The authors thank Dr. Herv&#233; Remigy of Thermo Fisher Scientific for useful advice. The cryo-EM experiments were performed at the Academia Sinica Cryo-EM Facility (ASCEM). ASCEM is supported by Academia Sinica (Grant No. AS-CFII-108-110) and Taiwan Protein Project (Grant No. AS-KPQ-109-TPP2). The authors also thank Ms. Hui-Ju Huang for the assistance with the sample preparation.

NOTE: This protocol aims to use a modified commercial vitrification apparatus to prepare the cryo-electron microscopy (cryo-EM) samples at specific temperatures, especially higher than 37 &#176;C. The overall experimental setup is shown in Figure 1. The protocol uses 55 &#176;C as an example. For the specific conditions at other temperatures, please refer to Supplementary Table 2 in reference12.
1. Preparation of the vitrification apparatus
<ol>
	<li>Make a 1 cm hole in a 50 mL centrifuge tube on its closed end.</li>
	<li>Place the tube in the vitrification apparatus chamber at the ultrasonic water outlet, as shown in Figure 2. 
	NOTE: The purpose is to minimize water condensation by guiding water vapor to the heat exchanger through the tube before reaching the entire chamber.</li>
	<li>Set up the vitrification apparatus temperature to the specified temperature (e.g., 55 &#176;C, as shown in Figure 3), and allow the vitrification apparatus chamber to reach to 55 &#176;C and 100% relative humidity. Let it stand for at least half an hour to stabilize the conditions before starting the experiment.</li>
</ol>
2. Warming up the sample and the tools
<ol>
	<li>Place the water bath on a hotplate and set the hotplate to the desired temperature (here 55 &#176;C). Check with a thermometer to ensure that the water reaches 55 &#176;C.</li>
	<li>Incubate the sample in the water bath and preheat the pipette tip on the edge of the hotplate for 2 min or longer before the blotting experiment. 
	&#8203;NOTE: The highest temperature setting for the vitrification apparatus chamber is 60 &#176;C. To prepare higher temperature grids for cyro-EM experiment (e.g., 70 &#176;C), the sample is incubated in the water bath at 80 &#176;C, and the average between the sample temperature and the vitrification apparatus temperature is estimated to be the actual temperature of the sample on the grid (70 &#176;C in this case). See the Discussion section for further details and limitations on this estimation.</li>
</ol>
3. Preparation for the blotting experiment
<ol>
	<li>Glow discharge a holey carbon-supported grid at 25 mA for 30 s, or alternative to the values depending on the device used.</li>
	<li>Incubate the tweezers with the grid in the vitrification apparatus for 2 min or longer.</li>
	<li>Fill the ethane container with ethane according to standard procedures. Do not let the ethane overflow. 
	NOTE: This step takes about 10 min and should be followed immediately with the blotting experiment to avoid freezing.</li>
	<li>Place the vitrification filter paper into the vitrification apparatus chamber no sooner than 5 min before the blotting experiment. 
	NOTE: Placing the filter paper in the chamber too soon will cause it to become too wet.</li>
</ol>
4. Blotting experiment
NOTE: When holding the grid, ensure that the grid is stable and there is a minimal contact area with the tweezers (Figure 4). This is done to maintain the best cooling efficiency of ethane and to avoid non-vitreous ice.
<ol>
	<li>Use a pipette tip to apply 7-9 &#956;L of the sample to the grid. Then wait for 1-2 s, blot for 1-1.5 s, and quickly plunge the sample to liquid ethane.</li>
	<li>Transfer the grid from liquid ethane to the cryo box, which is stored in liquid nitrogen. 
	&#8203;NOTE: This step must be performed very carefully because the tweezers is still hot, so the entire cooling tank is full of vapor at this time.</li>
</ol>
5. Quality check for the grids
<ol>
	<li>Clip the grids and upload them to a cryo-EM instrument.</li>
	<li>Use the display screen of the cryo-EM instrument and the low dose function of the software to screen the ice condition on the grid and the distribution of the sample on the grid. 
	&#8203;NOTE: Often, the grids are very dry, or the ice layer is too thick. The success rate of the grids prepared at high temperatures is substantially lower than that at room temperature or 4 &#176;C. Representative results of good grids and non-satisfactory grids are shown in the next section.</li>
	<li>If the quality of the resulting grid is not good, repeat the process of grid preparation with varied conditions (such as waiting time, blotting time, etc.). If the quality of the resulting grid is good, repeat the same steps to make grids at a different temperature.</li>
</ol>
6. Data collection
<ol>
	<li>Transfer the good quality grids to a high resolution cryo-EM instrument.</li>
	<li>Perform data collection and data analyses according to established procedures. 
	NOTE: As shown in our previous publication, the resolution of the structure is not affected by the high temperature12.</li>
</ol>

