Name: a mass spectrometry-based proteomics approach for global and high-confidence protein r-methylation analysis
Uploaded: 2022-04-28T12:20:00
Description: Watch this Scientific Journal Video about A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis at JoVE.com

MM and EM are PhD students within the European School of Molecular Medicine (SEMM). EM is the recipient of a 3-years FIRC-AIRC bursary (Project Code: 22506). Global analyses of R-methyl-proteomes in the TB group are supported by the AIRC IG Grant (Project Code: 21834).

1. Cell culturing and protein extraction (time: 3 - 4 weeks required)
<ol>
	<li>Grow HeLa cells in parallel in media supplied with either Light (L) or Heavy (H) Methionine, respectively (see Table 1 for media composition). Upon at least eight cell divisions, collect an aliquot of cells from each SILAC channel and perform the incorporation test. 
	NOTE: To check for the incorporation efficiency, test by LC-MS/MS analysis that the percentage of heavy Methionine (Met-4) in the Heavy channel is as nea...

<ol>
	<li>Bulau, P., 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=Quantitative+assessment+of+arginine+methylation+in+free+versus+protein-incorporated+amino+acids+in+vitro+and+in+vivo+using+protein+hydrolysis+and+high-performance+liquid+chromatography.">Quantitative assessment of arginine methylation in free versus protein-incorporated amino acids in vitro and in vivo using protein hydrolysis and high-performance liquid chromatography.</a> Biotechniques. 40 (3), 305-310 (2006).</li><li>Blanc, R. S., Richard, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Arginine+methylation:+the+coming+of+age.">Arginine methylation: the coming of age.</a> Molecular Cell. 65 (1), 8-24 (2017).</li><li>Sylvestersen, K. B., Horn, H., Jungmichel, S., Jensen, L. J., Nielsen, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomic+analysis+of+arginine+methylation+sites+in+human+cells+reveals+dynamic+regulation+during+transcriptional+arrest.">Proteomic analysis of arginine methylation sites in human cells reveals dynamic regulation during transcriptional arrest.</a> Molecular &amp; Cellular Proteomics. 13 (8), 2072-2088 (2014).</li><li>Yang, Y., Bedford, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+arginine+methyltransferases+and+cancer.">Protein arginine methyltransferases and cancer.</a> Nature Reviews Cancer. 13 (1), 37-50 (2013).</li><li>Bezzi, 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=Regulation+of+constitutive+and+alternative+splicing+by+PRMT5+reveals+a+role+for+Mdm4+pre-mRNA+in+sensing+defects+in+the+spliceosomal+machinery.">Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery.</a> Genes &amp; Development. 27 (17), 1903-1916 (2013).</li><li>Auclair, Y., Richard, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+arginine+methylation+in+the+DNA+damage+response.">The role of arginine methylation in the DNA damage response.</a> DNA Repair. 12 (7), 459-465 (2013).</li><li>Spadotto, V., 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=PRMT1-mediated+methylation+of+the+microprocessor-associated+proteins+regulates+microRNA+biogenesis.">PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis.</a> Nucleic Acids Research. 48 (1), 96-115 (2020).</li><li>Musiani, D., Massignani, E., Cuomo, A., Yadav, A., Bonaldi, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biochemical+and+computational+approaches+for+the+large-scale+analysis+of+protein+arginine+methylation+by+mass+spectrometry.">Biochemical and computational approaches for the large-scale analysis of protein arginine methylation by mass spectrometry.</a> Current Protein and Peptide Science. 21 (7), 725-739 (2020).</li><li>Ong, S. -. E., Mittler, G., Mann, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identifying+and+quantifying+in+vivo+methylation+sites+by+heavy+methyl+SILAC.">Identifying and quantifying in vivo methylation sites by heavy methyl SILAC.</a> Nature Methods. 1 (2), 119-126 (2004).</li><li>Hart-Smith, G., Yagoub, D., Tay, A. P., Pickford, R., Wilkins, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large+scale+mass+spectrometry-based+identifications+of+enzyme-mediated+protein+methylation+are+subject+to+high+false+discovery+rates.">Large scale mass spectrometry-based identifications of enzyme-mediated protein methylation are subject to high false discovery rates.