&#8722;1:1,000</td>
		</tr>
	</tbody>
</table>
Table 1: List of antibodies and used working dilutions.
<ol start="2">
	<li>Alternatively, use each pair of MeCP2-antibodies that works well with conventional ELISA.</li>
</ol>
2. Treatment of HDFs with TAT-MeCP2 fusion protein
NOTE: TAT-MeCP2 was recombinantly expressed in Escherichia coli and purified using standard chromatographic techniques as previously described8 and stored at -80 &#176;C.
<ol>
	<li>Plate 1 x 106 human dermal fibroblast (HDF) cells in 100 mm dishes and grow the cells overnight at 37 &#176;C with 5% CO2 until they reach about 90% confluency.</li>
	<li>Take out one vial of TAT-MeCP2 fusion protein. Thaw on ice and mix gently.</li>
	<li>Dilute TAT-MeCP2 to a final concentration of 500 nM in 50 mL of HDF culture media.</li>
	<li>Remove the media from 100 mm dishes and incubate the cells with 500 nM TAT-MeCP2 at 37 &#176;C for various incubation periods up to 24 h.</li>
	<li>Remove the TAT-MeCP2 solution from the cells. Wash the cells 2x with pre-warmed Dulbecco&#8217;s phosphate-buffered saline (DPBS).</li>
	<li>Treat the cells with 2 mL of 0.05% trypsin-EDTA solution for 5 min at 37 &#176;C10.</li>
	<li>Add 6 mL of HDF culture media to inactivate the trypsin and collect the cells in 15 mL tubes.</li>
	<li>Pellet the cells by centrifugation at 500 x g for 5 min at room temperature.</li>
	<li>Remove the supernatant and wash the cells 2x with ice-cold DPBS. Store the pellet on ice and proceed with sample preparation.</li>
</ol>
3. Sample preparation
<ol>
	<li>HDF lysates
	<ol>
		<li>Determine the highest protein levels of MeCP2 using the REAP method for subcellular fractionation into the cytoplasmic and nuclear subcellular compartments according to Suzuki et al.11. Limit fractionation to no more than six samples per experiment.</li>
	</ol>
	</li>
	<li>Mouse brain lysates
	<ol>
		<li>Prepare 100 mL of each hypotonic lysis reagent and extraction buffer.
		<ol>
			<li>For the hypotonic lysis reagent, mix well 10 mM HEPES, 1.5 mM magnesium chloride and 10 mM potassium chloride.</li>
			<li>For the extraction buffer, mix well 20 mM HEPES, 1.5 mM magnesium chloride, 0.42 M sodium chloride, 0.2 mM EDTA, and 25% (v/v) glycerol.</li>
			<li>Adjust the pH of both buffers to 7.9.</li>
			<li>Add 1 mM dithiothreitol (DTT) and 1x protease inhibitor cocktail to both buffers freshly. Chill on ice before use.</li>
		</ol>
		</li>
		<li>Suspend 100 mg of total mouse brain (strain: C57BL/6J, wildtype male and female and B6.129P2(C)-Mecp2tm1.1Bird/J, hemizygous male and heterozygous female; age: 4&#8722;8 weeks old) in 1 mL of ice-cold hypotonic lysis reagent.</li>
		<li>Homogenize the brain with a pre-chilled Dounce all-glass tissue homogenizer by 15 strokes of homogenizer A (loose, for large clearance) and B (tight, for small clearance), respectively.</li>
		<li>Transfer the homogenized cells to a clean tube and centrifuge at 10,000 x g for 20 min at 4 &#176;C. Discard the supernatant (or keep it as cytoplasmatic fraction for further use).</li>
		<li>Resuspend the pellet in 140 &#181;L of extraction buffer per 100 mg of starting material. Place the tube in a pre-cooled thermoblock and mix gently for 30 min at 4 &#176;C.</li>
		<li>Centrifuge the tube at 16,000 g for 10 min at 4 &#176;C. Transfer the supernatant (i.e., the nuclear fraction) to a new pre-chilled tube and store at -80 &#176;C until use. 
		NOTE: The protein concentration of lysates derived from mouse brain and HDFs can be assessed by the BCA protein assay.</li>
	</ol>
	</li>
</ol>
4. MeCP2-ECLIA protocol
<ol>
	<li>Preparation of washing solution, blocking buffer and assay diluent solution (day 1)
	<ol>
		<li>Add 500 &#181;L of Tween 20 to 1 L of PBS to prepare a 0.05% Tween 20 in PBS solution, mix vigorously and label as &#8220;washing solution&#8221;. 
		NOTE: Ensure that only freshly prepared washing buffer is used.</li>
		<li>Prepare a blocking solution of 3% blocker A (Table of Materials) in phosphate-buffered saline (PBS). Mix by gentle stirring, filter sterilize and keep them in the fridge until use for a maximum of two weeks.</li>
		<li>Add 5 mL of blocking solution to 10 mL of PBS to prepare assay diluent solution (1% blocker A in PBS).</li>
	</ol>
	</li>
	<li>Coating of high bind plates
	<ol>
		<li>Take out a 96-well multi-array single spot high bind plate. 
		NOTE: High bind plates have a greater binding capacity and therefore a larger dynamic range than standard plates with hydrophobic surfaces.</li>
		<li>Thaw the monoclonal mouse anti-MeCP2 antibody on ice and mix 0.67 &#181;L of the antibody with 4 mL of PBS (1:6,000 antibody dilution in PBS). Vortex the antibody solution to mix well and label the tube as &#8220;coating solution&#8221;.</li>
		<li>Carefully dispense 25 &#181;L of coating solution in the bottom corner of each well using a multichannel pipettor; this is called the solution coating method. Tap the 96-well plate gently on each side to ensure that the coating solution covers the bottom of each well.</li>
		<li>Seal the plate with an adhesive foil and incubate the plate in the fridge at 4 &#176;C overnight (12&#8722;16 h).</li>
	</ol>
	</li>
	<li>Blocking (day 2)
	<ol>
		<li>Take out the plate from the fridge and remove the foil.</li>
		<li>Remove the antibody coating solution by flicking it into the waste basket and tap the plate on a paper towel to remove all the coating solution from the wells.</li>
		<li>Add 125 &#181;L of blocking solution per well. Seal the plate again and place it on an orbital microplate shaker.</li>
