This work was supported by American Cancer Society Institutional Research Grant IRG-14-195-01 (M. Sharon Stack is Principal Investigator; X.L. is a subrecipient investigator). This publication was made possible with partial support from Grant Numbers KL2 TR002530 and UL1 TR002529 (A. Shekhar, PI) from the National Institutes of Health, National Center for Advancing Translational Sciences, Clinical and Translational Sciences Award. X. L. is a recipient of Indiana CTSI KL2 Young Investigator Award. S. F. is supported by Walther Cancer Foundation Advancing Basic Cancer grants. X. W. is supported by the National Natural Science Foundation of China General Program (Grant No. 817773047).

1. Nitration of Angiotensin II
<ol>
	<li>To generate nitrated peptide, dilute 10 &#956;L of Angiotensin II (DRVYIHPF) parent solution (2 mM in water) in 390 &#956;L PBS solution (10 mM NaH2PO4, 150 mM NaCl, pH 7.4) at the final concentration of 50 &#956;M.</li>
	<li>Add 10 &#956;L of peroxynitrite (200 mM in 4.7% NaOH) to the Angiotensin II solution to make the final concentration of peroxynitrite 5 mM. 
	NOTE: Peroxynitrite is unstable and easy to resolve when it is in acid form, so parent solution of peroxynitrite is kept in basic solution and stored in -80 &#176;C.</li>
	<li>Adjust the pH value of the solution to 7-8 by 1 M HCl. To initiate the nitration reaction, shake the tube at 400 rpm for 5 min.</li>
	<li>Use a commercially available reverse phase SPE column (see Table of Materials) for the desalting.
	<ol>
		<li>Prepare 2 solutions for the desalting, 5% methanol in water for the washing and 80% methanol in water for the elution.</li>
		<li>Add 500 &#956;L of methanol, followed by 500 &#956;L of water to pre-condition the column, put 1 mL pipettor with the tip on the top of the column, press the pipettor to accelerate the flow.</li>
		<li>Load 410 &#956;L of the sample in step 1.3 on the column, discard the flow through.</li>
		<li>After washing with 500 &#956;L of 5% methanol, use 300 &#956;L of 80% methanol to elute the nitropeptide, which is then fully dried by speed-vac in the default setting at room temperature. 
		NOTE: Desalting is very important for the reactions, since the solvent left in the previous step may have a negative effect on the next steps.</li>
	</ol>
	</li>
</ol>
2. Alkylation of primary amines by dimethyl labeling
<ol>
	<li>Reconstitute the powdered nitro-Angiotensin II in 100 &#956;L of 100 mM triethylammonium bicarbonate (TEAB) solution. 
	NOTE: The pH value of the solution should be between 7 and 9, and make sure no primary amine is added in the solution.</li>
	<li>Add 4 &#956;L of 4% formaldehyde to the solution, mix briefly. 
	CAUTION: Formaldehyde vapors are toxic; perform the experiments in a fume hood.</li>
	<li>Add 4 &#956;L of 0.6 M NaBH3CN to the solution, shake the tube at 400 rpm for 1 h at room temperature.</li>
	<li>Quench the labeling reaction by adding 16 &#956;L of 1% ammonia solution, incubate at room temperature for 5 min.</li>
	<li>Add 8 &#956;L of formic acid to acidify the solution and perform desalting using reverse phase SPE column as described in step 1.4.</li>
</ol>
3. Reduction of nitrotyrosine to aminotyrosine
<ol>
	<li>Reconstitute the dimethyl labeled nitro-Angiotensin II in 500 &#956;L of PBS (10 mM NaH2PO4, 150 mM NaCl, pH 7.4).</li>
	<li>Add 10 &#956;L of 1 M sodium dithionate to the solution and incubate at room temperature for 1 h. After the reduction reaction, the yellow color of the solution becomes clear. 
	NOTE: Weigh 174.1 mg sodium dithionate and dissolve it in water to make the final volume is 1 mL. This solution can be stored at -20 &#176;C no longer than a week.</li>
