We thank Pierre Thibault, Eric Bonneil, Jo&#235;l Lanoix, Caroline C&#244;t&#233; (Institute for Research in Immunology and Cancer, Universit&#233; de Montr&#233;al) and Anthony Purcell (Monash University) for their insightful comments. This work was supported by funding from the Fonds de recherche du Qu&#233;bec - Sant&#233; (FRQS), the Cole Foundation, CHU Sainte-Justine, and the Charles-Bruneau Foundations, Canada Foundation for Innovation, the National Sciences and Engineering Research Council (NSERC) (#RGPIN-2020-05232) and the Canadian Institutes of Health Research (CIHR) (#174924).

The protocol provided here was adapted from established protocols13,14,15,16,17,18,19,20. The overall procedure for the immunoaffinity purification (IP) of MHC class I and II peptides is illustrated in Figure 1. See Table of Materials for details about the cell lines and antibodies used.
1. Beads coupling with the antibodies (Day 1): Coupling antibodies to sepharose CNBr-activated beads
NOTE: Prepare fresh solutions for each new experiment. Refer to Table of Materials and Supplementary Table 1 for the list of reagents and solutions recipes. All the steps are carried out at room temperature (RT). When using a new antibody, check the binding efficiency by collecting key aliquots (see the indication OPTIONAL) and performing Coomassie blue staining SDS-PAGE (Figure 2).
<ol>
	<li>Activation of the sepharose CNBr beads
	<ol>
		<li>Weigh 80 mg of sepharose CNBr-activated beads per sample and transfer them to a 15 mL conical tube.</li>
		<li>To facilitate resuspension of dried beads, first, add 5 mL of 1 mM HCl and pipette up and down 5 times. Then, fill the conical tube with an additional 8.5 mL of 1 mM HCl.</li>
		<li>Rotate at 20 rpm (revolutions per minute) for 30 min at RT using a rotator device. Centrifuge the beads at 200 x g for 2 min at RT and remove the supernatant by aspiration.</li>
		<li>Add 500 &#181;L of coupling buffer to the beads pellet and transfer to a new 2.0 mL centrifuge tube and keep aside for step 1.2.2.</li>
	</ol>
	</li>
	<li>Coupling of antibodies to CNBr-activated beads
	<ol>
		<li>Prepare the antibody selected for the isolation of the MHC class I or II peptides in a new 2.0 mL microcentrifuge tube by adding 2 mg of the antibody (according to the concentration specified by the manufacturer). Complete the volume to 1 mL with the coupling buffer solution to get a final concentration of 2 mg/mL.</li>
		<li>Centrifuge the beads from step 1.1.4 at 200 x g for 2 min at RT and then remove the supernatant by aspiration.</li>
		<li>Add the antibody solution to the 2.0 mL microcentrifuge tube containing the activated beads.</li>
		<li>(OPTIONAL) Take an aliquot of 18 &#181;L (INPUT), add 6 &#181;L of 4x SDS-PAGE buffer, and freeze immediately.</li>
		<li>Rotate the microcentrifuge tube from step 1.2.3 at 20 rpm for 120 min using a rotator device. Centrifuge the beads at 200 x g for 2 min and then remove the supernatant.</li>
		<li>(OPTIONAL) Take an aliquot of 18 &#181;L of the supernatant (unbound antibody), add 6 &#181;L of 4x SDS-PAGE buffer and freeze immediately.</li>
	</ol>
	</li>
	<li>Blocking and washing of antibody coupled-beads
	<ol>
		<li>Add 1 mL of 0.2 M glycine to the microcentrifuge tube containing the antibody-coupled beads from step 1.2.5. Rotate at 20 rpm for 60 min at RT using a rotator device.</li>
		<li>Centrifuge the beads at 200 x g for 2 min, then remove the supernatant. Add 1 mL of PBS (Phosphate-buffered saline).</li>
		<li>Centrifuge the beads at 200 x g for 2 min, then remove the supernatant.</li>
		<li>(OPTIONAL) Take an aliquot of 18 &#181;L of the supernatant (unbound antibody, last wash), add 6 &#181;L of 4x SDS-PAGE buffer and freeze immediately.</li>
		<li>Add 1 mL of PBS to the beads in step 1.3.3.</li>
		<li>(OPTIONAL) Take an aliquot of 18 &#181;L of beads mixture (beads coupled with antibody), add 6 &#181;L of 4x SDS-PAGE buffer, and freeze immediately.</li>
		<li>Keep at 4 &#176;C until use the same day in step 2.5. 
		&#8203;NOTE: Beads can be prepared the day before the immunocapture, but longer storage has not been tested.</li>
	</ol>
	</li>
</ol>
2. Cell lysis and immunocapture with antibody coupled-beads (Day 1)
NOTE: The level of MHC molecules varies from one cell type to another, and the quantification of MHC/HLA molecules per cell is suggested21&#160;(Figure 4A). We recommend a minimum of 1 x 108 cells for each IP. This number of cells corresponds to 6-10 mg of protein from JY, EL4, and A20 cells solubilized with 0.5% Chaps buffer. To prepare cell pellets for IPs, cells should be harvested, centrifuged, and washed twice with 5 mL of PBS. Then, cell pellets can be stored in a 1.5 mL microcentrifuge tube or a 15 mL conical tube at -80 &#176;C until the time of the IP. Note that IPs can be performed on fresh harvested or frozen cell pellets.
<ol>
	<li>To isolate MHC class I or II peptides, thaw a frozen pellet of 1 x 108 cells by warming the bottom of the tube with the palm. Add 500 &#181;L of PBS to the pellet and pipette up and down until the suspension is homogenous. 
	NOTE: Depending on the cell type, the cell pellet volume can vary substantially. If 500 &#181;L of PBS is not enough to dissolve the cell pellet, use more PBS until the cells disaggregate easily while pipetting up and down.</li>
	<li>Measure the total volume of the pellet resuspended in PBS and transfer into a new tube 2 mL microcentrifuge tube. Split into more tubes if needed.</li>
	<li>Add a volume of cell lysis buffer (1% chaps buffer in PBS containing protease inhibitors, 1 pellet/10 mL of buffer) equivalent to the volume of cell pellet resuspended in PBS measured in the previous step. The final concentration of the lysis buffer is 0.5% Chaps.</li>
	<li>Rotate at 10 rpm for 60 min at 4 &#176;C using a rotator device. Centrifuge the cell lysate at 18,000 x g for 20 min at 4 &#176;C with full brake and transfer the supernatant (containing the MHC-peptides complexes) in a new 2.0 mL microcentrifuge tube.</li>
	<li>Recover the antibody-coupled beads from step 1.3.7 by centrifugation at 200 x g for 2 min and remove the supernatant.</li>
	<li>Transfer the cell lysate supernatant in step 2.4 to the antibody-coupled beads and incubate with rotation (10 rpm) for 14-18 h (overnight) at 4 &#176;C using a rotator device.</li>
</ol>
3. Elution of MHC peptides (Day 2)
NOTE: Polypropylene column allows elution of MHC-peptide complexes while retaining the beads into the column. In order to evaluate the proportion of MHC-peptides complexes bounded to the beads before and after acidic elution with 1% TFA (trifluoroacetic acid), it is possible to perform a western blot with aliquots taken at key steps during the protocol (see the indication OPTIONAL). Western blotting shown in Figure 3 reveals the enrichment of MHC-peptide complexes following acidic elution with 1% TFA. The absence of signal in this fraction would indicate that the elution step was not successful. Note that the proportion of unbound MHC-peptides complexes to the beads can also be evaluated in parallel by western blotting using an aliquot described in step 3.1.6.
<ol>
	<li>Elution of MHC-peptide complexes from the antibody coupled-beads
	<ol>
		<li>Remove the bottom lid of the polypropylene column, place the column onto the polypropylene column rack and install an empty container underneath to collect flow through. 