		<li>Incubate the plate for 90 min at room temperature with constant shaking at 800 rpm.</li>
	</ol>
	</li>
	<li>Preparations of standards and samples
	<ol>
		<li>During the incubation time, prepare the MeCP2 and/or TAT-MeCP2 protein standards and various samples. 
		NOTE: Lysis buffer used for standard dilution must be the same as that used in the analyzed samples.</li>
		<li>Take out one vial of MePC2 and/or TAT-MeCP2 protein stock solution (250 &#181;g/mL), mouse brain lysates and HDF lysates from -80 &#176;C. Thaw them on ice.</li>
		<li>Dilute the standard stock solution (MeCP2 and/or TAT-MeCP2) in clean tubes according to Table 2.</li>
		<li>Dilute the samples in lysis buffer as follows: 1&#8722;20 &#181;g of mouse brain lysate per 25 &#181;L of lysis buffer, and 0.25&#8722;1 &#181;g of HDF lysate per 25 &#181;L of lysis buffer. Prepare enough volume of each sample to carry out analysis in triplicate.</li>
	</ol>
	</li>
</ol>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Standard</td>
			<td>Concentration</td>
			<td>Dilution</td>
		</tr>
		<tr>
			<td>Standard 1</td>
			<td>1,800 ng/mL</td>
			<td>1.08 &#181;L Standard stock solution + 148.92 &#181;L Lysis buffer</td>
		</tr>
		<tr>
			<td>Standard 2</td>
			<td>600 ng/mL</td>
			<td>50 &#181;L Standard 1 + 100 &#181;L Lysis buffer</td>
		</tr>
		<tr>
			<td>Standard 3</td>
			<td>200 ng/mL</td>
			<td>50 &#181;L Standard 2 + 100 &#181;L Lysis buffer</td>
		</tr>
		<tr>
			<td>Standard 4</td>
			<td>66.67 ng/mL</td>
			<td>50 &#181;L Standard 3 + 100 &#181;L Lysis buffer</td>
		</tr>
		<tr>
			<td>Standard 5</td>
			<td>22.22 ng/mL</td>
			<td>50 &#181;L Standard 4 + 100 &#181;L Lysis buffer</td>
		</tr>
		<tr>
			<td>Standard 6</td>
			<td>7.41 ng/mL</td>
			<td>50 &#181;L Standard 5 + 100 &#181;L Lysis buffer</td>
		</tr>
		<tr>
			<td>Standard 7</td>
			<td>2.47 ng/mL</td>
			<td>50 &#181;L Standard 6 + 100 &#181;L Lysis buffer</td>
		</tr>
		<tr>
			<td>Standard 8</td>
			<td>0.82 ng/mL</td>
			<td>50 &#181;L Standard 7 + 100 &#181;L Lysis buffer</td>
		</tr>
		<tr>
			<td>Standard 9</td>
			<td>0.27 ng/mL</td>
			<td>50 &#181;L Standard 8 + 100 &#181;L Lysis buffer</td>
		</tr>
		<tr>
			<td>Standard 10</td>
			<td>0 ng/mL</td>
			<td>150 &#181;L Lysis buffer</td>
		</tr>
	</tbody>
</table>
Table 2: Standard series from 0 to 1,800 ng/mL.
<ol start="5">
	<li>Adding the samples and standard solutions
	<ol>
		<li>Remove the blocking solution by flicking it into the waste basket and tap the plate on a paper towel to remove all the blocking solution from the wells.</li>
		<li>Wash the plate 3x with 150 &#181;L of washing solution by adding the washing solution and immediately removing it.</li>
		<li>Add 25 ul of standards and samples to the bottom corner of the well using a single channel pipette.</li>
		<li>Seal the plate and incubate the plate for 4 h at room temperature with constant shaking at 800 rpm.</li>
	</ol>
	</li>
	<li>Unlabeled detection antibody
	<ol>
		<li>Thaw the polyclonal rabbit anti-MeCP2 antibody on ice. Dilute the antibody 1:6,000 in assay diluent solution.</li>
		<li>Remove the standards and samples by flicking it into the waste basket and tap the plate on a paper towel.</li>
		<li>Wash the plate 3x with 150 &#181;L of washing solution by adding the washing solution and immediately removing it.</li>
		<li>Add 25 &#181;L of unlabeled detection antibody to each well with the multichannel pipettor. Seal the plate and incubate it for 1 h with constant shaking at 800 rpm at room temperature.</li>
	</ol>
	</li>
	<li>Specific conjugated antibody
	<ol>
		<li>Take out the specific secondary antibody (Table of Materials) from the fridge and place it on ice. Dilute the antibody 1:666.67 in assay diluent solution and mix gently.</li>
		<li>Remove the free unlabeled secondary antibody by flicking it into the waste basket and tap the plate on a paper towel.</li>
		<li>Wash the plate 3x with 150 &#181;L of washing solution by adding the washing solution and immediately removing it.</li>
		<li>Add 25 &#181;L of specific conjugated antibody (Table of Materials) to each well with the multichannel pipettor. Seal the plate and incubate for 1 h with constant shaking at 800 rpm at room temperature.</li>
	</ol>
	</li>
	<li>Reading the plate
	<ol>
		<li>Remove the free conjugated antibody (Table of Materials) by flicking it into the waste basket and tap the plate on a paper towel.</li>
		<li>Wash the plate 3x with 150 &#181;L of washing solution.</li>
		<li>Add 150 &#956;L of 1x Tris-based Gold read buffer&#160;(Table of Materials) with surfactant containing tripropylamine as a co-reactant for light generation to the plate. Avoid any air bubbles by using reverse pipetting techniques.</li>
		<li>Place the plate on the microplate detection platform (Table of Materials) and start the measurement immediately. Use the settings for 96-well plate acquisition.</li>
		<li>Capture the electrochemiluminescence signals by a built-in CCD camera in an electrochemiluminescence detection system (Table of Materials) and record the signal counts, which correspond to relative light units (RLU) and are directly proportional to the intensity of light. 