	<li>Use the reverse phase SPE column for the desalting as described in step 1.4.</li>
</ol>
4. Biotinylation, enrichment, and detection
<ol>
	<li>Reconstitute the dimethyl labeled amino Angiotensin II in 500 &#956;L of PBS (10 mM NaH2PO4, 150 mM NaCl, pH 7.4).</li>
	<li>Add 5 &#956;L of 40 nM NHS-S-S-biotin, dissolved in DMSO, to the solution, after 2 h incubation at room temperature, use 1 &#956;L of 5% hydroxylamine to quench the reaction.</li>
	<li>In the meantime, equilibrate streptavidin agarose beads by adding 500 &#956;L of PBS (10 mM NaH2PO4, 150 mM NaCl, pH 7.4), centrifuging at 580 x g for 5 min at room temperature and discarding the supernatant. Perform the equilibration 3 times.</li>
	<li>Add 100 &#956;L streptavidin agarose beads to the reaction system, incubate 1 h on a rotary shaker at room temperature. Wash 4 times with PBS (10 mM NaH2PO4, 150 mM NaCl, pH 7.4). For each washing step, add 500 &#956;L of PBS to the beads, mix well, then centrifuge at 580 x g for 5 min at room temperature and discard the supernatant.</li>
	<li>Use 400 &#956;L of 10 mM dithiothreitol (DTT) to incubate with agarose beads at 50 &#176;C for 45 min, spin down at 580 x g for 5 min at room temperature and discard the beads, add 20 &#956;L of 0.5 M idoacetamide (IAM) to the supernatant for 20 min in darkness. 
	NOTE: DTT is used to break the disulfide bond between the link of biotin and peptide, the latter is released from beads and further alkylated by IAM.</li>
	<li>Use reverse phase SPE column for the desalting shown in step 1.4.</li>
	<li>After resolving the dry peptides in 20 &#956;L of 0.1% formic acid (FA), subject the product of each section to liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis.
	<ol>
		<li>Separate the modified Ang II peptides by a 60 min gradient elution (0-8 min, 2% B; 8-10 min, 5% B; 10-35 min, 18% B; 35-50 min, 28% B; 50-52 min, 80% B; 52-58 min, 80% B; 58-59 min, 2% B; 59-60 min, 2% B) at a flow rate 0.300 &#956;l/min with nano-HPLC system which is directly interfaced with the high resolution mass spectrometer. 
		NOTE: The analytical column is in 75 &#956;m ID, 150 mm length, packed with C-18 resin. Mobile phase A consisted of 0.1% formic acid, and mobile phase B consisted of 100% acetonitrile and 0.1% formic acid.</li>
		<li>Operate the mass spectrometer in the data-dependent acquisition mode, set a single full-scan mass spectrum (300-1800 m/z, 60 000 resolution) followed by 20 data-dependent MS/MS scans at 28% normalized collision energy.</li>
		<li>Open mass spectra data and identify the peaks of the product in each step to confirm the chemical reaction has been successfully performed.</li>
	</ol>
	</li>
</ol>
5. Quantification of nitropeptide
<ol>
	<li>Prepare 3 sets of nitro-Angiotensin II solutions from step 1.4, each set containing 2 concentrations of nitro-Angiotensin II: Set #1, 20 nmol in tube A and 20 nmol in tube B, each in 100 &#956;l TEAB solution; Set #2, 10 nmol in tube C and 20 nmol in tube D, each in 100 &#956;l TEAB solution; Set #3, 40 nmol in tube E and 10 nmol in tube F, each in 100 &#956;l TEAB solution. 
	Note: The two concentrations of nitro-Angiotensin II in each set are used for dimethyl labeling, to react with formaldehyde (light) and formaldehyde-D2 (heavy), respectively.</li>
	<li>For each set, add 4 &#956;L of 4% formaldehyde and formaldehyde-D2 to the sample to be labeled as light and heavy, respectively. Follow the steps 2.3 to 2.5 to finish dimethyl labeling.</li>
	<li>Mix the light and heavy labeled samples.</li>
	<li>Follow the steps from 3.1 to 4.6 for the reduction, biotinylation, enrichment, and detection.</li>
</ol>