		NOTE: One column per sample is required.</li>
		<li>Rinse the polypropylene column with 10 mL of buffer A and let it drain by gravity. If the flow speed of liquid elution is too slow, further cut the bottom tip of the polypropylene column.</li>
		<li>Measure and collect the beads-lysate mixture (~2 mL) from step 2.5 and transfer it into the polypropylene column.</li>
		<li>(OPTIONAL) Take an aliquot of 20 &#181;L (or 1/100 out of the total volume) for western blotting and freeze immediately. This fraction corresponds to the total MHC-peptides complexes incubated with the beads.</li>
		<li>Let the liquid mixture elute by gravity.</li>
		<li>(OPTIONAL) Collect and measure the flow-through and take an aliquot of 20 &#181;L (or 1/100 out of the total volume) for western blotting and freeze immediately. This fraction represents the residual unbound MHC-peptides complexes.</li>
		<li>To recover the beads-lysate mixture as much as possible, rinse the tube from step 3.1.3 with 1 mL of buffer A and transfer it to the polypropylene column.</li>
		<li>Wash the beads retained in the polypropylene column by adding 10 mL of buffer A. Let the washing buffer elute by gravity.</li>
		<li>Repeat the washing step with 10 mL of buffer B, 10 mL of buffer A and then 10 mL of buffer C.</li>
		<li>Remove the polypropylene column from the rack and place it on the top of a new 2.0 mL microcentrifuge tube. Hold the column and the tube together with the hand.</li>
		<li>Add 300 &#181;L of 1% TFA to the polypropylene column and mix the beads by pipetting up and down 5 times. 
		NOTE: The beads will be retained in the polypropylene column, and the MHC-bound peptides will elute in the 2.0 mL microcentrifuge tube.</li>
		<li>Transfer the eluate in a new 2.0 mL microcentrifuge tube. Repeat step 3.1.11 and pool the 2 eluates (the eluates containing the MHC-peptide complexes should correspond to a total of 600 &#181;L and will be used at step 3.2.4).</li>
		<li>(OPTIONAL) Collect an aliquot of 6 &#181;L (or 1/100 of the total volume) for western blotting and freeze immediately. This fraction corresponds to the MHC-peptides complexes eluted from the beads.</li>
	</ol>
	</li>
	<li>Desalting and elution of MHC peptides 
	NOTE: Desalting and elution of MHC peptides steps could be done by installing the C18 column onto a 2.0 mL microcentrifuge tube. For a better fit, install the anneals provided by the manufacturer between the C18 column and the 2.0 mL microcentrifuge tube. In this protocol, a C18 column is used with a volume capacity of 5-200 &#181;L (6-60 &#181;g). All the steps are carried out at RT.
	<ol>
		<li>Add 200 &#181;L of Methanol on top of the C18 column, then centrifuge at 1546 x g for 3 min. Discard the flow-through.</li>
		<li>Add 200 &#181;L of 80%ACN (acetonitrile)/0.1%TFA on top of the C18 column, then centrifuge at 1546 x g for 3 min. Discard the flow-through.</li>
		<li>Add 200 &#181;L of 0.1%TFA on top of the C18 column, then centrifuge at 1546 x g for 3 min. Discard the flow-through.</li>
		<li>Load 200 &#181;L of the MHC-peptide complexes from step 3.1.12 on top of the C18 column. Centrifuge at 1546 x g for 3 min and discard the flow through.</li>
		<li>Repeat step 3.2.4 twice until the complete volume has been loaded. Note that MHC peptides are retained in the C18 column.</li>
		<li>Add 200 &#181;L of 0.1%TFA to the C18 column, then centrifuge at 1546 x g for 3 min. Discard the flow-through.</li>
		<li>Transfer the C18 column into a new 2.0 mL microcentrifuge tube. Elute MHC peptides from the C18 column by adding 150 &#181;L of 28%ACN/0.1%TFA.</li>
		<li>Centrifuge at 1546 x g for 3 min.</li>
		<li>Transfer the flow-through in a new 1.5 mL microcentrifuge tube. Be careful not to discard the flow-through; it contains the isolated MHC class I or II peptides.</li>
		<li>Repeat steps 3.2.7-3.2.9 twice for a total volume of 450 &#181;L.</li>
		<li>Freeze the 450 &#181;L of eluate (purified MHC class I or II peptides) at -20 &#176;C until samples are analyzed by LC-MSMS.</li>
		<li>Prior to LC-MS/MS analysis, the purified MHC class I or II peptides from step 3.2.11 are evaporated to dryness using a vacuum concentrator with presets of 45 &#176;C for 2 h, vacuum level: 100 mTorr and vacuum ramp: 5. 
		&#8203;NOTE: The evaporation of frozen samples is highly efficient. Dried peptides can be re-frozen until analysis.</li>
	</ol>
	</li>
</ol>
4. Identification of MHC class I and II peptides by LC-MS/MS
NOTE: Analyze the MHC class I and II immunopeptidome using a High-performance Orbitrap and high-resolution quadrupole time-of-flight mass spectrometers6. The following information is given as an indication only, taking into account that the various existing tandem mass spectrometry instruments operate according to different operational standards. A brief outline of the steps are discussed below :
<ol>
	<li>Solubilize the dried samples (from step 3.2.12) in 50 &#181;L of 4% formic acid (FA).</li>
	<li>Load three injections of 16 &#181;L for each sample and separate on a home-made reversed-phase column (150-&#181;m i.d. by 250 mm length, Jupiter 3 &#181;m C18 300 &#197;) with a gradient from 5%-30% ACN-0.1% FA and a 600 nL/min flow rate on a nano-flow UHPLC connected to an MS.</li>
	<li>Acquire each full MS spectrum at a resolution of 120000, an AGC of 4 x 105 with automatic mode for the injection time and spectra using tandem-MS (MS-MS) on the most abundant multiply charged precursor ions for a maximum of 3 s. 
	NOTE: Tandem-MS experiments are performed using higher-energy collisional dissociation (HCD) at a collision energy of 30%, a resolution of 30,000, an AGC of 1.5 x 105, and an injection time of 300 ms.</li>
	<li>Process the data files from the three injections/sample using a proteomics LC-MS/MS analysis software (e.g., PEAKS X) using the mouse and human databases (UniProtKB/Swiss-Prot (2019_09)).</li>
	<li>Select &#39;Unspecified Enzyme Digestion&#39; for the enzyme parameter, and 10 ppm and 0.01 Da for mass tolerances on precursor and fragment ions, respectively. 
	&#8203;NOTE: Variable modifications are deamidation (NQ) and oxidation (M). All other search parameters are the default values. Final peptide lists are filtered using ALC of 80% and with a false discovery rate (FDR) of 1 % using the proteomics LC-MS/MS analysis software.</li>
</ol>
5. Visualization of immunopeptidomics data
NOTE: The quality of immunopeptidomics data generated by MS can be assessed in multiple ways, as recently described22,23. To visualize the data and assess their overall quality, composition, and MHC-specificity, the MhcVizPipe (MVP) software tool can be used.
<ol>
	<li>Follow all the instructions and related documentation to install and run the MVP software available at the Caron Lab GitHub website24. 
	NOTE: MVP provides a rapid and consolidated view of sample quality, composition, and MHC-specificity. MVP parallelizes the use of well-established immunopeptidomics algorithms (NetMHCpan25, NetMHCIIpan26, and GibbsCluster27) and generates organized and easy-to-understand reports in HTML (HyperText Markup Language) format. The reports are fully portable and can be viewed on any computer with a modern web browser. See Supplementary Data 1-4 for examples of HTML reports.</li>
</ol>