		NOTE: Upon electrochemical stimulation, the ruthenium label bound to the carbon electrode emits luminescence light at 620 nm. Analyze data with the instrument-accompanied software (Table of Materials).</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Debad, J. D., Glezer, E. N., Wohlstadter, J., Sigal, G. B., Leland, J. K., Bard, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clinical+and+biological+applications+of+ECL.">Clinical and biological applications of ECL.</a> Electrogenerated Chemiluminescence. , 359-383 (2004).</li><li>Yuzaburo, N., Michinori, U., Osamu, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+Sensitive+Electrochemiluminescence+Immunoassay+Using+the+Ruthenium+Chelate-Labeled+Antibody+Bound+on+the+Magnetic+Micro+Beads.">Highly Sensitive Electrochemiluminescence Immunoassay Using the Ruthenium Chelate-Labeled Antibody Bound on the Magnetic Micro Beads.</a> Analytical Sciences. 15 (11), 1087-1093 (1999).</li><li>Liu, W., Hu, Y., Yang, Y., Hu, T., Wang, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+two+immunoassays+for+quantification+of+hepatitis+B+surface+antigen+in+Chinese+patients+with+concomitant+hepatitis+B+surface+antigen+and+hepatitis+B+surface+antibodies.">Comparison of two immunoassays for quantification of hepatitis B surface antigen in Chinese patients with concomitant hepatitis B surface antigen and hepatitis B surface antibodies.</a> Archives of Virology. 160 (1), 191-198 (2015).</li><li>Shah, R. R., Bird, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MeCP2+mutations:+progress+towards+understanding+and+treating+Rett+syndrome.">MeCP2 mutations: progress towards understanding and treating Rett syndrome.</a> Genome Medicine. 9 (1), 17 (2017).</li><li>Chahrour, 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=MeCP2,+a+key+contributor+to+neurological+disease,+activates+and+represses+transcription.">MeCP2, a key contributor to neurological disease, activates and represses transcription.</a> Science. 320 (5880), 1224-1229 (2008).</li><li>Lyst, M. J., Bird, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rett+syndrome:+a+complex+disorder+with+simple+roots.">Rett syndrome: a complex disorder with simple roots.</a> Nature Reviews Genetics. 16 (5), 261-275 (2015).</li><li>Katz, D. 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=Rett+Syndrome:+Crossing+the+Threshold+to+Clinical+Translation.">Rett Syndrome: Crossing the Threshold to Clinical Translation.</a> Trends in Neurosciences. 39 (2), 100-113 (2016).</li><li>Steinkellner, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+electrochemiluminescence+based+assay+for+quantitative+detection+of+endogenous+and+exogenously+applied+MeCP2+protein+variants.">An electrochemiluminescence based assay for quantitative detection of endogenous and exogenously applied MeCP2 protein variants.</a> Scientific Reports. 9 (1), 7929 (2019).</li><li>Laccone, F. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Synthetic MeCP2 sequence for protein substitution therapy. , (2007).</li><li>Koutsokeras, A., Kabouridis, P. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Secretion+and+uptake+of+TAT-fusion+proteins+produced+by+engineered+mammalian+cells.">Secretion and uptake of TAT-fusion proteins produced by engineered mammalian cells.</a> Biochimica et Biophysica Acta (BBA) - General Subjects. 1790 (2), 147-153 (2009).</li><li>Suzuki, K., Bose, P., Leong-Quong, R. Y., Fujita, D. J., Riabowol, K. R. E. A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=REAP:+A+two+minute+cell+fractionation+method.">REAP: A two minute cell fractionation method.</a> BMC Research Notes. 3, 294 (2010).</li><li>Xia, H., Mao, Q., Davidson, B. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+HIV+Tat+protein+transduction+domain+improves+the+biodistribution+of+beta-glucuronidase+expressed+from+recombinant+viral+vectors.">The HIV Tat protein transduction domain improves the biodistribution of beta-glucuronidase expressed from recombinant viral vectors.</a> Nature Biotechnology. 19 (7), 640-644 (2001).</li><li>Schwarze, S. R., Ho, A., Vocero-Akbani, A., Dowdy, S. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+protein+transduction:+delivery+of+a+biologically+active+protein+into+the+mouse.">In vivo protein transduction: delivery of a biologically active protein into the mouse.</a> Science. 285 (5433), 1569-1572 (1999).</li><li>Nagahara, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transduction+of+full-length+TAT+fusion+proteins+into+mammalian+cells:+TAT-p27Kip1+induces+cell+migration.">Transduction of full-length TAT fusion proteins into mammalian cells: TAT-p27Kip1 induces cell migration.</a> Nature Medicine. 4 (12), 1449-1452 (1998).</li><li>Trazzi, S., 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=CDKL5+protein+substitution+therapy+rescues+neurological+phenotypes+of+a+mouse+model+of+CDKL5+disorder.">CDKL5 protein substitution therapy rescues neurological phenotypes of a mouse model of CDKL5 disorder.</a> Human Molecular Genetics. 27 (9), 1572-1592 (2018).</li><li>Van Esch, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MECP2+Duplication+Syndrome.">MECP2 Duplication Syndrome.</a> Molecular Syndromology. 2 (3-5), 128-136 (2012).</li><li>Collins, A. 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=Mild+overexpression+of+MeCP2+causes+a+progressive+neurological+disorder+in+mice.">Mild overexpression of MeCP2 causes a progressive neurological disorder in mice.</a> Human Molecular Genetics. 13 (21), 2679-2689 (2004).</li><li>Luikenhuis, S., Giacometti, E., Beard, C. F., Jaenisch, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression+of+MeCP2+in+postmitotic+neurons+rescues+Rett+syndrome+in+mice.">Expression of MeCP2 in postmitotic neurons rescues Rett syndrome in mice.</a> Proceedings of the National Academy of Sciences of the United States of America. 101 (16), 6033-6038 (2004).</li></ol>