<ol>
	<li>Yip, K. M., Fischer, N., Paknia, E., Chari, A., Stark, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic-resolution+protein+structure+determination+by+cryo-EM.">Atomic-resolution protein structure determination by cryo-EM.</a> Nature. 587, 157-161 (2020).</li><li>Nakane, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-particle+cryo-EM+at+atomic+resolution.">Single-particle cryo-EM at atomic resolution.</a> Nature. 587, 152-156 (2020).</li><li>Chen, C. Y., 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=Use+of+Cryo-EM+to+uncover+structural+bases+of+pH+effect+and+cofactor+bi-specificity+of+ketol-acid+reductoisomerase.">Use of Cryo-EM to uncover structural bases of pH effect and cofactor bi-specificity of ketol-acid reductoisomerase.</a> Journal of the American Chemical Society. 141, 6136-6140 (2019).</li><li>Cabra, V., Sams&#243;, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Do's+and+don'ts+of+cryo-electron+microscopy:+A+primer+on+sample+preparation+and+high+quality+data+collection+for+macromolecular+3D+reconstruction.">Do's and don'ts of cryo-electron microscopy: A primer on sample preparation and high quality data collection for macromolecular 3D reconstruction.</a> Journal of Visualized Experiments. (95), e52311 (2015).</li><li>Klebl, D. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Need+for+speed:+Examining+protein+behavior+during+CryoEM+grid+preparation+at+different+timescales.">Need for speed: Examining protein behavior during CryoEM grid preparation at different timescales.</a> Structure. 28 (11), 1238-1248 (2020).</li><li>Passmore, L. A., Russo, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Specimen+preparation+for+high+resolution+cryo-EM.">Specimen preparation for high resolution cryo-EM.</a> J. Methods in Enzymology. 579, 51-86 (2016).</li><li>Laughlin, T. G., Bayne, A. N., Trempe, J. -. F., Savage, D. F., Davies, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+of+the+complex+I-like+molecule+NDH+of+oxygenic+photosynthesis.">Structure of the complex I-like molecule NDH of oxygenic photosynthesis.</a> Nature. 566, 411-414 (2019).</li><li>Gao, Y., 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=Structures+and+operating+principles+of+the+replisome.">Structures and operating principles of the replisome.</a> Science. 363, (2019).</li><li>Zhao, Y., Chen, S., Swensen, A. C., Qian, W. -. J., Gouaux, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Architecture+and+subunit+arrangement+of+native+AMPA+receptors+elucidated+by+cryo-EM.">Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM.</a> Science. 364, 355-362 (2019).</li><li>Chen, B., 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=Structural+dynamics+of+ribosome+subunit+association+studied+by+mixing-spraying+time-resolved+cryogenic+electron+microscopy.">Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy.</a> Structure. 23, 1097-1105 (2015).</li><li>Singh, A. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+basis+of+temperature+sensation+by+the+TRP+channel+TRPV3.">Structural basis of temperature sensation by the TRP channel TRPV3.</a> Nature Structure and Molecular Biology. 26, 994-998 (2019).</li><li>Chen, C. Y., Chang, Y. C., Lin, B. L., Huang, C. H., Tsai, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Temperature-resolved+cryo-EM+uncovers+structural+bases+of+temperature-dependent+enzyme+functions.">Temperature-resolved cryo-EM uncovers structural bases of temperature-dependent enzyme functions.</a> Journal of the American Chemical Society. 141, 19983-19987 (2019).</li></ol>

The authors declare no competing financial interests.