</a> Molecular &amp; Cellular Proteomics. 15 (3), 989-1006 (2016).</li><li>Bedford, M. T., Clarke, S. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+arginine+methylation+in+mammals:+who,+what,+and+why.">Protein arginine methylation in mammals: who, what, and why.</a> Molecular Cell. 33 (1), 1-13 (2009).</li><li>Larsen, S. 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=Proteome-wide+analysis+of+arginine+monomethylation+reveals+widespread+occurrence+in+human+cells.">Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells.</a> Science Signaling. 9 (443), (2016).</li><li>Massignani, E., 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=hmSEEKER:+Identification+of+hmSILAC+doublets+in+MaxQuant+output+data.">hmSEEKER: Identification of hmSILAC doublets in MaxQuant output data.</a> Proteomics. 19 (5), 1800300 (2019).</li><li>Bradford, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+rapid+and+sensitive+method+for+the+quantitation+of+microgram+quantities+of+protein+utilizing+the+principle+of+protein-dye+binding.">A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.</a> Analytical Biochemistry. 72, 248-254 (1976).</li><li>Smith, P. K., 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=Measurement+of+protein+using+bicinchoninic+acid.">Measurement of protein using bicinchoninic acid.</a> Analytical Biochemistry. 150 (1), 76-85 (1985).</li><li>Getz, E. B., Xiao, M., Chakrabarty, T., Cooke, R., Selvin, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparison+between+the+sulfhydryl+reductants+tris(2-carboxyethyl)phosphine+and+dithiothreitol+for+use+in+protein+biochemistry.">A comparison between the sulfhydryl reductants tris(2-carboxyethyl)phosphine and dithiothreitol for use in protein biochemistry.</a> Analytical Biochemistry. 273 (1), 73-80 (1999).</li><li>Nielsen, M. 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=Iodoacetamide-induced+artifact+mimics+ubiquitination+in+mass+spectrometry.">Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry.</a> Nature Methods. 5 (6), 459-460 (2008).</li><li>Huesgen, P. F., 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=LysargiNase+mirrors+trypsin+for+protein+C-terminal+and+methylation-site+identification.">LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification.</a> Nature Methods. 12 (1), 55-58 (2015).</li><li>Rappsilber, J., Mann, M., Ishihama, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protocol+for+micro-purification,+enrichment,+pre-fractionation+and+storage+of+peptides+for+proteomics+using+StageTips.">Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips.</a> Nature Protocols. 2 (8), 1896 (2007).</li><li>Hartel, N. G., Chew, B., Qin, J., Xu, J., Graham, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deep+protein+methylation+profiling+by+combined+chemical+and+immunoaffinity+approaches+reveals+novel+PRMT1+targets.">Deep protein methylation profiling by combined chemical and immunoaffinity approaches reveals novel PRMT1 targets.</a> Molecular &amp; Cellular Proteomics. 18 (11), 2149-2164 (2019).</li><li>Bremang, 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=Mass+spectrometry-based+identification+and+characterisation+of+lysine+and+arginine+methylation+in+the+human+proteome.">Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome.</a> Molecular bioSystems. 9 (9), 2231-2247 (2013).</li><li>Geoghegan, V., Guo, A., Trudgian, D., Thomas, B., Acuto, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+identification+of+arginine+methylation+in+primary+T+cells+reveals+regulatory+roles+in+cell+signalling.">Comprehensive identification of arginine methylation in primary T cells reveals regulatory roles in cell signalling.</a> Nature Communications. 6 (1), 1-8 (2015).</li><li>Tabb, D. L., Huang, Y., Wysocki, V. H., Yates, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Influence+of+basic+residue+content+on+fragment+ion+peak+intensities+in+low-energy+collision-induced+dissociation+spectra+of+peptides.">Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides.</a> Analytical Chemistry. 76 (5), 1243-1248 (2004).</li><li>Guthals, A., Bandeira, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Peptide+identification+by+tandem+mass+spectrometry+with+alternate+fragmentation+modes.">Peptide identification by tandem mass spectrometry with alternate fragmentation modes.</a> Molecular &amp; Cellular Proteomics. 11 (9), 550-557 (2012).</li><li>Swaney, D. 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=Supplemental+activation+method+for+high-efficiency+electron-transfer+dissociation+of+doubly+protonated+peptide+precursors.">Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors.</a> Analytical Chemistry. 79 (2), 477-485 (2007).</li><li>Kundinger, S. R., Bishof, I., Dammer, E. B., Duong, D. M., Seyfried, N. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Middle-down+proteomics+reveals+dense+sites+of+methylation+and+phosphorylation+in+arginine-rich+RNA-binding+proteins.">Middle-down proteomics reveals dense sites of methylation and phosphorylation in arginine-rich RNA-binding proteins.</a> Journal of Proteome Research. 19 (4), 1574-1591 (2020).</li><li>Batth, T. S., Francavilla, C., Olsen, J. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Off-line+high-pH+reversed-phase+fractionation+for+in-depth+phosphoproteomics.">Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics.</a> Journal of Proteome Research. 13 (12), 6176-6186 (2014).</li><li>Yang, F., Shen, Y., Camp, D. G., Smith, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-pH+reversed-phase+chromatography+with+fraction+concatenation+for+2D+proteomic+analysis.">High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis.</a> Expert Review of Proteomics. 9 (2), 129-134 (2012).</li><li>Hartel, N. G., Chew, B., Qin, J., Xu, J., Graham, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deep+protein+methylation+profiling+by+combined+chemical+and+immunoaffinity+approaches+reveals+novel+PRMT1+targets.">Deep protein methylation profiling by combined chemical and immunoaffinity approaches reveals novel PRMT1 targets.</a> Molecular &amp; Cellular Proteomics. 18 (11), 2149-2164 (2019).</li><li>Uhlmann, 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=A+method+for+large-scale+identification+of+protein+arginine+methylation.">A method for large-scale identification of protein arginine methylation.</a> Molecular &amp; Cellular Proteomics. 11 (11), 1489-1499 (2012).</li><li>Wang, K., 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-free+approach+for+the+global+analysis+of+protein+methylation.">Antibody-free approach for the global analysis of protein methylation.</a> Analytical chemistry. 88 (23), 11319-11327 (2016).</li><li>Moore, K. E., 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=A+general+molecular+affinity+strategy+for+global+detection+and+proteomic+analysis+of+lysine+methylation.">A general molecular affinity strategy for global detection and proteomic analysis of lysine methylation.</a> Molecular cell. 50 (3), 444-456 (2013).</li><li>Wu, 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=A+chemical+proteomics+approach+for+global+analysis+of+lysine+monomethylome+profiling.">A chemical proteomics approach for global analysis of lysine monomethylome profiling.</a> Molecular &amp; Cellular Proteomics. 14 (2), 329-339 (2015).</li><li>Sylvestersen, K. B., Horn, H., Jungmichel, S., Jensen, L. J., Nielsen, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomic+analysis+of+arginine+methylation+sites+in+human+cells+reveals+dynamic+regulation+during+transcriptional+arrest.">Proteomic analysis of arginine methylation sites in human cells reveals dynamic regulation during transcriptional arrest.</a> Molecular &amp; Cellular Proteomics. 13 (8), 2072-2088 (2014).</li><li>Tay, A. P., Geoghegan, V., Yagoub, D., Wilkins, M. R., Hart-Smith, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MethylQuant:+A+Tool+for+Sensitive+Validation+of+Enzyme-Mediated+Protein+Methylation+Sites+from+Heavy-Methyl+SILAC+Data.">MethylQuant: A Tool for Sensitive Validation of Enzyme-Mediated Protein Methylation Sites from Heavy-Methyl SILAC Data.</a> Journal of Proteome Research. 17 (1), 359-373 (2018).</li></ol>