The authors declare that they have no competing financial interests.

Two mouse cell lines (EL4 and A20), one human cell line (JY), and five commercially available antibodies [M1 (anti-H2Db/Kb), Y3 (anti-H2Kb), M5 (anti-H2-IAd/IEd), W6/32 (anti-HLA-ABC), and L243 (anti-HLA-DR)] were tested and validated in the context of this protocol and provide high-quality immunopeptidomics data. Other anti-HLA antibodies are available (e.g., anti-HLA-A2 BB7.2) but were not tested here. Note that the W6/32 antibody is widely used and the most established antibody in the field; it enables the isolation of peptides presented by all HLA-ABC molecules in humans and was previously reported by expert laboratories to work from various biological sources such as fresh or frozen tissues8,39, peripheral blood mononuclear cells and bone marrow mononuclear cell40, biopsies41, xenografts41,42, autopsies43 and plasma samples44,45.
The preparation of fresh solutions that are used throughout the protocol is critical. In particular, the use of fresh acidic solutions in glass bottles is critical to avoid subsequent contamination of the samples analyzed by MS. In addition, when the protocol is done for the first time and/or with a new antibody, it is important to assess that the antibody is indeed coupled to the CNBr Sepharose beads using a blue Coomassie gel. The washing steps of the antibody coupled beads following immunocapture of the MHC-peptide complexes is also critical to avoid contamination of non-MHC peptides. Finally, special care is required to not discard the eluates following the elution of the MHC-peptide complexes with 1% TFA and the elution of the peptides from the C18 column with ACN28%/0.1% FA.
Existing protocols available in the literature describe additional steps to further purify the peptides at the end of the isolation procedure, e.g., peptide fractionation by different methods14,46 or ultrafiltration using 10-30 kDa filters13,47. The current protocol does not provide details on those additional steps and is sufficient to provide high-quality immunopeptidomics data. However, such steps could be considered by non-experts to modify and troubleshoot to further optimize the peptide isolation procedure.
The type of beads and the type of acidic elution buffer that are used to elute MHC-complexes from the beads can also be modified for troubleshooting13,14,15,16,17,18,19. In this regard, sepharose CNBr-activated beads are generally a good starting point since they are relatively inexpensive in addition to show flexibility in terms of binding with various types of antibodies. In the current protocol, sepharose CNBr-activated beads were shown to perform relatively well using five different commercially available antibodies (i.e., M1, Y3, W6/32, L243, and M5). Besides sepharose CNBr-activated beads, Protein A or G or A/G sepharose 4 Fast Flow beads are also easy to handle, and although relatively more expensive, can generate similar results. Another factor to consider is the affinity of the antibody for protein A or G. Furthermore, sepharose magnetic beads are also very easy to use but are relatively expensive. Independently of the type of beads selected by non-experts, it is encouraged to collect aliquots at critical steps of the protocol and perform blue Coomassie-stained SDS-PAGE gels to track the binding efficiency of the antibody to the beads, as shown in Figure 2.
Another important factor influencing the successfulness of MHC peptides isolation refers to the type of acidic elution buffer used to isolate the MHC-peptide complexes from the beads. Different buffers have been reported including 0.1%, 1% or 10% TFA, 0.2% FA and 10% acetic acid. 1% TFA was the elution buffer working for all the antibodies tested. This step could also be traced by western blotting against the MHC molecules used to capture MHC peptides, as shown in Figure 3.
All buffers containing acetonitrile (ACN) and/or trifluoroacetic acid (TFA) are aggressive and can lead to contamination of the sample with small molecular and polymeric substances such as plasticizers if in contact with plastic. To avoid such issues, all solutions containing an organic solvent and/or TFA are prepared fresh daily and stored in a glass bottle until use. The majority of the steps are performed in Protein LoBind plastic tube. These tubes are specifically designed for proteomics and are made of the highest quality, virgin polypropylene free of biocides, plasticizers, and latex. They are also produced with optimized, highly polished molds without the use of slip agents. These precautions are important to consider to enable the generation of high-quality immunopeptidomics data.
The antibody is an important limitation for the isolation of MHC-bound peptides. The W6/32 antibody enables the isolation of peptides presented by all HLA-ABC class I molecules in humans and is the most widely used and established antibody in the field. High-resolution HLA typing of uncharacterized human cell lines or biospecimens is not a necessity upon application of the W6/32 antibody but is nevertheless recommended for certain applications to facilitate data interpretation48. HLA/MHC typing information can also be found in public resources for multiple cell lines and mouse models49. Besides the W6/32 antibody, the four other antibodies (M1, M5, Y3, and L243) that were tested and validated in the context of this protocol are all commercially available. On the other hand, many other antibodies that were reported in previous immunopeptidomics studies have not been largely adopted by the community and are not commercially available or are available through the culture of hybridoma cell lines, which is relatively expensive.
Another important limitation for the isolation of MHC-bound peptides is the amount of starting material required. The amount required is inversely proportional to the expression level of MHC molecules on the cell surface, which can be quantified by flow cytometry (Figure 4A). Cells showing high expression levels of MHC molecules (e.g., dendritic cells and hematopoietic cells in general) generally yield high-quality immunopeptidomics data. Expert labs use from as low as 50 million cells50, but 100 million to 1 billion cells are recommended for non-experts. Use of tissue biopsy (&#60;13 mg)41, xenograft42,43, autopsy44, and plasma45,46 samples were also reported but remain challenging for non-expert laboratories. Also, the total number of MHC-associated peptides expected is well documented for established cell lines (here, between ~2000 and ~10000 peptides depending on the cell line and antibody used), but the absolute amounts of naturally presented peptides that are efficiently pulled down by the technique remain debated. Indeed, previous studies estimated that the efficiency of the isolation procedure is peptide-dependent and can be from as low as 0.5%-2%51. Other limitations in immunopeptidomics are the reproducibility of the methods and the inability of the NetMHCpan suite tools to correctly annotate peptides to MHC alleles that are less characterized. In this regard, further development and application of relatively new data-independent acquisition MS methods7,32,52,&#160;as well as new peptide clustering and MHC peptide binding prediction algorithms31,34,53,54 are expected to improve the reproducibility and the accuracy of peptide annotation in immunopeptidomics. Immunopeptidomics is facing other limitations regarding MS acquisition and computational analysis of MHC-associated peptides and are covered elsewhere1,6,55.
While the isolation of HLA-ABC-associated peptides from human samples using the W6/32 antibody is well established and widely applied by many research groups, the isolation of mouse MHC class I- and II-associated peptides is relatively less established. Hence, robust protocols for the isolation of mouse MHC ligands are needed. Here, we provide a protocol optimized for the isolation of MHC class I peptides and MHC class II peptides from two mouse cell lines of C57BL/6 and BALB/c origin, respectively. Specifically, the protocol enables the isolation of class I H2Kb- and H2Db-associated peptides using the M1 antibody, as well as class II H2-IAd and H2-IEd-associated peptides using the M5 antibody. Thus, dissemination and application of the current protocol should facilitate basic and translational immunopeptidomics research in various mouse models.
The protocol can be used to establish and standardize an immunopeptidomics workflow, as well as to benchmark new protocols. For instance, it can be adapted and further optimized to perform immunopeptidomics screening in various biological matrices ranging from blood/plasma to fresh or frozen tissue to FFPE (Formalin-Fixed Paraffin-Embedded). Moreover, the protocol will foster the intra- and inter-laboratory reproducibility of the sample preparation procedure in immunopeptidomics and is therefore expected to find wide application in basic and clinical research.