In step 1 of the protocol, make sure that the centrifuge tube has been installed well and does not fall when the experiment is in progress. Due to the accumulation of a large number of water droplets in the chamber, which could change the adsorption capacity of the filter paper, it is recommended that the overall time of the experiment should not exceed 30 min after the vitrification apparatus chamber reached the equilibration temperature. If the operation time exceeds 30 min, the operator needs to replace the filter paper and wait for the cabin to balance the temperature and humidity again. At step 8 of the protocol, the suggested sample volume of 7-9 &#181;L is larger than usual since otherwise, the sample evaporates quickly at high temperature, leading to empty squares on the grid. On the other hand, it is highly recommended that the sample applied does not exceed 9 &#181;L. Otherwise, it is very likely that the sample will drip down during the process of moving the tweezer before blotting. Overall, a key to the success of this technique is stable and fast gripping of grids and correct and stable execution of each time-limited action. Furthermore, it is recommended that each round of experiments deals with only one specific high temperature. Before proceeding to perform the experiment at another temperature, all systems must be fully recovered and reset.
Due to the high temperature and high humidity of the chamber, the window is often covered with fog leading to difficulties in launching the experiment. Use of a little soapsuds is recommended to clear the window. If grids are not good, possible reasons are that the steps described above are not followed precisely and/or that the steps take too long. Try to repeat the preparation of sample grids with precision and swiftness. If the grids are still not good after repeats, then try to adjust the conditions. The more frequent problem observed in this experiment is no ice on the grid at the high temperature. If so, try to reduce the blotting time further. On the other hand, if the ice is too thick, try to increase the blotting time.
A limitation of the high-temperature cryo-EM is that the maximum heating temperature on the vitrification apparatus is 60 &#176;C. To reach to the higher temperature, the sample was heated above 60 &#176;C (e.g., 80 &#176;C), and the average between the sample temperature and the vitrification temperature was estimated to be the real temperature of the sample on the grid (70 &#176;C, in this case). There could be some inaccuracy based on this estimation. A possible future solution is to build a thermocouple to measure the grid temperature accurately right before plunge-freezing. Another potential limitation is the stability of the protein at high temperatures. A separate experiment using circular dichroism should be performed to ensure that the protein is stable at the temperature for the planned cryo-EM experiment.
Another limitation is that only two types of commercially available vitrification apparatus can be heated to above 37 &#176;C and up to 60 &#176;C as mentioned above (e.g., Thermo Fischer Vitrobot and Leica EM-GP). The vitrification apparatuses from other vendors are either limited to room temperature or adjustable only between 4 &#176;C and 37 &#176;C. However, it is possible for research groups to build their own plunging devices with extended temperature ranges in the future.
Our protocol is modified from existing protocols4,5,6, with the purpose of preparing the grids at temperatures higher than room temperature. Without making the modifications described here, the chance of success for making good high-temperature sample grids suitable for cryo-EM image collection is very small.
Two papers in 2019 have demonstrated that protein structures are temperature dependent, in correlation with the temperature dependence of protein functions, in the range of 4 &#176;C to 42 &#176;C for the TRP channel TRPV311 and 4 &#176;C to 70 &#176;C for Sso-KARI12. These reports are likely to encourage a change in cryo-EM research in that more future studies will be performed at functionally relevant temperatures, usually at 37 &#176;C. The stability of the purified protein at this temperature could be a concern. However, it is required to incubate the protein sample at this temperature for only 2 min according to our protocol. Alternatively, physiological conditions can be achieved by imaging proteins in cells using tomography and sub-tomo averaging. Furthermore, cryo-EM can be used to study the mechanism and intermediates of protein unfolding at high temperatures, likely in the range of 40 &#176;C to 80 &#176;C. These studies will all benefit from the protocol described here.