<ol>
	<li>Radi, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nitric+oxide,+oxidants,+and+protein+tyrosine+nitration.">Nitric oxide, oxidants, and protein tyrosine nitration.</a> Proceedings of the National Academy of Sciences of the United States of America. 101, 4003-4008 (2004).</li><li>Radi, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+tyrosine+nitration:+biochemical+mechanisms+and+structural+basis+of+functional+effects.">Protein tyrosine nitration: biochemical mechanisms and structural basis of functional effects.</a> Accounts of Chemical Research. 46, 550-559 (2013).</li><li>Zhan, X., Desiderio, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MALDI-induced+fragmentation+of+leucine+enkephalin,+nitro-Tyr-leucine+enkaphalin,+and+d5-Phe-nitro-Tyr-leucine+enkephalin.">MALDI-induced fragmentation of leucine enkephalin, nitro-Tyr-leucine enkaphalin, and d5-Phe-nitro-Tyr-leucine enkephalin.</a> Int. J Mass Spectrometry. 287, 77-86 (2009).</li><li>Batthy&#225;ny, 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=Tyrosine-Nitrated+Proteins:+Proteomic+and+Bioanalytical+Aspects.">Tyrosine-Nitrated Proteins: Proteomic and Bioanalytical Aspects.</a> Antioxidants &amp; Redox Signaling. 26, 313-328 (2017).</li><li>Feeney, M. B., Sch&#246;neich, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomic+approaches+to+analyze+protein+tyrosine+nitration.">Proteomic approaches to analyze protein tyrosine nitration.</a> Antioxidants &amp; Redox Signaling. 19, 1247-1256 (2013).</li><li>Zhan, X., Desiderio, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nitroproteins+from+a+human+pituitary+adenoma+tissue+discovered+with+a+nitrotyrosine+affinity+column+and+tandem+mass+spectrometry.">Nitroproteins from a human pituitary adenoma tissue discovered with a nitrotyrosine affinity column and tandem mass spectrometry.</a> Analytical Biochemistry. 354, 279-289 (2006).</li><li>Zhan, X., Wang, X., Desiderio, D. 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S., Bischoff, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemical+labeling+and+enrichment+of+nitrotyrosine-containing+peptides.">Chemical labeling and enrichment of nitrotyrosine-containing peptides.</a> Talanta. 80, 1503-1512 (2010).</li><li>Chiappetta, G., 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+identification+of+protein+nitration+sites.">Quantitative identification of protein nitration sites.</a> Proteomics. 9, 1524-1537 (2009).</li><li>Dekker, F., Abello, N., Wisastra, R., Bischoff, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enrichment+and+detection+of+tyrosine-nitrated+proteins.">Enrichment and detection of tyrosine-nitrated proteins.</a> Current Protocols in Protein Science. , (2012).</li><li>Zhang, Q., 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+selective+enrichment+and+analysis+of+nitrotyrosine-containing+peptides+in+complex+proteome+samples.">A method for selective enrichment and analysis of nitrotyrosine-containing peptides in complex proteome samples.</a> Journal of Proteome Research. 6, 2257-2268 (2007).</li><li>Feng, 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=Myeloid-derived+suppressor+cells+inhibit+T+cell+activation+through+nitrating+LCK+in+mouse+cancers.">Myeloid-derived suppressor cells inhibit T cell activation through nitrating LCK in mouse cancers.</a> Proceedings of the National Academy of Sciences of the United States of America. 115, 10094-10099 (2018).</li><li>Boersema, P. 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The authors have nothing to disclose.

The protocol here describes the nitropeptide enrichment and profiling. Using Angiotensin II as the model peptide, we illustrated the procedure shown in Figure 1. After obtaining the nitro-Angiotensin II, the primary amine on the peptide should be blocked to avoid the further amine conjugation, which is one of the most critical steps within the protocol. In the current protocol, dimethyl labeling is used to block the primary amines for two reasons: first, it enables the acquisition of quantit...