Over the last decade, the interest in investigating the repertoire of MHC-associated peptides has exceeded the academic sector and reached the biotech and pharmaceutical industries. Indeed, in cancer, the discovery of actionable tumor-specific neoantigens represents a major research focus in the industrial sector to develop clinical immunotherapies leading to personalized oncology1,2,3. Fundamentally, MHC-associated peptides are presented throughout the entire body, reflect the intracellular stage of the cell, and are significant in various disease conditions such as autoimmunity, transplantation, infectious diseases, inflammation, cancer, and allergies1,4. Thus, MHC-associated peptides, or human leukocyte antigen (HLA) ligands in humans, are of great medical interest and are collectively referred to as the immunopeptidome5.
MS is a powerful analytical approach to characterize the immunopeptidome6,7, including the discovery of tumor-specific neoantigens8,9,10,11. A typical workflow to perform an immunopeptidomics experiment includes three main steps: 1) sample preparation for the isolation of MHC-associated peptides, 2) data acquisition by MS, and 3) data analysis using various computational software tools12. The generation of high-quality samples described in this visualized protocol is critical for the success of any project in MS-based immunopeptidomics. The protocol described below focuses on isolating MHC class I- and II-associated peptides from well-established cell lines that are suitable for generating high-quality immunopeptidomics data. Representative results from those cell lines are shown in the current protocol.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>A20 cell line</td>
			<td>ATCC</td>
			<td>TIB-208</td>
			<td>mouse B lymphoblast</td>
		</tr>
		<tr>
			<td>Acetonitrile, LC/MS Grade</td>
			<td>FisherScientific</td>
			<td>A955-4</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-Human HLA A, B, C (W6/32) - MHC class I</td>
			<td>BioXcell</td>
			<td>BE0079</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-Human/Monkey HLA-DR (L243) - MHC class II</td>
			<td>BioXcell</td>
			<td>BE0308</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-Mouse H2 (M1/42.3.9.8) - MHC class I</td>
			<td>BioXcell</td>
			<td>BE0077</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-Mouse H2-IAd/IEd (M5/114) - MHC class II</td>
			<td>BioXcell</td>
			<td>BE00108</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-Mouse H2Kb (Y3) - MHC class I</td>
			<td>BioXcell</td>
			<td>BE0172</td>
			<td></td>
		</tr>
		<tr>
			<td>BupH Phosphate Buffered Saline Packs (PBS)</td>
			<td>ThermoFisher</td>
			<td>28372</td>
			<td>Pouch contents dissolved in a final volume of 500 mL deionized water (FisherScientific, W64)</td>
		</tr>
		<tr>
			<td>CHAPS (3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate)</td>
			<td>EMDMilipore</td>
			<td>220201-10MG</td>
			<td></td>
		</tr>
		<tr>
			<td>CNBr-activated Sepharose</td>
			<td>Cytivia</td>
			<td># 17-0430-01</td>
			<td></td>
		</tr>
		<tr>
			<td>EL4 cell line</td>
			<td>ATCC</td>
			<td>TIB-39</td>
			<td>mouse T lymphoblast</td>
		</tr>
		<tr>
			<td>epTIPS LoRetention Tips, 1000 &#181;L/Eppendorf</td>
			<td>FisherScientific</td>
			<td>02-717-352</td>
			<td>Better results with low retention material</td>
		</tr>
		<tr>
			<td>epTIPS LoRetention Tips, 200 &#181;L/Eppendorf</td>
			<td>FisherScientific</td>
			<td>02-717-351</td>
			<td>Better results with low retention material</td>
		</tr>
		<tr>
			<td>Formic Acid, LC/MS Grade</td>
			<td>FisherScientific</td>
			<td>A117-50</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>FisherScientific</td>
			<td>RDCG0250500</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric acid solution</td>
			<td>FisherScientific</td>
			<td>60-007-11</td>
			<td></td>
		</tr>
		<tr>
			<td>JY cell line</td>
			<td>Sigma Aldrich</td>
			<td>94022533-1VL</td>
			<td>EBV-immortalised B cell lymphoblastoid line</td>
		</tr>
		<tr>
			<td>Methanol, LC/MS Grade</td>
			<td>FisherScientific</td>
			<td>A456-4</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly prep chromatography columns (polypropylene column)</td>
			<td>Bio-Rad</td>
			<td>731-1550</td>
			<td>referred as polypropylene column in the protocol</td>
		</tr>
		<tr>
			<td>Proteases inhibitor</td>
			<td>ThermoFisher</td>
			<td>A32963</td>
			<td>1 pellet per 10 mL of cell lysis buffer</td>
		</tr>
		<tr>
			<td>Qifikit</td>
			<td>Dako</td>
			<td>K007811-8</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Bicarbonate</td>
			<td>Amresco</td>
			<td># 0865-1kg</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Chloride</td>
			<td>FisherScientific</td>
			<td>MSX04201</td>
			<td></td>
		</tr>
		<tr>
			<td>Solid phase extraction disk, ultramicrospin column C18</td>
			<td>The nest group</td>
			<td>SEMSS18V</td>
			<td>capacity of 6&#8211;60 &#181;g, max volume of 200 &#181;L</td>
		</tr>
		<tr>
			<td>Trifluoroacetic Acid (TFA), LC-MS Grade</td>
			<td>FisherScientific</td>
			<td>PI85183</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>FisherScientific</td>
			<td>T395-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris-HCl</td>
			<td>FisherScientific</td>
			<td>#10812846001</td>
			<td></td>
		</tr>
		<tr>
			<td>Tube LoBind 1.5 mL/Eppendorf</td>
			<td>FisherScientific</td>
			<td>E925000090</td>
			<td>Better results with low retention material</td>
		</tr>
		<tr>
			<td>Tube LoBind 2 mL/Eppendorf</td>
			<td>FisherScientific</td>
			<td>13-698-795</td>
			<td>Better results with low retention material</td>
		</tr>
		<tr>
			<td>Water, LC/MS Grade</td>
			<td>FisherScientific</td>
			<td>W64</td>
			<td></td>
		</tr>
	</tbody>
</table>