The cryo-EM technology for solving the structures of protein complexes has continued to improve, particularly in the direction of obtaining high-resolution structures1,2. In the meantime, the landscape of its application has also been expanded by varying the sample conditions such as pH or ligands prior to the vitrification process3, which involves the preparation of sample grids followed by plunge freezing4,5. Another important condition is the temperature. Although cryo-EM experiments, like X-ray crystallography, are performed at low temperatures, the structure solved by cryo-EM reflects the structure at the solution state prior to vitrification. Until recently, the majority of single particle analysis (SPA) cryo-EM studies use samples that are kept on ice (i.e., at 4 &#176;C) prior to vitrification6, though a number of studies use samples at around room temperature7,8,9,10 or as high as 42 &#176;C11. In a recent report, we performed temperature-dependent studies of the enzyme ketol-acid reductoisomerase (KARI) from the thermophilic archaeon Sulfolobus solfataricus (Sso) at six different temperatures from 4 &#176;C to 70&#176;C12. Our studies suggest that it is important to prepare sample grids at functionally relevant temperatures and that cryo-EM is the only structural method that is practically feasible for solving the structure of the same protein complex at multiple temperatures.
The major difficulty for vitrification at high temperatures is to minimize vapor condensation and achieve thin ice. Here we report the detailed protocol used for preparing sample grids at high temperatures in our previous study of the Sso-KARI12. We assume that the readers or viewers are already experienced in the overall sample preparation and data processing procedures for cryo-EM experiments and emphasize the aspects relevant to high temperature.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Falcon tube</td>
			<td>Falcon</td>
			<td>352070</td>
			<td>size: 50 mL</td>
		</tr>
		<tr>
			<td>Filter paper</td>
			<td>Ted Pella</td>
			<td>47000-100</td>
			<td>&#216;55/20mm, Grade 595</td>
		</tr>
		<tr>
			<td>HI1210</td>
			<td>Leica</td>
			<td></td>
			<td>water bath</td>
		</tr>
		<tr>
			<td>K100X</td>
			<td>Electron Microscopy Sciences</td>
			<td></td>
			<td>glow discharge</td>
		</tr>
		<tr>
			<td>Quantifoil, 1.2/1.3 200Mesh Cu grid</td>
			<td>Ted Pella</td>
			<td>658-200-CU-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Titan Krios G3</td>
			<td>Thermo Fisher Scientific</td>
			<td>1063996</td>
			<td>low dose imaging</td>
		</tr>
		<tr>
			<td>Vitrobot Mark IV</td>
			<td>Thermo Fisher Scientific</td>
			<td>1086439</td>
			<td></td>
		</tr>
		<tr>
			<td>Vitrobot Tweezer</td>
			<td>Ted Pella</td>
			<td>47000-500</td>
			<td></td>
		</tr>
	</tbody>
</table>

preparation of high-temperature sample grids for cryo-em

The sample grids for cryo-electron microscopy (cryo-EM) experiments are usually prepared at a temperature optimal for the storage of biological samples, mostly at 4 &#176;C and occasionally at room temperature. Recently, we discovered that the protein structure solved at low temperature may not be functionally relevant, particularly for proteins from thermophilic archaea. A procedure was developed to prepare protein samples at higher temperatures (up to 70 &#176;C) for cryo-EM analysis. We showed that the structures from samples prepared at higher temperatures are functionally relevant and temperature dependent. Here we describe a detailed protocol for preparing sample grids at high temperature, using 55 &#176;C as an example. The experiment made use of a vitrification apparatus modified using an additional centrifuge tube, and samples were incubated at 55 &#176;C. The detailed procedures were fine-tuned to minimize vapor condensation and obtain a thin layer of ice on the grid. Examples of successful and unsuccessful experiments are provided.