Nitration of tyrosine residues in proteins to form 3-nitrotyrosine regulates many biological processes. Due to the different chemical properties between tyrosine and 3-nitrotyrosine, a nitrated protein may have perturbed signaling activity1,2. Therefore, it is important to develop methods that can enrich and identify nitration sites on proteins efficiently. As 3-nitrotyrosine is a low abundance modification on proteins compared to other forms of PTM, such as phosphorylation and acetylation, it is challenging to identify endogenous nitration sites directly from cell lines or tissue samples. Nevertheless, the methodology of using mass spectrometry (MS) to characterize the fragmentation pattern of nitrotpeptide has been developed (for example, Zhan &#38; Desiderio3), which lays the foundation for new methods of nitroproteomics.&#160;
Currently, an enrichment step followed by MS is the most powerful strategy for nitropeptide profiling4,5. The enrichment methods can be classified into two classes. One class is based on antibodies that can recognize 3-nitrotyrosine specifically, whereas the other class is based on the chemical derivation that reduces a nitro group to an amine group4,5. For the antibody-based method, nitrotyrosine affinity column is used for the enrichment, from which the eluted material is further resolved and analyzed by high resolution MS6,7. For the chemical derivation-based method, the amine groups at the N-terminus of the peptide or lysine should be blocked in the first step either by acetylation, isobaric tags for relative and absolute quantitation (iTRAQ), or tandem mass tags (TMT) reagents. Next, a reducer is used to reduce nitrotyrosine to aminotyrosine followed by modifying the newly formed amine group, which includes biotin ligation, sulphydryl peptide conversion, or other types of tagging systems8,9,10,11. Most of the protocols established so far are based on in vitro over-nitrated proteins, instead of endogenously nitrated proteins.
In the present study, a modified procedure of the chemical derivation of nitrotyrosine is developed for the nitropeptide enrichment and identification, which shows enhanced sensitivity during MS detection and is suitable for quantification purpose. Our recent study employing this method in biological systems identified that nitration of lymphocyte-specific protein tyrosine kinase (LCK) at Tyr394 by RNS produced from myeloid-derived suppressor cells (MDSCs) plays an important role in the immunosuppression of the tumor microenvironment12. Therefore, our method of nitropeptide identification can be applied to complex biological samples as well. Here, we describe our protocol by using the model peptide Angiotensin II, of which the fragmentation pattern is known and widely used in nitroproteomic studies8,9,10,11, as an example.

<table border="0" cellpadding="0" cellspacing="0" style="width:756px;" width="756">
	<tbody>
		<tr height="20">
			<td height="20">Acclaim pepmap 100 C18 column</td>
			<td style="width:197px;">Thermo-Fisher</td>
			<td style="width:119px;">164534</td>
			<td style="width:195px;"></td>
		</tr>
		<tr height="20">
			<td height="20">1 M TEAB solution</td>
			<td>Sigma-Aldrich</td>
			<td>T7408</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20">50% hydroxylamine</td>
			<td>Thermo-Fisher</td>
			<td>90115</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20">Acetonitrile</td>
			<td>Thermo-Fisher</td>
			<td>A955</td>
			<td>MS Grade</td>
		</tr>
		<tr height="20">
			<td height="20">dithiothreitol</td>
			<td>Sigma-Aldrich</td>
			<td>43819</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20">formaldehyde</td>
			<td>Sigma-Aldrich</td>
			<td>F8775</td>
			<td>Molecular Biology Grade</td>
		</tr>
		<tr height="22">
			<td height="22">formaldehyde-D2</td>
			<td>Toronto Research Chemicals</td>
			<td>F691353</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22">formic acid</td>
			<td>Sigma-Aldrich</td>
			<td>695076</td>
			<td>ACS reagent</td>
		</tr>
		<tr height="22">
			<td height="22">Fusion Lumos mass spectrometer</td>
			<td>Thermo</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20">isoacetamide</td>
			<td>Sigma-Aldrich</td>
			<td>I1149</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20">Methanol</td>
			<td>Thermo-Fisher</td>
			<td>A456</td>
			<td>MS Grade</td>
		</tr>
		<tr height="20">
			<td height="20">NHS-S-S-bition</td>
			<td>Thermo-Fisher</td>
			<td>21441</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20">Oasis HLB column (10 mg)</td>
			<td>Waters</td>
			<td>186000383</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20">peroxynitrite</td>
			<td>Merck-Millipore</td>
			<td>516620</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20">sodium cyanoborohydrite</td>
			<td>Sigma-Aldrich</td>
			<td>42077</td>
			<td>PhamaGrade</td>
		</tr>
		<tr height="20">
			<td height="20">sodium dithionate</td>
			<td>Sigma-Aldrich</td>
			<td>157953</td>
			<td>Technical Grade</td>
		</tr>
		<tr height="20">
			<td height="20">Streptavidin Sepharose</td>
			<td>GE Healcare</td>
			<td>GE17-5113-01</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20">Ultimate 3000 nanoLC</td>
			<td>Thermo</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