immunopeptidomics: isolation of mouse and human mhc class i- and ii-associated peptides for mass spectrometry analysis

Immunopeptidomics is an emerging field that fuels and guides the development of vaccines and immunotherapies. More specifically, it refers to the science of investigating the composition of peptides presented by major histocompatibility complex (MHC) class I and class II molecules using mass spectrometry (MS) technology platforms. Among all the steps in an MS-based immunopeptidomics workflow, sample preparation is critically important for capturing high-quality data of therapeutic relevance. Here, step-by-step instructions are described to isolate MHC class I and II-associated peptides by immunoaffinity purification from quality control samples, from mouse (EL4 and A20), and human (JY) cell lines more specifically. The various reagents and specific antibodies are thoroughly described to isolate MHC-associated peptides from these cell lines, including the steps to verify the beads-binding efficiency of the antibody and the elution efficiency of the MHC-peptide complexes from the beads. The protocol can be used to establish and standardize an immunopeptidomics workflow, as well as to benchmark new protocols. Moreover, the protocol represents a great starting point for any non-experts in addition to foster the intra- and inter-laboratory reproducibility of the sample preparation procedure in immunopeptidomics.

The general workflow to isolate MHC-peptide complexes for the analysis of immunopeptidomes by MS is illustrated in Figure 1. Representative results for the verification of the beads-binding efficiency of the antibody (Figure 2) (using the Y3 anti-H2Kb antibody) and the elution efficiency of the MHC-peptide complexes from the beads (Figure 3) (using the W6/32 anti-HLA-ABC antibody) are shown. Flow cytometry-based quantification assays21 were also applied to measure the absolute number of MHC class I molecules per EL4 cell (H2Kb and H2Db) and JY cell (HLA-ABC), as shown in Figure 4A.
The intra- and inter-individual reproducibility of the results using the current protocol are shown in Figure 4B-E. Representative results are shown for MHC class I peptides identified from 1 x 108 EL4 cells and 1 x 108 JY cells. Results were generated from two different lab members (User 1 and User 2). For User 1, the mean number of MHCI-specific peptides detected from EL4 and JY cells was 1341 and 6361, respectively; for User 2, 1933 and 7238, respectively (Figure 4B,D). The average coefficient of variation (CV) for the number of peptides detected across three different biological replicates/experiments varies from 1.9%-11% (Figure 4B,D). Although the CVs for the number of peptides detected across the three different experiments were relatively small, the identity of the peptides varied considerably (Figure 4C,E). Indeed, representative Venn diagrams show that the proportion of peptides that were reproducibly detected across three biological replicates ranged from 39% (User 2, EL4 cells) to 63% (User 1, JY cells) (Figure 4C,E and Supplementary Table 2).
Heatmaps generated by the MVP software show predicted MHC binding strength of the identified peptides using the NetMHCpan suite tools25,26,28. Two GibbsCluster routine options, which are termed &#39;Unsupervised GibbsCluster&#39; and &#39;Allele-Specific GibbsCluster&#39;, are also performed by MVP to extract MHC peptide-binding motifs. Note that MVP has limitations; its primary goal is not to extract allele-specific motifs and annotate peptides in a highly accurate manner but to rather provide a bird&#39;s eye view on the overall quality, composition, and MHC-specificity of the samples.
For mouse MHC class I (H2Db and H2Kb) peptides in EL4 cells (Figure 5A; upper panels and Supplementary Data 1), a representative heatmap shows that 89% of all detected 8-12-mer peptides are predicted to be Strong Binders (SB: NetMHCpan %Rank &#60;0.5) or Weak Binders (WB: NetMHCpan %Rank &#60;2) for H2Db or H2Kb molecules. Sequence clusters generated from the 8-12-mer peptides are in concordance with reported logos for H2Db (asparagine at P5 and Leucine at P9) and H2Kb (phenylalanine at P5 and leucine at P8) (Figure 5)29. It is worth mentioning that a third dominant motif (histidine at P7 and leucine at P9) as well as additional &#39;artefactual&#39; motifs can be observed using the M1 antibody (Supplementary Data 1). In fact, the M1 antibody is known to cross-react with the non-classical Qa2 molecule, and therefore, Qa2-associated peptides are also detected by MS (Supplementary Data 1). Here, for simplicity, Figure 5 focuses on showing the well-established peptide binding motifs for the two classical H2b alleles (i.e., H2Db or H2Kb) expressed in EL4 cells.
For human HLA class I (HLA-ABC) peptides in JY cells (Figure 5A; lower panels and Supplementary Data 2), a representative heatmap shows that 97% of all detected 8-12-mer peptides are predicted to be SB or WB for HLA-A*0201, -B*0702 or -C*0702. Peptides were clustered to visualize peptide binding motifs for HLA-A*0201 and -B*0702. Binding motif for HLA-C*0702 is not shown in Figure 5A because the C*0702 allele has a relatively low expression level. Therefore too few C*0702 peptides were isolated and identified to generate a representative C*0702 motif.Note that the C*0702 motif can be visualized in other studies30,31,32 or from the NetMHCpan 4.1 Motif Viewer website33.
For human HLA class II (HLA-DR) peptides in JY cells (Figure 5B; upper panels and Supplementary Data S3), a representative heatmap shows that 70% of all detected 9-22-mer peptides are predicted to be SB or WB for HLA-DRB1*0404 and -DRB1*1301. Peptide binding motifs for these two alleles are shown (Figure 5B). Note that the peptide-binding motifs shown here may not be in complete concordance with the recently reported logos for HLA-DRB1*0404 and -DRB1*130134. This discrepancy highlights the current inability of MVP/NetMHCpan to precisely annotate peptides to HLA class II alleles that are less characterized, such as HLA-DRB1*0404 and -DRB1*1301 expressed in JY cells. Additional information on class II peptide binding motifs can be found in other studies34,35 and from the NetMHCIIpan 4.0 Motif Viewer website36.
Finally, for mouse MHC class II (H2-IAd and H2-IEd) peptides in A20 cells (Figure 5B; lower panels and Supplementary Data 4), a representative heatmap shows that 87% of all detected 9-22-mer peptides are predicted to be SB or WB for H2-IAd or H2-IEd. Peptide binding motifs for these two alleles are in concordance with reported logos37.
Complete HTML reports generated by the MVP software to assess the overall quality and MHC-specificity of the samples are available in Supplementary Data 1-4.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/63052/63052fig01.jpg" /> 