The low magnification overview is shown in Figure 5A,B. Panel A is an example of a successful grid. There is an ice gradient from top left (thicker) to bottom right (thinner or empty). Such a grid makes it easier to find an appropriate thickness of the ice layer in the middle area suitable for data collection, such as the blue and green boxes. The grid B is too dry. The squares in the grid have bright contrast, which means that the ice layer is too thin or there is no ice layer at all. Only the two squares indicated by the red arrows are suitable for data collection.
Furthermore, examples of the low-dose images from different grids are shown in Figure 5C,D. The image in panel C shows that most of the ice is in the crystalline form, not suitable for data collection. On the other hand, image in panel D shows that the ice layer is mostly in an amorphous state, suitable for data collection.
Please note that this is a short paper focusing on grid preparation at high temperatures. The grid only contains the sample for data collection. A good grid has a good chance, though not a definite chance, to generate good data for solving a high-resolution structure. The real cryo-EM data and final structures for the examples described in this paper are already described in the published paper12. In short, we have obtained grids good enough for data collection, solved the structures of two Sso-KARI complexes at six different temperatures each, and compared the structures from different temperatures for each complex, as well as the structures between the two complexes from the same temperature. The results indicate that the structure of each complex is temperature-dependent and that the temperature-dependent changes are different between the two complexes. Importantly, the successive structural changes correlate well with the successive temperature changes, which is a strong indication for the success of the temperature-dependent sample grid preparation.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/62772/62772fig01.jpg" /> 
Figure 1:&#160;The overall experimental setup for high-temperature cryo-EM sample preparation. The items shown include vitrification apparatus, incubator, timer, pipette tip placement, cooling tank, and tweezers. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62772/62772fig01large.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/62772/62772fig02.jpg" /> 
Figure 2:&#160;Modification of the vitrification apparatus chamber. A 50 mL tube is installed at the ultrasonic spray outlet as indicated by the red arrow12. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62772/62772fig02large.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/62772/62772fig03.jpg" /> 
Figure 3:&#160;Appearance of the vitrification apparatus during the experiment. The screen shows the temperature at 55 &#176;C and the humidity at 100%. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62772/62772fig03large.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/62772/62772fig04.jpg" /> 
Figure 4: Using tweezers to grab the grid. It is recommended that the tweezers grip the grid with as little contact as possible, but it must be able to hold the grid stably during the process of the operation. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62772/62772fig04large.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/62772/62772fig05.jpg" /> 
Figure 5:&#160;Representative results: Grid checking by Cryo-EM. (A,B) show the overall state of the grid. (C,D) show examples of the low-dose images from different grids. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62772/62772fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Preparation of High-Temperature Sample Grids for Cryo-EM at JoVE.com

Preparation of High-Temperature Sample Grids for Cryo-EM

This paper provides a detailed protocol for preparing sample grids at temperatures as high as 70 &#176;C, prior to plunge freezing for cryo-EM experiments.

The sample grids for cryo-electron microscopy (cryo-EM) experiments are usually prepared at a temperature optimal for the storage of biological samples, ...

preparation-of-high-temperature-sample-grids-for-cryo-em

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Biochemistry

3.4K Views.  Academia Sinica. This paper provides a detailed protocol for preparing sample grids at temperatures as high as 70 °C, prior to plunge freezing for cryo-EM experiments.

Video: Preparation of High-Temperature Sample Grids for Cryo-EM

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 ...

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. A prerequisite for the method is that highly ordered crystalline specimen need to be grown from the macromolecule to be studied, which then need to be prepared for the diffraction experiment. This preparation procedure typically involves removal of the crystal from the solution, in which it was grown, soaking of the crystal in ligand solution or cryo-protectant solution and then immobilizing the crystal on a mount suitable for the experiment. A serious problem for this procedure is that macromolecular crystals are often mechanically unstable and rather fragile. Consequently, the handling of such fragile crystals can easily become a bottleneck in a structure determination attempt. Any mechanical force applied to such delicate crystals may disturb the regular packing of the molecules and may lead to a loss of diffraction power of the crystals. Here, we present a novel all-in-one sample holder, which has been developed in order to minimize the handling steps of crystals and hence to maximize the success rate of the structure determination experiment. The sample holder supports the setup of crystal drops by replacing the commonly used microscope cover slips. Further, it allows in-place crystal manipulation such as ligand soaking, cryo-protection and complex formation without any opening of the crystallization cavity and without crystal handling. Finally, the sample holder has been designed in order to enable the collection of in situ X-ray diffraction data at both, ambient and cryogenic temperature. By using this sample holder, the chances to damage the crystal on its way from crystallization to diffraction data collection are considerably reduced since direct crystal handling is no longer required.