The authors have nothing to disclose.

To measure endogenous MeCP2, recombinant MeCP2 and TAT-MeCP2 levels, a 96-well plate ECLIA was developed. It has been shown that loss of MeCP2 protein function leads to RTT syndrome6, for which treatment is currently limited to symptom management and physical therapy. One promising treatment avenue is the so-called protein replacement therapy, where MeCP2 levels can be titrated up to their needed concentration12,13,<sup class="x...

The electrochemiluminescence immunoassay (ECLIA) is based on a process that utilizes labels designed to emit luminescence when electrochemically stimulated. It is a broadly applicable technique for the quantitative detection of biological analytes in basic industry and academic research, food industry as well as in clinical diagnostics1. Commonly, a disposable 96-well plate with carbon ink electrodes is used. These electrodes act as a solid-phase carrier for the immunoassay. A secondary antibody is conjugated to an electrochemiluminescent label and when electricity is applied to the system, light emission of the chemical label is triggered. An ultra-low noise charge-coupled device (CCD) records the light intensity which is directly proportional to the antigen bound to the capture antibody resulting in the quantification of the targeted analyte of the sample2. Compared to the enzyme-linked immunosorbent assay (ELISA), ECLIA is considered to be advantageous as it offers higher sensitivity and reproducibility as well as better automation and consistency3.
Here we analyzed the methyl-CpG binding protein 2 (MeCP2) levels in samples of human and murine origin as well as different variants of the recombinant protein using the newly developed ECLIA system. MecP2 is an X-linked nucleic acid-binding protein known to interact with methylated DNA sequences. This protein has been implicated in the regulation of gene expression4,5. Loss-of-function mutations in the gene which encodes this protein are the main culprits causing Rett syndrome (RTT), a severe neurodevelopmental disorder6. Another MeCP2-related disorder, MECP2 duplication syndrome, also leads to neurological symptoms that can overlap with those of RTT7. Notably, females are mostly affected by RTT while males are mostly afflicted by MECP2 duplication syndrome6,7.
These disorders are associated with insufficient or excess MeCP2 levels respectively in the central nervous system (CNS). Hence, treatment options for RTT that involve increasing MeCP2 levels in the CNS would need to avoid the detrimental effects associated with excess of MeCP27. Due to this fact, a highly sensitive and accurate quantification of MeCP2 protein levels, as provided by the ECLIA system, is crucial for the advancement of RTT as well as MECP2 duplication syndrome research. The precise measurements of endogenous and exogenous MeCP2 levels from human cell lines and mouse tissue samples as well as a recombinant protein consisting of human MeCP2 isoform B (also known as isoform e1), and a minimal N-terminal HIV-TAT transduction domain (TAT-MeCP2) that has the potential to cross the blood-brain-barrier8,9 are presented in this work.