Figure 1: Schematic of the complete procedure for the isolation of MHC class I and II peptides. (A-B)100 million cells are pelleted and lysed with 0.5% Chaps buffer. (C) The cell lysate is centrifuged, and the supernatant is added to CNBr-sepharose beads coupled to the desired antibody beforehand and (D) incubated 14-18 h at 4 &#176;C. (E) Following immunocapture, the beads are transferred into a polypropylene column and washed, and the MHC-peptide complexes are eluted with a 1% TFA solution. (F) The peptides are desalted and eluted using a C18 column. (G) Subsequently, peptides are speed vac dried and analyzed by tandem mass spectrometry. (H) The quality of the isolated MHC class I and II peptides can be assessed based on the HLA subtypes using the freely available MhcVizPipe software. Figure created with BioRender.com (NT22ZL8QSL). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/63052/63052fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/63052/63052fig02.jpg" /> 
Figure 2: Coomassie gel staining to track antibody binding efficiency to sepharose CNBr-activated beads. Aliquots of equivalent volumes were loaded onto 12% SDS-PAGE gel followed by Coomassie blue staining: beads + antibody pre-coupling (1), unbound antibody following coupling step (2), supernatant following last wash after coupling (3), and beads coupled with antibody (4). The efficiency of binding is illustrated by a significant decrease in signal staining intensity of the light and heavy chains of H2Kb when beads are covalently bound (Lane 4) to the CNBr beads compared to the antibody before coupling (Lane 1). The figure has been reprinted and adapted from bioRxiv38. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/63052/63052fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/63052/63052fig03.jpg" /> 
Figure 3: Western blotting for tracking MHC-peptide complexes following acidic elution from antibody-coupled CNBr-activated beads. Aliquots taken from the steps indicated in the protocol (1/100 of the total measured volume) were loaded onto a 12% SDS-PAGE gel and transferred onto nitrocellulose membrane: Beads + lysate following immunocapture and last wash (A); supernatant of last wash (B) and MHC-peptide complexes eluted from the beads (C). The strong detection signal of the MHC-peptide complexes in (C) using anti-HLA-ABC heavy chain antibody (Abcam, #ab 70328, 1:5000) confirmed the isolation of MHC-peptide complexes following acidic elution. Note that it is possible to assess the proportion of MHC-peptide complexes that were not captured by the antibody coupled beads by collecting the flow-through from step 3.1.6. An aliquot can be added to the western blot (not shown on this gel). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/63052/63052fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/63052/63052fig04.jpg" /> 
Figure 4: Identification of MHC class I peptides from JY and EL4 cells. (A) Histogram showing the absolute number of cell surface H2Db and H2Kb molecules per EL4 cell and of HLA-ABC molecules per JY cell. Quantification was performed by flow cytometry. Mean and standard error of the mean were obtained from three biological replicates. (B, D) Histogram showing the mean number and standard deviation of the mean of MHC class I peptides identified by two independent users (USER_1 [U1] and USER_2 [U2]). Mean number and standard deviation of the mean of MHC class I peptides detected from mouse EL4 cells (B) and human JY cells (D) are shown. Coefficients of variation (CV) across three independent biological replicates are indicated. (C, E) Venn diagrams showing the number of peptides that were reproducibly detected in EL4 (C) and JY cells (E) by two independent users (U1 and U2) across three independent biological replicates. Figure 4A has been reprinted and adapted from bioRxiv38. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/63052/63052fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/63052/63052fig05.jpg" /> 
Figure 5: Visualization of immunopeptidomics data using the MVP software tool. Data analysis of mouse and human (A) MHC class I and (B) MHC class II peptides.&#160;Representative binding affinity heatmaps (left panels) and peptide binding motifs (right panels) are shown. Heatmaps colors represent the MHC binding affinity predicted by NetMHCpan 4.1 (%rank). Strong Binders are red (%rank &#60;0.5), Weak Binders are blue (%rank &#60;2) and Non-Binders are yellow (%Rank &#62;2). Proportion (%) of 8-12mer peptides (A) and 9-22mer peptides (B) that are SB or WB is indicated in parenthesis. Peptide binding motifs were generated by MVP using the &#39;Allele-specific Gibbscluster&#39; option. These representative results were obtained from 1 x 108 cells and by using the following antibodies and cell lines: M1 antibody and EL4 cells for mouse MHC class I peptides; W6/32 antibody and JY cells for human MHC class I peptides; M5 antibody and A20 cells for mouse MHC class II peptides; L243 antibody and JY cells for human MHC class II peptides. Refer to the Supplementary Data 1-4 to access the full HTML reports generated by the MVP software. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/63052/63052fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Supplementary Data 1-4: <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/63052/SUPPLEMENTARY DATA S1-S4.zip" target="_blank">Please click here to download this File.</a>
Supplementary Data 1: HTML report generated by the MVP software from peptides that were isolated from 1 x 108 EL4 cells using the M1 antibody. Three biological replicates are shown. This report is related to Figure 4 and Figure 5 and representative peptides are listed in Supplementary Table 2.
Supplementary Data 2: HTML report generated by the MVP software from peptides that were isolated from 1 x 108 JY cells using the W6/32 antibody. Three biological replates are shown. This report is related to Figure 4, and Figure 5, and representative peptides are listed in Supplementary Table 2.
Supplementary Data 3: HTML report generated by the MVP software from peptides that were isolated from 1 x 108 JY cells using the L243 antibody. This report is related to Figure 5, and representative peptides are listed in Supplementary Table 2.
Supplementary Data 4: HTML report generated by the MVP software from peptides that were isolated from 1 x 108 A20 cells using the M5 antibody. This report is related to Figure 5, and representative peptides are listed in Supplementary Table 2.
Supplementary Table 1: List of buffers. Recipes for all the buffers used in the protocol are described. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/63052/List of Buffers-63052R1.xlsx" target="_blank">Please click here to download this Table.</a>
Supplementary Table 2: Representative lists of peptides associated with H2Db/Kb, HLA-ABC, HLA-DR, and H2-IAd/IEd. This table contains the lists of representative MHC class I and II peptides isolated from mouse EL4 and A20 cell lines, respectively, and HLA class I and II from human JY cell line. These data have been deposited on the ProteomeXchange (PXD028633). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/63052/SUPPLEMENTARY TABLE S2-R2.xlsx" target="_blank">Please click here to download this Table.</a>
DATA AVAILABILITY:
Datasets used in this manuscript were deposited on the ProteomeXchange (http://proteomecentral.proteomexchange.org/cgi/GetDataset):&#160;&#160;PXD028633.