The high confidence identification of in vivo protein/peptide methylation by global MS-based proteomics is challenging, due to the risk of high FDR, with several amino acid substitutions and methyl-esterification occurring during sample preparation that are isobaric to methylation and can cause wrong assignments in the absence of orthogonal MS validation strategies. The substoichiometric nature of this PTM further complicates the task of global methyl-proteomics, but can be overcome with the selective enrichment...

Arginine (R)-methylation is a post translational modification (PTM) that decorates around 1% of the mammalian proteome1. Protein Arginine Methyltransferases (PRMTs) are the enzymes catalyzing R-methylation reaction by the deposition of one or two methyl groups to the nitrogen (N) atoms of the guanidino group of the side chain of R in a symmetric or asymmetric manner. In mammals, PRMTs can be grouped into three classes-type I, type II, and type III-depending on their capability to deposit both mono-methylation (MMA) and asymmetric di-methylation (ADMA), MMA and symmetric di-methylation (SDMA) or only MMA, respectively2,3. PRMTs mainly target R residues located within glycine- and arginine-rich regions, known as GAR motifs, but some PRMTs, such as PRMT5 and CARM1, can methylate proline-glycine-methionine-rich (PGM) motifs4. R-methylation has emerged as a protein modulator of several biological processes, such as RNA splicing5, DNA repair6, miRNA biogenesis7, and translation2, fostering the research on this PTM.
Mass Spectrometry (MS) is recognized as the most effective technology to systematically study global R-methylation at protein-, peptide-, and site-resolution. However, this PTM requires some particular precautions for its high-confidence identification by MS. First, R-methylation is substoichiometric, with the unmodified form of the peptides being much more abundant than the modified ones, so that mass spectrometers operating in the Data Dependent Acquisition (DDA) mode will fragment high-intensity unmodified peptides more often than their lower-intensity methylated counterparts8. Moreover, most MS-based workflows for R-methylated site identification suffer from limitations at the bioinformatic analysis level. Indeed, the computational identification of methyl-peptides is prone to high False Discovery Rates (FDR), because this PTM is isobaric to various amino acid substitutions (e.g., glycine into alanine) and chemical modification, such as methyl-esterification of aspartate and glutamate9. Hence, methods based on the isotope labeling of methyl groups, such as Heavy Methyl Stable Isotope Labeling with Amino Acids in Cell culture (hmSILAC), have been implemented as orthogonal strategies for confident MS-identification of in vivo methylations, significantly reducing the rate of false positive annotations10.
Recently, various proteome-wide protocols to study R-methylated proteins have been optimized. The development of antibody-based strategies for the immuno-affinity enrichment of R-methyl-peptides has led to the annotation of several hundreds of R-methylated sites in human cells11,12. Furthermore, many studies3,13 reported that coupling antibody-based enrichment with peptide separation techniques such as HpH-RP chromatography fractionation can boost the overall number of methyl-peptides identified.
This article describes an experimental strategy designed for the systematic and high-confidence identification of R-methylated sites in human cells, based on various biochemical and analytical steps: protein extraction from hmSILAC-labeled cells, parallel double enzymatic digestion with Trypsin and LysargiNase proteases, followed by HpH-RP chromatographic fractionation of digested peptides, coupled with antibody-based immuno-affinity enrichment of MMA-, SDMA-, and ADMA-containing peptides. All affinity-enriched peptides are then analyzed by high-resolution Liquid Chromatography (LC)-MS/MS in DDA mode, and raw MS data are processed by MaxQuant algorithm for identificationof R-methyl-peptides. Finally, the MaxQuant output results are processed with hmSEEKER, an in-house developed bioinformatics tool to search pairs of heavy and light methyl-peptides. Briefly, hmSEEKER reads and filters methyl-peptides identifications from the msms file, then matches each methyl-peptide to its corresponding MS1 peak in the allPeptides file, and, finally, searches the peak of the heavy/light peptide counterpart. For each putative heavy-light pair, the Log2 H/L ratio (LogRatio), Retention Time difference (dRT), and Mass Error (ME) parameters are calculated, and doublets that are located within user-defined cut-offs are labeled as true positives. The workflow of the biochemical protocol is described in Figure 1.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Ammonium Bicarbonate (AMBIC)</td>