nitropeptide profiling and identification illustrated by angiotensin ii

Protein nitration is one of the most important post-translational modifications (PTM) on tyrosine residues and it can be induced by chemical actions of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in eukaryotic cells. Precise identification of nitration sites on proteins is crucial for understanding the physiological and pathological processes related to protein nitration, such as inflammation, aging, and cancer. Since the nitrated proteins are of low abundance in cells even under induced conditions, no universal and efficient methods have been developed for the profiling and identification of protein nitration sites. Here we describe a protocol for nitropeptide enrichment by using a chemical reduction reaction and biotin labeling, followed by high resolution mass spectrometry. In our method, nitropeptide derivatives can be identified with high accuracy. Our method exhibits two advantages compared to the previously reported methods. First, dimethyl labeling is used to block the primary amine on nitropeptides, which can be used to generate quantitative results. Second, a disulfide bond containing NHS-biotin reagent is used for the enrichment, which can be further reduced and alkylated to enhance the detection signal on a mass spectrometer. This protocol has been successfully applied to the model peptide Angiotensin II in the current paper.

The flowchart for nitropeptide profiling in this manuscript is shown in Figure 1. Figure 2, 3, 4 and 5 show the mass spectra of Angiotensin II, nitro-Angiotensin II, dimethyl labeled nitro-Angiotensin II and dimethyl labeled amino Angiotensin II, respectively. The molecular weight of the compound can be reflected by the m/z values of the mono-isotope peak in each figure, indicating the chemical modification on A...

Watch this Scientific Journal Video about Nitropeptide Profiling and Identification Illustrated by Angiotensin II at JoVE.com

Nitropeptide Profiling and Identification Illustrated by Angiotensin II

Proteomic profiling of tyrosine-nitrated proteins has been a challenging technique due to the low abundance of the 3-nitrotyrosine modification. Here we describe a novel approach for nitropeptide enrichment and profiling by using Angiotensin II as the model. This method can be extended for other in vitro or in vivo systems.

Protein nitration is one of the most important post-translational modifications (PTM) on tyrosine residues and it can be induced by chemical actions of ...

nitropeptide-profiling-identification-illustrated-angiotensin

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Biochemistry

5.6K Views.  Westlake University. Proteomic profiling of tyrosine-nitrated proteins has been a challenging technique due to the low abundance of the 3-nitrotyrosine modification. Here we describe a novel approach for nitropeptide enrichment and profiling by using Angiotensin II as the model. This method can be extended for other in vitro or in vivo systems.

Video: Nitropeptide Profiling and Identification Illustrated by Angiotensin II

Identification of Small Molecule-binding Proteins in a Native Cellular Environment by Live-cell Photoaffinity Labeling

Identifying the molecular target(s) of small molecules is a challenging but necessary step towards understanding their mechanism of action. While several target identification methods have been developed and used to successfully elucidate the binding proteins of a variety of small molecules, these techniques have drawbacks that make them unsuitable for detecting certain types of small molecule-target interactions. In particular, non-covalent interactions that depend on native cellular conditions, such as those of membrane proteins whose structures may be perturbed upon cell lysis, are often not amenable to affinity-based target identification methods. Here, we demonstrate a method wherein a probe containing a photolabile group is used to covalently crosslink to the small molecule binding protein within the environment of the live cell, allowing the detection and isolation of the target protein without the need for maintenance of the interaction after cell lysis. This technique is a valuable tool for studying biologically interesting small molecules with unknown mechanisms, both in the context of basic biology as well as drug discovery.

We describe here a method for identification of small molecule-binding proteins using photoaffinity labeling. The advantage of this technique is that binding and covalent labeling of the target proteins occurs within the live cellular environment, removing the risk of disrupting native protein structure and binding conditions upon cell lysis.

Identifying the molecular target(s) of small molecules is a challenging but necessary step towards understanding their mechanism of action. While several ...

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological processes. Affinity purification coupled to mass spectrometry (AP-MS) has become the method of choice for identifying protein-protein interactions. However, conventional AP-MS studies provide information on protein interactions, but the organizational information is lost. To address this issue, we developed a strategy to unravel the distinct functional assemblies a protein might be involved in, by resolving affinity-purified protein complexes prior to their characterization by mass spectrometry. Protein complexes isolated through affinity purification of a bait protein using an epitope tag and competitive elution are separated through blue native electrophoresis. Comparison of protein migration profiles through correlation profiling using quantitative mass spectrometry allows assignment of interacting proteins to distinct molecular entities. This method is able to resolve protein complexes of close molecular weights that might not be resolved by traditional chromatographic techniques such as gel filtration. With little more work than conventional AP-geLC-MS/MS, we demonstrate this strategy may in many cases be adequate for obtaining protein complex topological information concomitantly to identifying protein interactions.

Here we present protocols for affinity purification of protein complexes and their separation by blue native PAGE, followed by protein correlation profiling using label free quantitative mass spectrometry. This method is useful to resolve interactomes into distinct protein complexes.

Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological ...

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particular technical progress in liquid chromatography (LC) coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep-proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an extensive LC/LC-MS/MS platform, and post-MS computational interference correction to accurately quantitate whole proteomes. This protocol includes the following main steps: protein extraction and digestion, TMT labeling, 2-dimensional (2D) LC, high-resolution mass spectrometry, and computational data processing. Quality control steps are included for troubleshooting and evaluating experimental variation. More than 10,000 proteins in mammalian samples can be confidently quantitated with this protocol. This protocol can also be applied to the quantitation of post translational modifications with minor changes. This multiplexed, robust method provides a powerful tool for proteomic analysis in a variety of complex samples, including cell culture, animal tissues, and human clinical specimens.

We present a protocol to accurately quantitate proteins with isobaric labelling, extensive fractionation, bioinformatics tools, and quality control steps in combination with liquid chromatography interfaced to a high-resolution mass spectrometer.

Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particular technical progress in liquid chromatography (LC) ...

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

Translation of mRNA into proteins is a complex process involving several layers of regulation. It is often assumed that changes in mRNA transcription reflect changes in protein synthesis, but many exceptions have been observed. Recently, a technique called ribosome profiling (or Ribo-Seq) has emerged as a powerful method that allows identification, with high accuracy, which regions of mRNA are translated into proteins and quantification of translation at the genome-wide level. Here, we present a generalized protocol for genome-wide quantification of translation using Ribo-Seq in budding yeast. In addition, combining Ribo-Seq data with mRNA abundance measurements allows us to simultaneously quantify translation efficiency of thousands of mRNA transcripts in the same sample and compare changes in these parameters in response to experimental manipulations or in different physiological states. We describe a detailed protocol for generation of ribosome footprints using nuclease digestion, isolation of intact ribosome-footprint complexes via sucrose gradient fractionation, and preparation of DNA libraries for deep sequencing along with appropriate quality controls necessary to ensure accurate analysis of in vivo translation.

Translational regulation plays an important role in the control of protein abundance. Here, we describe a high-throughput method for quantitative analysis of translation in the budding yeast Saccharomyces cerevisiae.

Translation of mRNA into proteins is a complex process involving several layers of regulation. It is often assumed that changes in mRNA transcription ...

Polysome Profiling in Leishmania, Human Cells and Mouse Testis

Proper protein expression at the right time and in the right amounts is the basis of normal cell function and survival in a fast-changing environment. For a long time, the gene expression studies were dominated by research on the transcriptional level. However, the steady-state levels of mRNAs do not correlate well with protein production, and the translatability of mRNAs varies greatly depending on the conditions. In some organisms, like the parasite Leishmania, the protein expression is regulated mostly at the translational level. Recent studies demonstrated that protein translation dysregulation is associated with cancer, metabolic, neurodegenerative and other human diseases. Polysome profiling is a powerful method to study protein translation regulation. It allows to measure the translational status of individual mRNAs or examine translation on a genome-wide scale. The basis of this technique is the separation of polysomes, ribosomes, their subunits and free mRNAs during centrifugation of a cytoplasmic lysate through a sucrose gradient. Here, we present a universal polysome profiling protocol used on three different models - parasite Leishmania major, cultured human cells and animal tissues. Leishmania cells freely grow in suspension and cultured human cells grow in adherent monolayer, while mouse testis represents an animal tissue sample. Thus, the technique is adapted to all of these sources. The protocol for the analysis of polysomal fractions includes detection of individual mRNA levels by RT-qPCR, proteins by Western blot and analysis of ribosomal RNAs by electrophoresis. The method can be further extended by examination of mRNAs association with the ribosome on a transcriptome level by deep RNA-seq and analysis of ribosome-associated proteins by mass spectroscopy of the fractions. The method can be easily adjusted to other biological models.