A novel sample holder for macromolecular X-ray crystallography along with a suitable handling protocol is presented. The system allows crystal growth, crystal soaking and in situ diffraction data collection at both, ambient and cryogenic temperature without the need of any crystal manipulation or mounting.

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. ...

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation

Sample preparation for mass spectrometry analysis in proteomics requires enzymatic cleavage of proteins into a peptide mixture. This process involves numerous incubation and liquid transfer steps in order to achieve denaturation, reduction, alkylation, and cleavage. Adapting this workflow onto an automated workstation can increase efficiency and reduce coefficients of variance, thereby providing more reliable data for statistical comparisons between sample types. We previously described an automated proteomic sample preparation workflow1. Here, we report the development of a more efficient and better controlled workflow with the following advantages: 1) The number of liquid transfer steps is reduced from nine to six by combining reagents; 2) Pipetting time is reduced by selective tip pipetting using a 96-position pipetting head with multiple channels; 3) Potential throughput is increased by the availability of up to 45 deck positions; 4) Complete enclosure of the system provides improved temperature and environmental control and reduces the potential for contamination of samples or reagents; and 5) The addition of stable isotope labeled peptides, as well as &#946;-galactosidase protein, to each sample makes monitoring and quality control possible throughout the entire process. These hardware and process improvements provide good reproducibility and improve intra-assay and inter-assay precision (CV of less than 20%) for LC-MS based protein and peptide quantification. The entire workflow for digesting 96 samples in a 96-well plate can be completed in approximately 5 hours.

Here, we present an automated plasma protein digestion method for mass spectrometry-based quantitative proteomic analysis. In this protocol, the liquid transferring and incubation steps for protein denaturation, reduction, alkylation, and trypsin digestion reactions are streamlined and automated. It takes approximately five hours to prepare a 96-well plate with desired precision.

Sample preparation for mass spectrometry analysis in proteomics requires enzymatic cleavage of proteins into a peptide mixture. This process involves ...

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 ...

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Proteomic technologies are powerful methodologies that can aid our understanding of mechanisms of action in biological systems by providing a global view of the impact of a disease, treatment, or other condition on the proteome as a whole. This report provides a detailed protocol for the extraction, quantification, precipitation, digestion, labeling, and subsequent data analysis of protein samples. Our optimized TMT labeling protocol requires a lower tag-label concentration and achieves consistently reliable data. We have used this protocol to evaluate protein expression profiles in a variety of mouse tissues (i.e., heart, skeletal muscle, and brain) as well as cells cultured in vitro. In addition, we demonstrate how to evaluate thousands of proteins from the resulting dataset.

We present an optimized tandem mass tag (TMT) labeling protocol that includes detailed information for each of the following steps: protein extraction, quantification, precipitation, digestion, labeling, submission to a proteomics facility, and data analyses.

Proteomic technologies are powerful methodologies that can aid our understanding of mechanisms of action in biological systems by providing a global view ...