			<td>Sigma-Aldrich</td>
			<td>09830</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium Persulfate (APS)</td>
			<td>Sigma-Aldrich</td>
			<td>497363</td>
			<td></td>
		</tr>
		<tr>
			<td>C18 Sep-Pak columns vacc 6cc (1g)</td>
			<td>Waters</td>
			<td>WAT036905</td>
			<td></td>
		</tr>
		<tr>
			<td>Colloidal Coomassie staining Instant</td>
			<td>Sigma-Aldrich</td>
			<td>ISB1L-1L</td>
			<td></td>
		</tr>
		<tr>
			<td>cOmplete Mini, EDTA-free</td>
			<td>Roche-Sigma Aldrich</td>
			<td>11836170001</td>
			<td>Protease Inhibitor</td>
		</tr>
		<tr>
			<td>Dialyzed Fetal Bovine Serum (FBS)</td>
			<td>GIBCO ThermoFisher</td>
			<td>26400-044</td>
			<td></td>
		</tr>
		<tr>
			<td>DL-Dithiothreitol (DTT)</td>
			<td>Sigma-Aldrich</td>
			<td>3483-12-3</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM Medium</td>
			<td>GIBCO ThermoFisher</td>
			<td>requested</td>
			<td>&#160;with stabile glutamine and without methionine</td>
		</tr>
		<tr>
			<td>EASY-nano LC 1200 chromatography system</td>
			<td>ThermoFisher</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>EASY-Spray HPLC Columns</td>
			<td>ThermoFisher</td>
			<td>ES907</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerolo</td>
			<td>Sigma-Aldrich</td>
			<td>G5516</td>
			<td></td>
		</tr>
		<tr>
			<td>HeLa cells</td>
			<td>ATCC</td>
			<td>ATCC CCL-2</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Sigma-Aldrich</td>
			<td>H3375</td>
			<td></td>
		</tr>
		<tr>
			<td>Iodoacetamide (IAA)</td>
			<td>Sigma-Aldrich</td>
			<td>144-48-9</td>
			<td></td>
		</tr>
		<tr>
			<td>Jupiter C12-RP column</td>
			<td>Phenomenex</td>
			<td>00G-4396-E0</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Methionine</td>
			<td>Sigma-Aldrich</td>
			<td>M5308</td>
			<td>Light (L) Methionine</td>
		</tr>
		<tr>
			<td>L-Methionine-(methyl-13C,d3)</td>
			<td>Sigma-Aldrich</td>
			<td>299154</td>
			<td>Heavy (H) Methionine</td>
		</tr>
		<tr>
			<td>LysargiNase</td>
			<td>Merck Millipore</td>
			<td>EMS0008</td>
			<td></td>
		</tr>
		<tr>
			<td>Microtip Cell Disruptor Sonifier 250</td>
			<td>Branson</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>N,N,N&#8242;,N&#8242;-Tetramethylethylenediamine (TEMED)</td>
			<td>Sigma-Aldrich</td>
			<td>T9281</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>GIBCO ThermoFisher</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>PhosSTOP</td>
			<td>Roche-Sigma Aldrich</td>
			<td>4906837001</td>
			<td>Phosphatase Inhibitor</td>
		</tr>
		<tr>
			<td>Pierce C18 Tips</td>
			<td>ThermoFisher</td>
			<td>87782</td>
			<td></td>
		</tr>
		<tr>
			<td>Pierce&#160; 0.1% Formic Acid (v/v) in Acetonitrile, LC-MS Grade</td>
			<td>ThermoFisher</td>
			<td>85175</td>
			<td>LC-MS Solvent B</td>
		</tr>
		<tr>
			<td>Pierce&#160; 0.1% Formic Acid (v/v) in Water, LC-MS Grade</td>
			<td>ThermoFisher</td>
			<td>85170</td>
			<td>LC-MS Solvent A</td>
		</tr>
		<tr>
			<td>Pierce&#160; Acetonitrile (ACN), LC-MS Grade</td>
			<td>ThermoFisher</td>
			<td>51101</td>
			<td></td>
		</tr>
		<tr>
			<td>Pierce&#160; Water, LC-MS Grade</td>
			<td>ThermoFisher</td>
			<td>51140</td>
			<td></td>
		</tr>
		<tr>
			<td>Polyacrylamide</td>
			<td>Sigma-Aldrich</td>
			<td>92560</td>
			<td></td>
		</tr>
		<tr>
			<td>Precision Plus Protein&#160; All Blue Prestained Protein Standards</td>
			<td>Bio-Rad</td>
			<td>1610373</td>
			<td></td>
		</tr>
		<tr>
			<td>PTMScan antibodies &#945;-ADMA</td>
			<td>Cell Signaling Technology</td>
			<td>13474</td>
			<td></td>
		</tr>
		<tr>
			<td>PTMScan antibodies &#945;-MMA</td>
			<td>Cell Signaling Technology</td>
			<td>12235</td>
			<td></td>
		</tr>
		<tr>
			<td>PTMScan antibodies &#945;-SDMA</td>
			<td>Cell Signaling Technology</td>
			<td>13563</td>
			<td></td>
		</tr>
		<tr>
			<td>Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer</td>
			<td>ThermoFisher</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sequencing Grade Modified Trypsin</td>
			<td>Promega</td>
			<td>V5113</td>
			<td></td>
		</tr>
		<tr>
			<td>Trifluoroacetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>T6508</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultimate 3000 HPLC</td>
			<td>Dionex</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Urea</td>
			<td>Sigma-Aldrich</td>
			<td>U5378</td>
			<td></td>
		</tr>
		<tr>
			<td>Vacuum Concentrator 5301</td>
			<td>Eppendorf</td>
			<td></td>
			<td>Speed vac</td>
		</tr>
	</tbody>
</table>

a mass spectrometry-based proteomics approach for global and high-confidence protein r-methylation analysis

Protein Arginine (R)-methylation is a widespread protein post-translational modification (PTM) involved in the regulation of several cellular pathways, including RNA processing, signal transduction, DNA damage response, miRNA biogenesis, and translation.
In recent years, thanks to biochemical and analytical developments, mass spectrometry (MS)-based proteomics has emerged as the most effective strategy to characterize the cellular methyl-proteome with single-site resolution. However, identifying and profiling in vivo protein R-methylation by MS remains challenging and error-prone, mainly due to the substoichiometric nature of this modification and the presence of various amino acid substitutions and chemical methyl-esterification of acidic residues that are isobaric to methylation. Thus, enrichment methods to enhance the identification of R-methyl-peptides and orthogonal validation strategies to reduce False Discovery Rates (FDR) in methyl-proteomics studies are required.
Here, a protocol specifically designed for high-confidence R-methyl-peptides identification and quantitation from cellular samples is described, which couples metabolic labeling of cells with heavy isotope-encoded Methionine (hmSILAC) and dual protease in-solution digestion of whole cell extract, followed by off-line High-pH Reversed Phase (HpH-RP) chromatography fractionation and affinity enrichment of R-methyl-peptides using anti-pan-R-methyl antibodies. Upon high-resolution MS analysis, raw data are first processed with the MaxQuant software package and the results are then analyzed by hmSEEKER, a software designed for the in-depth search of MS peak pairs corresponding to light and heavy methyl-peptide within the MaxQuant output files.

The article describes a workflow for the high-confidence identification of global protein R-methylation, which is based on the combination of the enzymatic digestion of the protein extract with two distinct proteases in parallel, followed by HpH-RP liquid chromatography fractionation of proteolytic peptides and immuno-affinity enrichment of R-methyl-peptides with anti-pan-R-methyl antibodies (Figure 1).
The cells were grown in the presence of Methionine, either na...

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A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis

Protein Arginine (R)-methylation is a wide-spread post-translational modification regulating multiple biological pathways. Mass spectrometry is the best technology to globally profile the R-methyl-proteome, when coupled to biochemical approaches for modified peptide enrichment. The workflow designed for the high confidence identification of global R-methylation in human cells is described here.

Protein Arginine (R)-methylation is a widespread protein post-translational modification (PTM) involved in the regulation of several cellular pathways, ...