Polysome Profiling in Leishmania, Human Cells and Mouse Testis

The overall goal of polysome profiling technique is analysis of translational activity of individual mRNAs or transcriptome mRNAs during protein synthesis. The method is important for studies of protein synthesis regulation, translation activation and repression in health and multiple human diseases.

Proper protein expression at the right time and in the right amounts is the basis of normal cell function and survival in a fast-changing environment. For ...

Capture and Identification of RNA-binding Proteins by Using Click Chemistry-assisted RNA-interactome Capture (CARIC) Strategy

A comprehensive identification of RNA-binding proteins (RBPs) is key to understanding the posttranscriptional regulatory network in cells. A widely used strategy for RBP capture exploits the polyadenylation [poly(A)] of target RNAs, which mostly occurs on eukaryotic mature mRNAs, leaving most binding proteins of non-poly(A) RNAs unidentified. Here we describe the detailed procedures of a recently reported method termed click chemistry-assisted RNA-interactome capture (CARIC), which enables the transcriptome-wide capture of both poly(A) and non-poly(A) RBPs by combining the metabolic labeling of RNAs, in vivo UV cross-linking, and bioorthogonal tagging.

Capture and Identification of RNA-binding Proteins by Using Click Chemistry-assisted RNA-interactome Capture CARIC Strategy

A detailed protocol for applying the click chemistry-assisted RNA-interactome capture (CARIC) strategy to identify proteins binding to both coding and noncoding RNAs is presented.

A comprehensive identification of RNA-binding proteins (RBPs) is key to understanding the posttranscriptional regulatory network in cells. A widely used ...

Identification of Orexin and Endocannabinoid Receptors in Adult Zebrafish Using Immunoperoxidase and Immunofluorescence Methods

Immunohistochemistry (IHC) is a highly sensitive and specific technique involved in the detection of target antigens in tissue sections with labeled antibodies. It is a multistep process in which the optimization of each step is crucial to obtain the optimum specific signal. Through IHC, the distribution and localization of specific biomarkers can be detected, revealing information on evolutionary conservation. Moreover, IHC allows for the understanding of expression and distribution changes of biomarkers in pathological conditions, such as obesity. IHC, mainly the immunofluorescence technique, can be used in adult zebrafish to detect the organization and distribution of phylogenetically conserved molecules, but a standard IHC protocol is not estasblished. Orexin and endocannabinoid are two highly conserved systems involved in the control of food intake and obesity pathology. Reported here are protocols used to obtain information about orexin peptide (OXA), orexin receptor (OX-2R), and cannabinoid receptor (CB1R) localization and distribution in the gut and brain of normal and diet-induced obese (DIO) adult zebrafish models. Also described are methods for immunoperoxidase and double immunofluorescence, as well as preparation of reagents, fixation, paraffin-embedding, and cryoprotection of zebrafish tissue and preparation for an endogenous activity-blocking step and background counterstaining. The complete set of parameters is obtained from previous IHC experiments, through which we have shown how immunofluorescence can help with the understanding of OXs, OX-2R, and CB1R distribution, localization, and conservation of expression in adult zebrafish tissues. The resulting images with highly specific signal intensity led to the confirmation that zebrafish are suitable animal models for immunohistochemical studies of distribution, localization, and evolutionary conservation of specific biomarkers in physiological and pathological conditions. The protocols presented here are recommended for IHC experiments in adult zebrafish.

Presented here are protocols for immunohistochemical characterization and localization of orexin peptide, orexin receptors, and endocannabinoid receptors in the gut and brains of normal and diet-induced obesity (DIO) adult zebrafish models using immunoperixidase and double immunofluorescence methods.

Immunohistochemistry (IHC) is a highly sensitive and specific technique involved in the detection of target antigens in tissue sections with labeled ...