Cryo-EM and Single-Particle Analysis with Scipion

Cryo-electron microscopy has become one of the most important tools in biological research to reveal the structural information of macromolecules at near-atomic resolution. In single-particle analysis, the vitrified sample is imaged by an electron beam and the detectors at the end of the microscope column produce movies of that sample. These movies contain thousands of images of identical particles in random orientations. The data need to go through an image processing workflow with multiple steps to obtain the final 3D reconstructed volume. The goal of the image processing workflow is to identify the acquisition parameters to be able to reconstruct the specimen under study. Scipion provides all the tools to create this workflow using several image processing packages in an integrative framework, also allowing the traceability of the results. In this article the whole image processing workflow in Scipion is presented and discussed with data coming from a real test case, giving all the details necessary to go from the movies obtained by the microscope to a high resolution final 3D reconstruction. Also, the power of using consensus tools that allow combining methods, and confirming results along every step of the workflow, improving the accuracy of the obtained results, is discussed.

Single-particle analysis in cryo-electron microscopy is one of the main techniques used to determine the structure of biological ensembles at high resolution. Scipion provides the tools to create the whole pipeline to process the information acquired by the microscope and achieve a 3D reconstruction of the biological specimen.

Cryo-electron microscopy has become one of the most important tools in biological research to reveal the structural information of macromolecules at ...

A Sample Preparation Pipeline for Microcrystals at the VMXm Beamline

The mounting of microcrystals (&#60;10 &#181;m) for single crystal cryo-crystallography presents a non-trivial challenge. Improvements in data quality have been seen for microcrystals with the development of beamline optics, beam stability and variable beam size focusing from submicron to microns, such as at the VMXm beamline at Diamond Light Source1. Further improvements in data quality will be gained through improvements in sample environment and sample preparation. Microcrystals inherently generate weaker diffraction, therefore improving the signal-to-noise is key to collecting quality X-ray diffraction data and will predominantly come from reductions in background noise. Major sources of X-ray background noise in a diffraction experiment are from their interaction with the air path before and after the sample, excess crystallization solution surrounding the sample, the presence of crystalline ice and scatter from any other beamline instrumentation or X-ray windows. The VMXm beamline comprises instrumentation and a sample preparation protocol to reduce all these sources of noise.
Firstly, an in-vacuum sample environment at VMXm removes the air path between X-ray source and sample. Next, sample preparation protocols for macromolecular crystallography at VMXm utilize a number of processes and tools adapted from cryoTEM. These include copper grids with holey carbon support films, automated blotting and plunge cooling robotics making use of liquid ethane. These tools enable the preparation of hundreds of microcrystals on a single cryoTEM grid with minimal surrounding liquid on a low-noise support. They also minimize the formation of crystalline ice from any remaining liquid surrounding the crystals. 
We present the process for preparing and assessing the quality of soluble protein microcrystals using visible light and scanning electron microscopy before mounting the samples on the VMXm beamline for X-ray diffraction experiments. We will also provide examples of good quality samples as well as those which require further optimization and strategies to do so.

The signal-to-noise ratio of data is one of the most important considerations in performing X-ray diffraction measurements from microcrystals. The VMXm beamline provides a low-noise environment and microbeam for such experiments. Here, we describe sample preparation methods for mounting and cooling microcrystals for VMXm and other microfocus macromolecular crystallography beamlines.

The mounting of microcrystals (&#60;10 &#181;m) for single crystal cryo-crystallography presents a non-trivial challenge. Improvements in data quality ...

Sample Preparation and Relative Quantitation using Reductive Methylation of Amines for Peptidomics Studies

Peptidomics can be defined as the qualitative and quantitative analysis of peptides in a biological sample. Its main applications include identifying the peptide biomarkers of disease or environmental stress, identifying neuropeptides, hormones, and bioactive intracellular peptides, discovering antimicrobial and nutraceutical peptides from protein hydrolysates, and can be used in studies to understand the proteolytic processes. The recent advance in sample preparation, separation methods, mass spectrometry techniques, and computational tools related to protein sequencing has contributed to the increase of the identified peptides number and peptidomes characterized. Peptidomic studies frequently analyze peptides that are naturally generated in cells. Here, a sample preparation protocol based on heat-inactivation is described, which eliminates protease activity, and extraction with mild conditions, so there is no peptide bonds cleavage. In addition, the relative quantitation of peptides using stable isotope labeling by reductive methylation of amines is also shown. This labeling method has some advantages as the reagents are commercially available, inexpensive compared to others, chemically stable, and allows the analysis of up to five samples in a single LC-MS run.