Watch this Scientific Journal Video about Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis at JoVE.com

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Here, we present a protocol for the purification of MHC class I and class II peptide complexes from mouse and human cell lines providing high-quality immunopeptidomics data. The protocol focuses on sample preparation using commercially available antibodies.

Immunopeptidomics is an emerging field that fuels and guides the development of vaccines and immunotherapies. More specifically, it refers to the science ...

immunopeptidomics-isolation-mouse-human-mhc-class-i-ii-associated

Research

JoVE Journal

Biochemistry

11.1K Views.  CHU Sainte-Justine Research Center. Here, we present a protocol for the purification of MHC class I and class II peptide complexes from mouse and human cell lines providing high-quality immunopeptidomics data. The protocol focuses on sample preparation using commercially available antibodies. 

Video: Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Species Determination and Quantitation in Mixtures Using MRM Mass Spectrometry of Peptides Applied to Meat Authentication

We describe a simple protocol for identifying and quantifying the two components in binary mixtures of species possessing one or more similar proteins. Central to the method is the identification of 'corresponding proteins' in the species of interest, in other words proteins that are nominally the same but possess species-specific sequence differences. When subject to proteolysis, corresponding proteins will give rise to some peptides which are likewise similar but with species-specific variants. These are 'corresponding peptides'. Species-specific peptides can be used as markers for species determination, while pairs of corresponding peptides permit relative quantitation of two species in a mixture. The peptides are detected using multiple reaction monitoring (MRM) mass spectrometry, a highly specific technique that enables peptide-based species determination even in complex systems. In addition, the ratio of MRM peak areas deriving from corresponding peptides supports relative quantitation. Since corresponding proteins and peptides will, in the main, behave similarly in both processing and in experimental extraction and sample preparation, the relative quantitation should remain comparatively robust. In addition, this approach does not need the standards and calibrations required by absolute quantitation methods. The protocol is described in the context of red meats, which have convenient corresponding proteins in the form of their respective myoglobins. This application is relevant to food fraud detection: the method can detect 1% weight for weight of horse meat in beef. The corresponding protein, corresponding peptide (CPCP) relative quantitation using MRM peak area ratios gives good estimates of the weight for weight composition of a horse plus beef mixture.

We present a protocol for identifying and quantifying the components in mixtures of species possessing similar proteins. Mass spectrometry detects peptides for identification, and gives relative quantitation by ratios of peak areas. As a tool food for fraud detection, the method can detect 1% horse in beef.

We describe a simple protocol for identifying and quantifying the two components in binary mixtures of species possessing one or more similar proteins. ...

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. Hydrogen-Deuterium Exchange (HDX) measured at rapid time scales is uniquely suited to detect structures and hydrogen bonding networks that are briefly populated, allowing for the characterization of transient conformers in native ensembles. Coupling of HDX to mass spectrometry offers several key advantages, including high sensitivity, low sample consumption and no restriction on protein size. This technique has advanced greatly in the last several decades, including the ability to monitor HDX labeling times on the millisecond time scale. In addition, by incorporating the HDX workflow onto a microfluidic platform housing an acidic protease microreactor, we are able to localize dynamic properties at the peptide level. In this study, Time-Resolved ElectroSpray Ionization Mass Spectrometry (TRESI-MS) coupled to HDX was used to provide a detailed picture of residual structure in the tau protein, as well as the conformational shifts induced upon hyperphosphorylation.

Conformational flexibility plays a critical role in protein function. Herein, we describe the use of time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange for probing the rapid structural changes that drive function in ordered and disordered proteins.

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. ...

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 ...

Mass Spectrometry and Luminogenic-based Approaches to Characterize Phase I Metabolic Competency of In Vitro Cell Cultures

Xenobiotic metabolizing enzymes play a key function in the biotransformation of medicines and toxicants by adding functional groups that increase solubility and facilitate excretion. On some occasions those structural modifications lead to the formation of new toxic products. In order to reduce animal testing, chemical risk can be assessed using metabolically competent cells. The expression of metabolic enzymes, however, is not stable over time in many in vitro primary culture systems and is often partial or absent in cell lines. Therefore, the study of medicines, additives, and environmental pollutants metabolism in vitro should ideally be conducted in cell systems where metabolic activity has been characterized. We explain here an approach to measure the activity of a class of metabolic enzymes (Human Phase I) in 2D cell lines and primary 3D cultures using chemical probes and their metabolic products quantifiable by UPLC mass spectrometry and luminometry. The method can be implemented to test the metabolic activity in cell lines and primary cells derived from a variety of tissues.

Mass Spectrometry and Luminogenic-based Approaches to Characterize Phase I Metabolic Competency of In Vitro Cell Cultures

Metabolic competency of in vitro systems is a key requirement for the biotransformation and disposition of drugs and toxicants. In this protocol, we describe the application of reference metabolic probes to assess phase I metabolism in cell cultures.

Xenobiotic metabolizing enzymes play a key function in the biotransformation of medicines and toxicants by adding functional groups that increase ...

Lipid Droplet Isolation for Quantitative Mass Spectrometry Analysis

Lipid droplets are vital to the replication of a variety of different pathogens, most prominently the Hepatitis C Virus (HCV), as the putative site of virion morphogenesis. Quantitative lipid droplet proteome analysis can be used to identify proteins that localize to or are displaced from lipid droplets under conditions such as virus infections. Here, we describe a protocol that has been successfully used to characterize the changes in the lipid droplet proteome following infection with HCV. We use Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) and thus label the complete proteome of one population of cells with &#34;heavy&#34; amino acids to quantitate the proteins by mass spectrometry. For lipid droplet isolation, the two cell populations (i.e.&#160;HCV-infected/&#34;light&#34; amino acids and uninfected control/&#34;heavy&#34; amino acids) are mixed 1:1 and lysed mechanically in hypotonic buffer. After removing the nuclei and cell debris by low speed centrifugation, lipid droplet-associated proteins are enriched by two subsequent ultracentrifugation steps followed by three washing steps in isotonic buffer. The purity of the lipid droplet fractions is analyzed by western blotting with antibodies recognizing different subcellular compartments. Lipid droplet-associated proteins are then separated by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) followed by Coomassie staining. After tryptic digest, the peptides are quantified by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Using this method, we identified proteins recruited to lipid droplets upon HCV infection that might represent pro- or antiviral host factors. Our method can be applied to a variety of different cells and culture conditions, such as infection with pathogens, environmental stress, or drug treatment.