<table>
	<tbody>
		<tr>
			<td>1,4-Dithiothreitol (DTT)</td>
			<td>Sigma-Aldrich</td>
			<td>D9779</td>
			<td>Hypotonic lysis reagent, Extraction Buffer</td>
		</tr>
		<tr>
			<td>Bio-Rad Protein Assay Dye Reagent Concentrate</td>
			<td>Bio-Rad Laboratories Inc.</td>
			<td>500-0006</td>
			<td>Sample preperation</td>
		</tr>
		<tr>
			<td>Detection AB SULFO-TAG labeled anti-rabbit</td>
			<td>Meso Scale Diagnostics</td>
			<td>R32AB-1</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Discovery workbench 4.0</td>
			<td>Meso Scale Discovery</td>
			<td></td>
			<td>Software</td>
		</tr>
		<tr>
			<td>DMEM (1X)</td>
			<td>gibco by Life Technologies</td>
			<td>41966-029</td>
			<td>Sample preperation</td>
		</tr>
		<tr>
			<td>Dulbecco&#8217;s PBS (sterile)</td>
			<td>Sigma-Aldrich</td>
			<td>D8537-500ML</td>
			<td>Sample preperation, Washing solution, Coating solution</td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Sigma-Aldrich</td>
			<td>EDS</td>
			<td>Extraction Buffer</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Sigma-Aldrich</td>
			<td>F9665</td>
			<td>Sample preperation</td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Sigma-Aldrich</td>
			<td>G2025</td>
			<td>Extraction Buffer</td>
		</tr>
		<tr>
			<td>Gold Read Buffer T (1x) with surfactant</td>
			<td>Meso Scale Diagnostics</td>
			<td>R92TG</td>
			<td>MeCP2 ECLIA protocol</td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Sigma-Aldrich</td>
			<td>H3375</td>
			<td>Hypotonic lysis reagent, Extraction Buffer</td>
		</tr>
		<tr>
			<td>KIMBLE Dounce tissue grinder set</td>
			<td>Sigma-Aldrich</td>
			<td>D8938</td>
			<td>Sample preperation</td>
		</tr>
		<tr>
			<td>Laboratory Shaker, rocking motion (low speed)</td>
			<td>GFL</td>
			<td>3014</td>
			<td>MeCP2 ECLIA protocol</td>
		</tr>
		<tr>
			<td>Magnesium chloride hexahydrate (MgCl*6H20)</td>
			<td>Sigma-Aldrich</td>
			<td>M2670</td>
			<td>Hypotonic lysis reagent, Extraction Buffer</td>
		</tr>
		<tr>
			<td>MeCP2 (Human) Recombinant Protein (P01)</td>
			<td>Abnova Corporation</td>
			<td>H00004204-P01</td>
			<td>Cell treatment</td>
		</tr>
		<tr>
			<td>Microseal B seal</td>
			<td>Bio-Rad Laboratories Inc.</td>
			<td>MSB1001</td>
			<td>for plate sealing</td>
		</tr>
		<tr>
			<td>Monoclonal Anti-MeCP2, produced in mouse, clone Mec-168, purified immunoglobulin</td>
			<td>Sigma-Aldrich</td>
			<td>M6818-100UL; RRID:AB_262075</td>
			<td>Antibody, Coating solution</td>
		</tr>
		<tr>
			<td>MSD Blocker A</td>
			<td>Meso Scale Diagnostics</td>
			<td>R93BA-4</td>
			<td>Blocker</td>
		</tr>
		<tr>
			<td>MSD SECTOR Imager 2400</td>
			<td>Meso Scale Diagnostics</td>
			<td>I30AA-0</td>
			<td>MeCP2 ECLIA protocol</td>
		</tr>
		<tr>
			<td>Multi-Array 96-well Plate</td>
			<td>Meso Scale Diagnostics</td>
			<td>L15XB-3/L11BX-3</td>
			<td>MeCP2 ECLIA protocol</td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>gibco by Life Technologies</td>
			<td>15140122</td>
			<td>Sample preperation</td>
		</tr>
		<tr>
			<td>Polyclonal Anti-MeCP2, produced in rabbit</td>
			<td>Eurogentec S.A.</td>
			<td>custom-designed</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Potassium chloride (KCl)</td>
			<td>Merck KGaA</td>
			<td>1049361000</td>
			<td>Hypotonic lysis reagent</td>
		</tr>
		<tr>
			<td>Primary AB Mouse, anti-MeCP2 (1B11)</td>
			<td>Sigma-Aldrich</td>
			<td>SAB1404063; RRID:AB_10737296</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Primary AB Mouse, anti-MeCP2 (4B6)</td>
			<td>Sigma-Aldrich</td>
			<td>WH0004204M1; RRID:AB_1842411</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Primary AB Mouse, anti-MeCP2 (Mec-168)</td>
			<td>Sigma-Aldrich</td>
			<td>M6818; RRID:AB_262075</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Primary AB Mouse, anti-MeCP2 (Men-8)</td>
			<td>Sigma-Aldrich</td>
			<td>M7443; RRID:AB_477235</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Primary AB Rabbit, anti-MeCP2 (D4F3)</td>
			<td>Cell Signaling Technology</td>
			<td>3456S; RRID:AB_2143849</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Protease Inhibitor Cocktail (100X)</td>
			<td>Sigma-Aldrich</td>
			<td>8340</td>
			<td>Hypotonic lysis reagent, Extraction Buffer</td>
		</tr>
		<tr>
			<td>Secondary AB, Rabbit, anti-MeCP2</td>
			<td>Eurogentec S.A.</td>
			<td>custom</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Secondary AB, Rabbit, anti-MeCP2</td>
			<td>Merck</td>
			<td>07-013</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Sodium chloride (NaCl)</td>
			<td>Sigma-Aldrich</td>
			<td>S3014</td>
			<td>Extraction Buffer</td>
		</tr>
		<tr>
			<td>SULFO-TAG Labeled Anti-Rabbit Antibody (goat)</td>
			<td>Meso Scale Diagnostics</td>
			<td>W0015528S</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>TAT-MeCP2 fusion protein</td>
			<td>in-house production</td>
			<td></td>
			<td>Cell treatment</td>
		</tr>
		<tr>
			<td>Trypsin EDTA 0.25% (1X)</td>
			<td>gibco by Life Technologies</td>
			<td>25200-056</td>
			<td>Cell treatment</td>
		</tr>
		<tr>
			<td>Tween 20</td>
			<td>Sigma-Aldrich</td>
			<td>P9416</td>
			<td>Washing solution</td>
		</tr>
	</tbody>
</table>