This protocol is highly significant because it represents the state-of-the-art workflow for the global analysis of protein arginine methylation by mass spectrometry. This is the only method to identify and profile R-methylated protein with a single style resolution which is not achievable with other biochemical techniques. When coupled with the use of PRMT inhibitors, several of which are in clinical trials and anti-cancer drugs, this protocol allows for in-depth analysis of their mechanism of action.To begin, perform reduction of the thiol group of proteins using a stock solution of DTT dissolved in ultrapure water at a final concentration of 4.5 millimolar and let the reaction go for 30 minutes at 55 degrees Celsius. Perform alkylation of the thiol group of proteins by adding iodoacetamide at a concentration of 10 millimolar and incubating for 15 minutes at room temperature in the dark. To verify the proteolysis efficiency, save an aliquot of protein extract for subsequent analysis on SDS-PAGE Coomassie-stained gel and compare it with a corresponding amount of sample upon digestion.Dilute the remaining protein extract with four volumes of 20 millimolar HEPES at pH 8.0 to reach a final urea concentration of two molar. Split the sample into two parts, then add sequencing grade modified trypsin to one and LysargiNase protease to the other. Leave the samples overnight at 37 degrees Celsius in a ThermoMixer at 600 rotations per minute to allow for enzymatic digestion.For each chromatographic gradient, collect all fractions into a deep 96-well plate. Pool the fractions collected before the start of the gradient into one single fraction named pre. Concatenate the 60 fractions from the high pH reversed phase liquid chromatographic gradient by pooling them in a non-contiguous way into 14 final fractions.To obtain non-contiguous concatenation, pool the high pH reversed phase fractions as described in the text manuscript. Pool the fractions collected after the gradient into a unique fraction named post. Perform sequential immuno-affinity enrichment of the modified peptide separately for the two samples from trypsin and LysargiNase digestions.Dilute the 10X concentrated immuno-affinity purification or IAP buffer 10 times. Centrifuge the lyophilized peptides at 2, 000 G for five minutes to spin down the peptides to the bottom of the tube. Resuspend the peptides with 250 microliters of diluted IAP buffer per 15 milliliter tube and transfer to a 1.5 milliliter low binding tube.Use a litmus paper to check that the pH is greater than six. Keep a small aliquot of each fraction as input for the subsequent MS analysis. Split each fraction in two parts to perform the immuno enrichment of asymmetrically dimethylated, or ADMA, and symmetrically dimethylated, or SDMA, peptides in parallel.Prepare three vials of the selected anti-pan R-methylated antibodies conjugated to protein A agarose beads per 10 milligrams of the initial protein extract. Prepare the correct amount of antibody conjugated to agarose beads by centrifuging each vial at 2, 000 G for 30 seconds and removing the buffer from the beads. Wash the beads three times with one milliliter of 1X PBS by centrifuging them at 2, 000 G for 30 seconds.After the last wash, resuspend the beads in 40 microliters 1X PBS for each vial, pool them and then finally divide them equally into 16 fractions. Add 250 microliters of 1X IAP buffer to each tube and mix by inverting. Then incubate the tubes on a rotating wheel for two hours at four degrees Celsius.After the incubation, centrifuge the 1.5 milliliter tubes containing peptides and pan R-methyl antibody conjugated beads at 2, 000 G for 30 seconds to pellet the beads and transfer the flowthrough from each fraction into a clean 1.5 milliliter low binding tube. Add the beads to the flowthrough conjugated to antibodies against R-mono methylation and repeat the resuspension into PBS, incubation with IAP buffer, and centrifugation. During the incubation of the peptide samples with mono-methylization or MMA beads, wash the fractions that were previously immunoprecipitated with anti-ADMA and SDMA with 250 microliters IAP buffer twice and discard the supernatant after each wash.Then wash with LC-MS grade water three times. Elute the affinity enriched SDMA or ADMA peptides from the agarose beads by adding 50 microliters of 0.15 TFA to each tube. Leave this solution for 10 minutes at room temperature, inverting the tubes every two to three minutes.Transfer the first elution into clean 1.5 milliliter low binding tubes and repeat the elution with 50 microliters of 0.15 TFA. Pool the two elution fractions into one tube. Repeat this process for the R-mono-methylated peptides that were incubated with the anti-MMA antibody beads.After mixing the light and heavy labeled cells, proteins were extracted and subjected to digestion by trypsin and LysargiNase. An SDS-PAGE Coomassie-stained gel was used to verify the efficient enzymatic digestion of total proteins in peptides. The efficiency of the purification step performed by C18 Sep-Pak column was evaluated, confirming the absence of peptides in the flowthrough of the C18 column and in the first and second wash as well as their expected presence in the eluent.Proper MET4 incorporation in the heavy channel and correct heavy or light mixing were evaluated. The chromatogram from the offline high pH reversed phase liquid chromatography fractionation of peptides and the subsequent non-contiguous concatenation of fractions are shown here. Peptides were detected by 250 nanometer UV, while potentially remaining undigested proteins were evaluated by 280 nanometer UV.The full MS spectra of peptides representing true positive methyl peptide annotation were obtained.The M over Z differences observed between the three peaks are consistent with the presence of enzymatically methylated residue. The full MS spectra of peptides representing false positive methyl peptide annotation were obtained. The M over Z differences observed between the light methylated peptide and its punitive heavy counterpart deviates from the expected value by 0.0312.The protocol workflow is overall linear, but there are a few steps that needs special attention. For instance, the IPH chromatography separation with non-contiguous fraction concatenation, as well the IP setup. The same protocol can be coupled to either standard SILAC or label-free quantification to profile arginine methylation dynamics in response to a variety of perturbation.This protocol paves the way to the characterization of the extent and dynamics of protein methylation in several cell types and model systems supporting all aspect of basic and translational research focused on PRMTs.

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