Lipid droplets are important organelles for the replication of several pathogens, including the Hepatitis C Virus (HCV). We describe a method to isolate lipid droplets for quantitative mass spectrometry of associated proteins; it can be used under a variety of conditions, such as virus infection, environmental stress, or drug treatment.

Lipid droplets are vital to the replication of a variety of different pathogens, most prominently the Hepatitis C Virus (HCV), as the putative site of ...

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Noncoding RNAs play important roles in several nuclear processes, including regulating gene expression, chromatin structure, and DNA repair. In most cases, the action of noncoding RNAs is mediated by proteins whose functions are in turn regulated by these interactions with noncoding RNAs. Consistent with this, a growing number of proteins involved in nuclear functions have been reported to bind RNA and in a few cases the RNA-binding regions of these proteins have been mapped, often through laborious, candidate-based methods.
Here, we report a detailed protocol to perform a high-throughput, proteome-wide unbiased identification of RNA-binding proteins and their RNA-binding regions. The methodology relies on the incorporation of a photoreactive uridine analog in the cellular RNA, followed by UV-mediated protein-RNA crosslinking, and mass spectrometry analyses to reveal RNA-crosslinked peptides within the proteome. Although we describe the procedure for mouse embryonic stem cells, the protocol should be easily adapted to a variety of cultured cells.

We describe a protocol to identify RNA-binding proteins and map their RNA-binding regions in live cells using UV-mediated photocrosslinking and mass spectrometry.

Noncoding RNAs play important roles in several nuclear processes, including regulating gene expression, chromatin structure, and DNA repair. In most ...

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

The maintenance of the genome and its faithful replication is paramount for conserving genetic information. To assess high fidelity replication, we have developed a simple non-labeled and non-radio-isotopic method using a matrix-assisted laser desorption ionization with time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis for a proofreading study. Here, a DNA polymerase [e.g., the Klenow fragment (KF) of Escherichia coli DNA polymerase I (pol I) in this study] in the presence of all four dideoxyribonucleotide triphosphates is used to process a mismatched primer-template duplex. The mismatched primer is then proofread/extended and subjected to MALDI-TOF MS. The products are distinguished by the mass change of the primer down to single nucleotide variations. Importantly, a proofreading can also be determined for internal single mismatches, albeit at different efficiencies. Mismatches located at 2-4-nucleotides (nt) from the 3' end were efficiently proofread by pol I, and a mismatch at 5 nt from the primer terminus showed only a partial correction. No proofreading occurred for internal mismatches located at 6 - 9 nt from the primer 3' end. This method can also be applied to DNA repair assays (e.g., assessing a base-lesion repair of substrates for the endo V repair pathway). Primers containing 3' penultimate deoxyinosine (dI) lesions could be corrected by pol I. Indeed, penultimate T-I, G-I, and A-I substrates had their last 2 dI-containing nucleotides excised by pol I before adding a correct ddN 5'-monophosphate (ddNMP) while penultimate C-I mismatches were tolerated by pol I, allowing the primer to be extended without repair, demonstrating the sensitivity and resolution of the MS assay to measure DNA repair.

A non-labeled, non-radio-isotopic method for DNA polymerase proofreading and a DNA repair assay was developed by using high-resolution MALDI-TOF mass spectrometry and a single nucleotide extension strategy. The assay proved to be very specific, simple, rapid, and easy to perform for proofreading and repair patches shorter than 9-nucleotides.

The maintenance of the genome and its faithful replication is paramount for conserving genetic information. To assess high fidelity replication, we have ...

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.

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 ...

Sample Preparation for Probe Electrospray Ionization Mass Spectrometry

Mass spectrometry (MS) is a powerful tool in analytical chemistry because it provides very accurate information about molecules, such as mass-to-charge ratios (m/z), which are useful to deduce molecular weights and structures. While it is essentially a destructive analytical method, recent advancements in the ambient ionization technique have enabled us to acquire data while leaving tissue in a relatively intact state in terms of integrity. Probe electrospray ionization (PESI) is a so-called direct method because it does not require complex and time-consuming pretreatment of samples. A fine needle serves as a sample picker, as well as an ionization emitter. Based on the very sharp and fine property of the probe tip, destruction of the samples is minimal, allowing us to acquire the real-time molecular information from living things in situ. Herein, we introduce three applications of PESI-MS technique that will be useful for biomedical research and development. One involves the application to solid tissue, which is the basic application of this technique for the medical diagnosis. As this technique requires only 10 mg of the sample, it may be very useful in the routine clinical settings. The second application is for in vitro medical diagnostics where human blood serum is measured. The ability to measure fluid samples is also valuable in various biological experiments where a sufficient volume of sample for conventional analytical techniques cannot be provided. The third application leans toward the direct application of probe needles in living animals, where we can obtain real-time dynamics of metabolites or drugs in specific organs. In each application, we can infer the molecules that have been detected by MS or use artificial intelligence to obtain a medical diagnosis.

This article introduces sample preparation methods for a unique real-time analytical method based on the ambient mass spectrometry. This method lets us perform real-time analysis of the biological molecules in vivo without any special pretreatments.

Mass spectrometry (MS) is a powerful tool in analytical chemistry because it provides very accurate information about molecules, such as mass-to-charge ...

Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

Lipids are structurally diverse amphipathic molecules that are insoluble in water. Lipids are essential contributors to the organization and function of biological membranes, energy storage and production, cellular signaling, vesicular transport of proteins, organelle biogenesis, and regulated cell death. Because the budding yeast Saccharomyces cerevisiae is a unicellular eukaryote amenable to thorough molecular analyses, its use as a model organism helped uncover mechanisms linking lipid metabolism and intracellular transport to complex biological processes within eukaryotic cells. The availability of a versatile analytical method for the robust, sensitive, and accurate quantitative assessment of major classes of lipids within a yeast cell is crucial for getting deep insights into these mechanisms. Here we present a protocol to use liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) for the quantitative analysis of major cellular lipids of S. cerevisiae. The LC-MS/MS method described is versatile and robust. It enables the identification and quantification of numerous species (including different isobaric or isomeric forms) within each of the 10 lipid classes. This method is sensitive and allows identification and quantitation of some lipid species at concentrations as low as 0.2 pmol/&#181;L. The method has been successfully applied to assessing lipidomes of whole yeast cells and their purified organelles. The use of alternative mobile phase additives for electrospray ionization mass spectrometry in this method can increase the efficiency of ionization for some lipid species and can be therefore used to improve their identification and quantitation.

Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

We present a protocol using liquid chromatography coupled with tandem mass spectrometry to identify and quantify major cellular lipids in Saccharomyces cerevisiae. The described method for a quantitative assessment of major lipid classes within a yeast cell is versatile, robust, and sensitive.

Lipids are structurally diverse amphipathic molecules that are insoluble in water. Lipids are essential contributors to the organization and function of ...

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

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Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry