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class="post-14092 post type-post status-publish format-standard has-post-thumbnail category-proteomics tag-lc-ms entry" aria-label="Top 3 Tools Single-Cell Proteomics Researchers Need for a Big Breakthrough"><header class="entry-header"><h1 class="entry-title">Top 3 Tools Single-Cell Proteomics Researchers Need for a Big Breakthrough</h1> <span class="post-info-author"> By <a href="https://www.thermofisher.com/blog/analyteguru/tf-author/alec-valenta/" title="Posts by Alec Valenta" rel="author">Alec Valenta, Product Marketing Specialist, HPLC, Thermo Fisher Scientific</a> </span> <span class="post-info-date"> 05.24.2023 </span> </header><div class="entry-content"> <p>The emergence of single-cell proteomics (SCP) is set to revolutionize the field of precision medicine – a diagnostic approach that develops treatments to fit specific genetic and molecular characteristics.</p> <p>Understanding the etiology of complex diseases is rooted in cellular biochemistry. But before you can develop effective and targeted therapeutics, you need to identify how the metabolic pathways, expression and regulation of proteins change in diseased versus normal cells.</p> <div class="wp-block-image"> <figure class="alignright size-full is-resized"><img decoding="async" width="1000" height="750" src="https://www.thermofisher.com/blog/analyteguru/wp-content/uploads/sites/25/2023/06/Single-Cell-Proteomics-1.jpg" alt="Cells in single-cell proteomics" class="wp-image-14093" style="width:439px;height:329px" srcset="https://www.thermofisher.com/blog/analyteguru/wp-content/uploads/sites/25/2023/06/Single-Cell-Proteomics-1.jpg 1000w, https://www.thermofisher.com/blog/analyteguru/wp-content/uploads/sites/25/2023/06/Single-Cell-Proteomics-1-300x225.jpg 300w, https://www.thermofisher.com/blog/analyteguru/wp-content/uploads/sites/25/2023/06/Single-Cell-Proteomics-1-768x576.jpg 768w" sizes="(max-width: 1000px) 100vw, 1000px" /></figure></div> <p>Also, when you analyze large groups of heterogenous cells together (e.g., tissues, plasma, etc.) in traditional proteomics approaches, a significant amount of information about the content of individual cell types is effectively lost or averaged out.</p> <p>A deep understanding of disease states hinges on insight into the behavior of these individual cell types. The problem is the average “simple” cell has <a href="https://www.cell.com/pb-assets/journals/research/cell-systems/cels_384.pdf" target="_blank" rel="noreferrer noopener">millions of proteins</a>, so you need high-performance LC-MS technology to elucidate changes in protein expression, most importantly, without bias.</p> <p>That’s where successful proteomics researchers like <a href="https://twitter.com/karl_mechtler" target="_blank" rel="noreferrer noopener">Karl Mechtler</a> (Institute of Molecular Pathology, Vienna) shine. Our <a href="https://www.biorxiv.org/content/10.1101/2023.04.27.538542v1.full.pdf" target="_blank" rel="noreferrer noopener">new manuscript in Biorxiv</a> in collaboration with Dr. Mechtler’s group demonstrates a high throughput, <a href="https://www.analyteguru.com/t5/Blog/LC-Separation-in-Proteomics-Why-You-Can-t-Afford-to-Ignore-It/ba-p/20196" target="_blank" rel="noreferrer noopener">proteome coverage</a>, and quantitative precision in <a href="https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/proteomics-mass-spectrometry/single-cell-proteomics.html">single-cell proteomics</a> using our low-flow tools.</p> <p><strong>The major takeaway points from our groundbreaking work are</strong>:</p> <ul class="wp-block-list"> <li>Higher LC-MS sensitivity was achieved by employing a <a href="https://www.thermofisher.com/order/catalog/product/VN-S10-A-01" target="_blank" rel="noreferrer noopener">low nano-flow rate</a> (100 nL/min) and <a href="https://www.thermofisher.com/order/catalog/product/164946?SID=srch-srp-164946" target="_blank" rel="noreferrer noopener">narrow I.D. column</a>s (50 µm)</li> <li>High sample throughput (100 samples/day) is possible by using a trap-and-elute workflow and optimized methods</li> <li>A 10-min elution window provides <a href="https://www.thermofisher.com/order/catalog/product/BRE725539" target="_blank" rel="noreferrer noopener">high MS utilization</a> (~70 percent) without sacrificing data quality</li> <li>Reproducible inter-lab performance was observed in single-cell and standard diluted samples</li> <li>State-of-the-art separation technology enabled the identification of  >2,200 and >1,700 protein groups from 250 pg diluted standard and single-cell samples, respectively, using <a href="https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-systems/orbitrap-lc-ms/orbitrap-exploris-mass-spectrometers/velocity-data-independent-acquisition-platform.html" target="_blank" rel="noreferrer noopener">library-free DIA searches</a></li> </ul> <div class="wp-block-image"> <figure class="alignright size-full is-resized"><img decoding="async" width="800" height="533" src="https://www.thermofisher.com/blog/analyteguru/wp-content/uploads/sites/25/2023/06/Single-Cell-4-5.jpg" alt="Successful proteomics researchers" class="wp-image-14098" style="width:400px;height:267px" srcset="https://www.thermofisher.com/blog/analyteguru/wp-content/uploads/sites/25/2023/06/Single-Cell-4-5.jpg 800w, https://www.thermofisher.com/blog/analyteguru/wp-content/uploads/sites/25/2023/06/Single-Cell-4-5-300x200.jpg 300w, https://www.thermofisher.com/blog/analyteguru/wp-content/uploads/sites/25/2023/06/Single-Cell-4-5-768x512.jpg 768w, https://www.thermofisher.com/blog/analyteguru/wp-content/uploads/sites/25/2023/06/Single-Cell-4-5-96x65.jpg 96w" sizes="(max-width: 800px) 100vw, 800px" /></figure></div> <p class="has-medium-font-size">To our knowledge, this study represents the most comprehensive proteome coverage in the SCP workflow space to date.</p> <p>Teamwork truly makes the dreamwork!</p> <p>P.S. Don’t forget to explore our top three proteomics tools today:</p> <ol class="wp-block-list"> <li><a href="https://www.thermofisher.com/us/en/home/products-and-services/promotions/industrial/vanquish-neo-beyond-brilliant.html" target="_blank" rel="noreferrer noopener">Thermo Scientific Vanquish Neo UHPLC System</a></li> <li><a href="https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-systems/orbitrap-lc-ms/orbitrap-exploris-mass-spectrometers/orbitrap-exploris-480-mass-spectrometers.html" target="_blank" rel="noreferrer noopener">Thermo Scientific Orbitrap Exploris 480 Mass Spectrometer</a></li> <li><a href="https://www.thermofisher.com/us/en/home/industrial/chromatography/chromatography-consumables/hplc-uhplc-columns/low-flow-hplc-columns.html" target="_blank" rel="noreferrer noopener">Thermo Scientific low-flow columns</a></li> </ol> <p></p> <p></p> </div></article><section class="author-box"><h4 class="author-box-title">Alec Valenta</h4><div class="author-box-content" itemprop="description">Alec Valenta is a Product Marketing Specialist for Chromatography and Mass Spectrometry, Thermo Fisher Scientific</div></section><div class="adjacent-entry-pagination pagination"><div class="pagination-previous alignleft"><i class="fa fa-icon fa-chevron-left"></i> <a href="https://www.thermofisher.com/blog/analyteguru/quality-risk-management-dont-discard-standard-lab-practices/" rel="prev">Quality Risk Management: Don’t Discard Standard Lab Practices</a></div><div class="pagination-next alignright"><a href="https://www.thermofisher.com/blog/analyteguru/complex-carbohydrate-analysis-by-hpae-pad-made-easier-just-add-water/" rel="next">Complex Carbohydrate Analysis by HPAE-PAD Made Easier: ‘Just Add Water’</a> <i class="fa fa-icon fa-chevron-right"></i></div></div></main></div></div><footer class="site-footer"><div class="wrap"><div class="creds"><p class="footer-links"><a href="https://corporate.thermofisher.com/en/footer/privacy-statement.html" target="_blank" rel="noopener noreferrer">Privacy Statement</a><a href="https://corporate.thermofisher.com/en/footer/terms-and-conditions.html" target="_blank" rel="noopener noreferrer">Terms & Conditions</a><a href="/blog/locations/">Locations</a><a href="/blog/sitemap/">Sitemap</a></p><p>© 2024 <a href="https://www.thermofisher.com">Thermo Fisher Scientific</a>. 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