an electrochemiluminescence-based assay for mecp2 protein variants

The ECLIA is a versatile method which is able to quantify endogenous and recombinant protein amounts in a 96-well format. To demonstrate ECLIA efficiency, this assay was used to analyze intrinsic levels of MeCP2 in mouse brain tissue and the uptake of TAT-MeCP2 in human dermal fibroblasts. The MeCP2-ECLIA produces highly accurate and reproducible measurements with low intra- and inter-assay error. In summary, we developed a quantitative method for the evaluation of MeCP2 protein variants that can be utilized in high-throughput screens.

The principle of the ECLIA system is described in Figure 1. Standard curves for two MeCP2 variants are shown in Figure 2. Accurate quantification was possible over a wide range of concentrations (1&#8722;1,800 ng/mL). In Figure 3, MeCP2 levels of lysates derived from mouse brain and HDFs were analyzed. MeCP2 expression in brain nuclear lysates from heterozygous, wildtype and knockout mice were compared in Figure...

Watch this Scientific Journal Video about An Electrochemiluminescence-Based Assay for MeCP2 Protein Variants at JoVE.com

An Electrochemiluminescence-Based Assay for MeCP2 Protein Variants

The electrochemiluminescence immunoassay (ECLIA) is a novel approach for quantitative detection of endogenous and exogenously applied MeCP2 protein variants, which produces highly quantitative, accurate and reproducible measurements with low intra- and inter-assay error over a wide working range. Here, the protocol for the MeCP2-ECLIA in a 96-well format is described.

The ECLIA is a versatile method which is able to quantify endogenous and recombinant protein amounts in a 96-well format. To demonstrate ECLIA efficiency, ...

an-electrochemiluminescence-based-assay-for-mecp2-protein-variants

Research

JoVE Journal

Biochemistry

26.8K Views.  Medical University of Vienna (MUV). The electrochemiluminescence immunoassay (ECLIA) is a novel approach for quantitative detection of endogenous and exogenously applied MeCP2 protein variants, which produces highly quantitative, accurate and reproducible measurements with low intra- and inter-assay error over a wide working range. Here, the protocol for the MeCP2-ECLIA in a 96-well format is described.

Video: An Electrochemiluminescence-Based Assay for MeCP2 Protein Variants

Capturing the Interaction Kinetics of an Ion Channel Protein with Small Molecules by the Bio-layer Interferometry Assay

The bio-layer interferometry (BLI) assay is a valuable tool for measuring protein-protein and protein-small molecule interactions. Here, we first describe the application of this novel label-free technique to study the interaction of human EAG1 (hEAG1) channel proteins with the small molecule PIP2. hEAG1 channel has been recognized as potential therapeutic target because of its aberrant overexpression in cancers and a few gain-of-function mutations involved in some types of neurological diseases. We purified&#160;hEAG1 channel proteins from a mammalian stable expression system and measured the interaction with PIP2 by BLI. The successful measurement of the kinetics of binding between hEAG1 protein and PIP2 demonstrates that the BLI assay is a potential high-throughput approach used for novel small-molecule ligand screening in ion channel pharmacology.

The protocol here describes the interactions of purified hEAG1 ion channel protein with the small molecule lipid ligand phosphatidylinositol 4, 5-bisphosphate (PIP2). The measurement demonstrates that BLI could be a potential method for novel small-molecule ion channel ligand screening.

The bio-layer interferometry (BLI) assay is a valuable tool for measuring protein-protein and protein-small molecule interactions. Here, we first describe ...

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 ...

A Fluorescence Fluctuation Spectroscopy Assay of Protein-Protein Interactions at Cell-Cell Contacts

A variety of biological processes involves cell-cell interactions, typically mediated by proteins that interact at the interface between neighboring cells. Of interest, only few assays are capable of specifically probing such interactions directly in living cells. Here, we present an assay to measure the binding of proteins expressed at the surfaces of neighboring cells, at cell-cell contacts. This assay consists of two steps: mixing of cells expressing the proteins of interest fused to different fluorescent proteins, followed by fluorescence fluctuation spectroscopy measurements at cell-cell contacts using a confocal laser scanning microscope. We demonstrate the feasibility of this assay in a biologically relevant context by measuring the interactions of the amyloid precursor-like protein 1 (APLP1) across cell-cell junctions. We provide detailed protocols on the data acquisition using fluorescence-based techniques (scanning fluorescence cross-correlation spectroscopy, cross-correlation number and brightness analysis) and the required instrument calibrations. Further, we discuss critical steps in the data analysis and how to identify and correct external, spurious signal variations, such as those due to photobleaching or cell movement.
In general, the presented assay is applicable to any homo- or heterotypic protein-protein interaction at cell-cell contacts, between cells of the same or different types and can be implemented on a commercial confocal laser scanning microscope. An important requirement is the stability of the system, which needs to be sufficient to probe diffusive dynamics of the proteins of interest over several minutes.