This article describes a sample preparation method based on heat-inactivation to preserve endogenous peptides avoiding degradation post-mortem, followed by relative quantitation using isotopic labeling plus LC-MS.

Peptidomics can be defined as the qualitative and quantitative analysis of peptides in a biological sample. Its main applications include identifying the ...

Sample Preparation using a Lipid Monolayer Method for Electron Crystallographic Studies

Electron crystallography is a powerful tool for high-resolution structure determination. Macromolecules such as soluble or membrane proteins can be grown into highly ordered two-dimensional (2D) crystals under favorable conditions. The quality of the grown 2D crystals is crucial to the resolution of the final reconstruction via 2D image processing. Over the years, lipid monolayers have been used as a supporting layer to foster the 2D crystallization of peripheral membrane proteins as well as soluble proteins. This method can also be applied to 2D crystallization of integral membrane proteins but requires more extensive empirical investigation to determine detergent and dialysis conditions to promote partitioning to the monolayer. A lipid monolayer forms at the air-water interface such that the polar lipid head groups remain hydrated in the aqueous phase and the non-polar, acyl chains, tails partition into the air, breaking the surface tension and flattening the water surface. The charged nature or distinctive chemical moieties of the head groups provide affinity for proteins in solution, promoting binding for 2D array formation. A newly formed monolayer with the 2D array can be readily transfer into an electron microscope (EM) on a carbon-coated copper grid used to lift and support the crystalline array. In this work, we describe a lipid monolayer methodology for cryogenic electron microscopic (cryo-EM) imaging.

Lipid monolayers have been used as a foundation for forming two-dimensional (2D) protein crystals for structural studies for decades. They are stable at the air-water interface and can serve as a thin supporting material for electron imaging. Here we present the proven steps on preparing lipid monolayers for biological studies.

Electron crystallography is a powerful tool for high-resolution structure determination. Macromolecules such as soluble or membrane proteins can be grown ...

A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion

Recent advances in both instrumentation and image processing software have made single-particle cryo-electron microscopy (cryo-EM) the preferred method for structural biologists to determine high-resolution structures of a wide variety of macromolecules. Multiple software suites are available to new and expert users for image processing and structure calculation, which streamline the same basic workflow: movies acquired by the microscope detectors undergo correction for beam-induced motion and contrast transfer function (CTF) estimation. Next, particle images are selected and extracted from averaged movie frames for iterative 2D and 3D classification, followed by 3D reconstruction, refinement, and validation. Because various software packages employ different algorithms and require varying levels of expertise to operate, the 3D maps they generate often differ in quality and resolution. Thus, users regularly transfer data between a variety of programs for optimal results. This paper provides a guide for users to navigate a workflow across the popular software packages: cryoSPARC v3, RELION-3, and Scipion 3 to obtain a near-atomic resolution structure of the adeno-associated virus (AAV). We first detail an image processing pipeline with cryoSPARC v3, as its efficient algorithms and easy-to-use GUI allow users to quickly arrive at a 3D map. In the next step, we use PyEM and in-house scripts to convert and transfer particle coordinates from the best quality 3D reconstruction obtained in cryoSPARC v3 to RELION-3 and Scipion 3 and recalculate 3D maps. Finally, we outline steps for further refinement and validation of the resultant structures by integrating algorithms from RELION-3 and Scipion 3. In this article, we describe how to effectively utilize three processing platforms to create a single and robust workflow applicable to a variety of data sets for high-resolution structure determination.

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

This article describes how to effectively utilize three cryo-EM processing platforms, i.e., cryoSPARC v3, RELION-3, and Scipion 3, to create a single and robust workflow applicable to a variety of single-particle data sets for high-resolution structure determination.

Recent advances in both instrumentation and image processing software have made single-particle cryo-electron microscopy (cryo-EM) the preferred method ...