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

DNA primase synthesizes short RNA primers that initiate DNA synthesis of Okazaki fragments on the lagging strand by DNA polymerase during DNA replication. The binding of prokaryotic DnaG-like primases to DNA occurs at a specific trinucleotide recognition sequence. It is a pivotal step in the formation of Okazaki fragments. Conventional biochemical tools that are used to determine the DNA recognition sequence of DNA primase provide only limited information. Using a high-throughput microarray-based binding assay and consecutive biochemical analyses, it has been shown that 1) the specific binding context (flanking sequences of the recognition site) influences the binding strength of the DNA primase to its template DNA, and 2) stronger binding of primase to the DNA yields longer RNA primers, indicating higher processivity of the enzyme. This method combines PBM and primase activity assay and is designated as high-throughput primase profiling (HTPP), and it allows characterization of specific sequence recognition by DNA primase in unprecedented time and scalability.&#160;

Protein binding microarray (PBM) experiments combined with biochemical assays link the binding and catalytic properties of DNA primase, an enzyme that synthesizes RNA primers on template DNA. This method, designated as high-throughput primase profiling (HTPP), can be used to reveal DNA-binding patterns of a variety of enzymes.

DNA primase synthesizes short RNA primers that initiate DNA synthesis of Okazaki fragments on the lagging strand by DNA polymerase during DNA replication. ...

High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis

Proteins generally exert biological functions through interactions with other proteins, either in dynamic protein assemblies or as a part of stably formed complexes. The latter can be elegantly resolved according to molecular size using native polyacrylamide gel electrophoresis (BN-PAGE). Coupling of such separations to sensitive mass spectrometry (BN-MS) has been well-established and theoretically allows for exhaustive assessment of the extractable complexome in biological samples. However, this approach is rather laborious and provides limited complex size resolution and sensitivity. Also, its application has remained restricted to abundant mitochondrial and plastid proteins. Thus, for a majority of proteins, information regarding integration into stable protein complexes is still lacking. Presented here is an optimized approach for complexome profiling comprising preparative-scale BN-PAGE separation, sub-millimeter sampling of broad gel lanes by cryomicrotome slicing, and mass spectrometric analysis with label-free protein quantification. The procedures and tools for critical steps are described in detail. As an application, the report describes complexome analysis of a solubilized endosome-enriched membrane fraction from mouse kidneys, with 2,545 proteins profiled in total. The results demonstrate identification of uniform, low-abundance membrane proteins such as intracellular ion channels as well as high resolution, complex protein assembly patterns, including glycosylation isoforms. The results are in agreement with independent biochemical analyses. In summary, this methodology allows for comprehensive and unbiased identification of protein (super)complexes and their subunit composition, providing a basis for investigating stoichiometry, assembly, and interaction dynamics of protein complexes in any biological system.

A versatile cryoslicing BN-MS protocol using a microtome is presented for high-resolution complexome profiling.

Proteins generally exert biological functions through interactions with other proteins, either in dynamic protein assemblies or as a part of stably formed ...

Profiling Ubiquitin and Ubiquitin-like Dependent Post-translational Modifications and Identification of Significant Alterations

Ubiquitin (ub) and ubiquitin-like (ubl) dependent post-translational modifications of proteins play fundamental biological regulatory roles within the cell by controlling protein stability, activity, interactions, and intracellular localization. They enable the cell to respond to signals and to adapt to changes in its environment. Alterations within these mechanisms can lead to severe pathological situations such as neurodegenerative diseases and cancers. The aim of the technique described here is to establish ub/ubls dependent PTMs profiles, rapidly and accurately, from cultured cell lines. The comparison of different profiles obtained from different conditions allows the identification of specific alterations, such as those induced by a treatment for example. Lentiviral mediated cell transduction is performed to create stable cell lines expressing a two-tags (6His and Flag) version of the modifier (ubiquitin or a ubl such as SUMO1 or Nedd8). These tags permit the purification of ubiquitin and therefore of ubiquitinated proteins from the cells. This is done through a two-step purification process: The first one is performed in denaturing conditions using the 6His tag, and the second one in native conditions using the Flag tag. This leads to a highly specific and pure isolation of modified proteins which are subsequently identified and semi-quantified by liquid chromatography followed by tandem mass spectrometry (LC-MS/MS) technology. Easy informatics analysis of MS data using Excel software enables the establishment of PTM profiles by eliminating background signals. These profiles are compared between each condition in order to identify specific alterations which will then be studied more specifically, starting with their validation by standard biochemistry techniques.

This protocol aims at establishing ubiquitin (Ub) and ubiquitin-likes (Ubls) specific proteomes in order to identify alterations of these kind of post-translational modifications (PTMs), associated with a specific condition such as a treatment or a phenotype.

Ubiquitin (ub) and ubiquitin-like (ubl) dependent post-translational modifications of proteins play fundamental biological regulatory roles within the ...