This protocol describes a fluorescence fluctuation spectroscopy-based approach to investigate interactions among proteins mediating cell-cell interactions, i.e. proteins localized in cell junctions, directly in living cells. We provide detailed guidelines on instrument calibration, data acquisition and analysis, including corrections to possible artefact sources.

A variety of biological processes involves cell-cell interactions, typically mediated by proteins that interact at the interface between neighboring ...

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing approaches suffer from significant limitations, we have developed a new method for determining TF-DNA binding affinities with high sensitivity on a large scale. The assay relies on the established fluorescence anisotropy (FA) principle but introduces important technical improvements. First, we measure a full FA competitive titration curve in a single well by incorporating TF and a fluorescently labeled reference DNA in a porous agarose gel matrix. Unlabeled DNA oligomer is loaded on the top as a competitor and, through diffusion, forms a spatio-temporal gradient. The resulting FA gradient is then read out using a customized epifluorescence microscope setup. This improved setup greatly increases the sensitivity of FA signal detection, allowing both weak and strong binding to be reliably quantified, even for molecules of similar molecular weights. In this fashion, we can measure one titration curve per well of a multi-well plate, and through a fitting procedure, we can extract both the absolute dissociation constant (KD) and active protein concentration. By testing all single-point mutation variants of a given consensus binding sequence, we can survey the entire binding specificity landscape of a TF, typically on a single plate. The resulting position weight matrices (PWMs) outperform those derived from other methods in predicting in vivo TF occupancy. Here, we present a detailed guide for implementing HiP-FA on a conventional automated fluorescent microscope and the data analysis pipeline.

Here we present a novel method for determining binding affinities at equilibrium and in solution with high sensitivity on a large scale. This improves the quantitative analysis of transcription factor-DNA binding. The method is based on automated fluorescence anisotropy measurements in a controlled delivery system.

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing ...

A Fluorogenic Peptide Cleavage Assay to Screen for Proteolytic Activity: Applications for coronavirus spike protein activation

Enveloped viruses such as coronaviruses or influenza virus require proteolytic cleavage of their fusion protein to be able to infect the host cell. Often viruses exhibit cell and tissue tropism and are adapted to specific cell or tissue proteases. Moreover, these viruses can introduce mutations or insertions into their genome during replication that may affect the cleavage, and thus can contribute to adaptations to a new host. Here, we present a fluorogenic peptide cleavage assay that allows a rapid screening of peptides mimicking the cleavage site of viral fusion proteins. The technique is very flexible and can be used to investigate the proteolytic activity of a single protease on many different substrates, and in addition, it also allows exploration of the activity of multiple proteases on one or more peptide substrates. In this study, we used peptides mimicking the cleavage site motifs of the coronavirus spike protein. We tested human and camel derived Middle East Respiratory Syndrome coronaviruses (MERS-CoV) to demonstrate that single and double substitutions in the cleavage site can alter the activity of furin and dramatically change cleavage efficiency. We also used this method in combination with bioinformatics to test furin cleavage activity of feline coronavirus spike proteins from different serotypes and strains. This peptide-based method is less labor- and time intensive than conventional methods used for the analysis of proteolytic activity for viruses, and results can be obtained within a single day.

We present a fluorogenic peptide cleavage assay that allows a rapid screening of the proteolytic activity of proteases on peptides representing the cleavage site of viral fusion peptides. This method can also be used on any other amino acid motif within a protein sequence to test for the protease activity.

Enveloped viruses such as coronaviruses or influenza virus require proteolytic cleavage of their fusion protein to be able to infect the host cell. Often ...

Evaluation of Protein&#8211;Protein Interactions using an On-Membrane Digestion Technique

Numerous intracellular proteins physically interact in accordance with their intracellular and extracellular circumstances. Indeed, cellular functions largely depend on intracellular protein&#8211;protein interactions. Therefore, research regarding these interactions is indispensable to facilitating the understanding of physiologic processes. Co-precipitation of associated proteins, followed by mass spectrometry (MS) analysis, enables the identification of novel protein interactions. In this study, we have provided details of the novel technique of immunoprecipitation-liquid chromatography (LC)-MS/MS analysis combined with on-membrane digestion for the analysis of protein&#8211;protein interactions. This technique is suitable for crude immunoprecipitants and can improve the throughput of proteomic analyses. Tagged recombinant proteins were precipitated using specific antibodies; next, immunoprecipitants blotted onto polyvinylidene difluoride membrane pieces were subjected to reductive alkylation. Following trypsinization, the digested protein residues were analyzed using LC-MS/MS. Using this technique, we were able to identify several candidate associated proteins. Thus, this method is convenient and useful for the characterization of novel protein&#8211;protein interactions.

Here, we present a protocol for an on-membrane digestion technique for the preparation of samples for mass spectrometry. This technique facilitates the convenient analysis of protein&#8211;protein interactions.

Numerous intracellular proteins physically interact in accordance with their intracellular and extracellular circumstances. Indeed, cellular functions ...

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Protein dimerization events that occur only in the presence of a small-molecule ligand enable the development of small-molecule biosensors for the dissection and manipulation of biological pathways. Currently, only a limited number of chemically induced dimerization (CID) systems exist and engineering new ones with desired sensitivity and selectivity for specific small-molecule ligands remains a challenge in the field of protein engineering. We here describe a high throughput screening method, combinatorial binders-enabled selection of CID (COMBINES-CID), for the de novo engineering of CID systems applicable to a large variety of ligands. This method uses the two-step selection of a phage-displayed combinatorial nanobody library to obtain 1) &#34;anchor binders&#34; that first bind to a ligand of interest and then 2) &#34;dimerization binders&#34; that only bind to anchor binder-ligand complexes. To select anchor binders, a combinatorial library of over 109 complementarity-determining region (CDR)-randomized nanobodies is screened with a biotinylated ligand and hits are validated with the unlabeled ligand by bio-layer interferometry (BLI). To obtain dimerization binders, the nanobody library is screened with anchor binder-ligand complexes as targets for positive screening and the unbound anchor binders for negative screening. COMBINES-CID is broadly applicable to select CID binders with other immunoglobulin, non-immunoglobulin, or computationally designed scaffolds to create biosensors for in vitro and in vivo detection of drugs, metabolites, signaling molecules, etc.

Creating chemically induced protein dimerization systems with desired affinity and specificity for any given small molecule ligand would have many biological sensing and actuation applications. Here, we describe an efficient, generalizable method for de novo engineering of chemically induced dimerization systems via the stepwise selection of a phage-displayed combinatorial single-domain antibody library.

Protein dimerization events that occur only in the presence of a small-molecule ligand enable the development of small-molecule biosensors for the ...

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Chromatin is a higher-order structure that packages eukaryotic DNA. Chromatin undergoes dynamic alterations according to the cell cycle phase and in response to environmental stimuli. These changes are essential for genomic integrity, epigenetic regulation, and DNA metabolic reactions such as replication, transcription, and repair. Chromatin assembly is crucial for chromatin dynamics and is catalyzed by histone chaperones. Despite extensive studies, the mechanisms by which histone chaperones enable chromatin assembly remains elusive. Moreover, the global features of nucleosomes organized by histone chaperones are poorly understood. To address these problems, this work describes a unique single-molecule imaging technique named DNA curtain, which facilitates the investigation of the molecular details of nucleosome assembly by histone chaperones. DNA curtain is a hybrid technique that combines lipid fluidity, microfluidics, and total internal reflection fluorescence microscopy (TIRFM) to provide a universal platform for real-time imaging of diverse protein-DNA interactions.Using DNA curtain, the histone chaperone function of Abo1, the Schizosaccharomyces pombe bromodomain-containing AAA+ ATPase, is investigated, and the molecular mechanism underlying histone assembly of Abo1 is revealed. DNA curtain provides a unique approach for studying chromatin dynamics.

DNA curtain, a high-throughput single-molecule imaging technique, provides a platform for real-time visualization of diverse protein-DNA interactions. The present protocol utilizes the DNA curtain technique to investigate the biological role and molecular mechanism of Abo1, a Schizosaccharomyces pombe bromodomain-containing AAA+ ATPase.

Chromatin is a higher-order structure that packages eukaryotic DNA. Chromatin undergoes dynamic alterations according to the cell cycle phase and in ...

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome

Untargeted metabolomics techniques are being widely used in recent years. However, the rapidly increasing throughput and number of samples create an enormous amount of spectra, setting challenges for quality control of the mass spectrometry spectra. To reduce the false positives, false discovery rate (FDR) quality control is necessary. Recently, we developed a software for FDR control of untargeted metabolome identification that is based on a Target-Decoy strategy named XY-Meta. Here, we demonstrated a complete analysis pipeline that integrates XY-Meta and metaX together. This protocol shows how to use XY-meta to generate a decoy database from an existing reference database and perform FDR control using the Target-Decoy strategy for large-scale metabolome identification on an open-access dataset. The differential analysis and metabolites annotation were performed after running metaX for metabolites peaks detection and quantitation. In order to help more researchers, we also developed a user-friendly cloud-based analysis platform for these analyses, without the need for bioinformatics skills or any computer languages.

We constructed an untargeted metabolomic workflow that integrated XY-Meta and metaX together. In this protocol, we displayed how to use XY-Meta to generate a decoy spectral library from open access spectra reference, and then performed FDR control and used the metaX to quantitate the metabolites after identifying the metabolomics spectra.

Untargeted metabolomics techniques are being widely used in recent years. However, the rapidly increasing throughput and number of samples create an ...

An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation

Phosphorylation is a necessary posttranslational modification that regulates protein function and directs cell signaling outcomes. Current methods to measure protein phosphorylation cannot preserve the heterogeneity in phosphorylation across individual proteins. The single-molecule pull-down (SiMPull) assay was developed to investigate the composition of macromolecular complexes via immunoprecipitation of proteins on a glass coverslip followed by single-molecule imaging. The current technique is an adaptation of SiMPull that provides robust quantification of the phosphorylation state of full-length membrane receptors at the single-molecule level. Imaging thousands of individual receptors in this way allows for quantifying protein phosphorylation patterns. The present protocol details the optimized SiMPull procedure, from sample preparation to imaging. Optimization of glass preparation and antibody fixation protocols further enhances data quality. The current protocol provides code for the single-molecule data analysis that calculates the fraction of receptors phosphorylated within a sample. While this work focuses on phosphorylation of the epidermal growth factor receptor (EGFR), the protocol can be generalized to other membrane receptors and cytosolic signaling molecules.

The present protocol describes sample preparation and data analysis to quantify protein phosphorylation using an improved single-molecule pull-down (SiMPull) assay.

Phosphorylation is a necessary posttranslational modification that regulates protein function and directs cell signaling outcomes. Current methods to ...