Frequently Asked Questions - Proteome Sciences

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for="cat-28">TMT-SRM</label> </li> <li class="Checkbox"> <input id="cat-26" class="js-filterButton" data-id="26" type="checkbox"><label for="cat-26">SRM</label> </li> </ul> <a href="#" class="u-hidden js-clearFilters">Show All</a> </div> </div> </aside> </div> <div class="Grid-cell u-lg-sizeFull"> <div class="u-lg-hide"> <div></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">Will the SysQuant Global Phosphoproteomic workflow enable me to detect and quantify my pathway/proteins/phosphorylation sites of interest?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>While we cannot guarantee to see any specific protein, pathway or phosphorylation site, with a coverage of approximately 130,000 unique peptides and 41,000 unique phosphopeptides that map to approximately 15,000 unique phosphorylation sites, we have a very good chance of finding relevant biological processes in your study. We can also devise methods with include-lists to ensure the mass spectrometer triggers to analyze peptides of interest if they are present in the sample. Finally, all our SysQuant customers are offered an additional bioinformatics and data interpretation consultancy service which is tailor-made to each client to focus on their specific pathway/proteins/phosphorylation sites of interest.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">Why do you advise this type of enrichment for the analysis of phosphorylation over an antibody based approach?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>For SysQuant phosphoprotein enrichment, we use metal affinity chromatography as it has the best overall performance for enrichment of phosphorylated peptides relative to the sample requirements. We use IMAC resins to maximize coverage of singly and multiply phosphorylated peptides.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">What types of sample can be analysed using the SysQuant Global Phosphoproteomic workflow?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>SysQuant is designed for the analysis of tissues & cell lysates from discovery, pre-clinical & clinical studies across all therapeutic areas.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">What is the recommended amount of starting material per sample for a SysQuant study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>For each sample the minimum protein requirement is 1mg total protein with a maximum requirement of 2mg. This is approximately 40mg wet tissue, ½ a core needle biopsy or 10<sup>6</sup> – 10<sup>7</sup> cells. Protein recoveries are sample dependent and our team will discuss requirements for specific samples types during planning phase.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">What type of mass spectrometry is used for a SysQuant study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>For SysQuant workflows in general we typically use LC-MS/MS (MS2) running on UHPLC-Orbitrap Fusion Tribrid, ThermoScientific.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">Do we need to pre-treat our cells like a SILAC experiment?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>No, pre-treat of cells is not required for SysQuant. Best practice protocols for preparation of cells for a SysQuant study can be provided on request.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">How many proteins are identified in a SysQuant study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>SysQuant outputs are typically in the range 8,000 protein groups, 130,000 unique peptides and 15,000 unique phosphorylation sites with confidence score greater than pRS = 75%. Approximately 85% of all peptide spectral matches (PSM) have quantitation in all ten samples within each TMT 10plex across a SysQuant study.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">What coverage of the phosphoproteome is identified by the SysQuant workflow?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>There is no definition of a phosphoproteome in terms of numbers. We identify approximately 41,000 unique phosphopeptides in a typical human tissue study that map to approximately 15,000 unique phosphorylation site (with pRS score >=75% or high confident phospho-sites).</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">What is the sensitivity of the SysQuant workflow?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>We are often asked what is the sensitivity of the SysQuant workflow, however it is impossible to give definitive values; with greater than 8,000 proteins covered this will include many low abundance features.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">What percentage fold changes can be discerned between peptides and phosphopeptides in a SysQuant study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Using data from an in-house CNS SysQuant study of disease vs control samples we reliably can detect a significant fold change of 20% or more. For phosphorylation sites a change of approximately 25% was considered reliable.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">What is the analytical performance of the SysQuant workflow?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Using data from an in-house CNS SysQuant study of disease vs control samples a median biological CV (n=3) of 11.19% and a median analytical CV (n=4) of 7.81% at the peptide level was achieved. Analytical CV is based on the comparison of 4 reference samples analysed across four TMT<sup>®</sup> 10plex sets.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">What does the SysQuant data output look like?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>The standard data output of SysQuant is QuantSheet™, a Microsoft Excel file. We can also provide other formats such as .CSV or .txt on request. Please discuss specific requirements with our sales team.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="6" data-tag=""> <h2 class="u-redlineLeftSm">What additional bioinformatics and data interpretation packages are available for a SysQuant study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/sysquant-workflow">SysQuant</a> Global Phosphoproteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><ul> <li>PS offers its SysQuant customers a bioinformatics and data interpretation consultancy service.</li> <li>This service is designed to enable our SysQuant customers to unlock the valuable insight contained within their data.</li> <li>As a consultancy service the details and outputs are discussed with our customers on a case by case basis, to meet the needs of the customer and are typically charged at a daily rate.  Please contact us for more details on this.</li> </ul></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">Why do you recommend TMTcalibrator over TMT-MS3 or SRM/MRM for fluid biomarker discovery?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Using the ability to multiplex samples with Tandem Mass Tags, TMTcalibrator uniquely combines fluids and tissues or cells lines to bias biomarker discovery towards disease-related biomarkers. The use of an excess of disease tissue sample ensures that all representative biomarkers are present in each analysis and forces the mass spectrometer to mostly select tissue-derived peptides for analysis. Because the same peptide present in the body fluid will also be selected for analysis at the same time, due to the isobaric TMT labelling, we substantially increase sensitivity and reduce the frequency of peptides from the normal higher abundance fluid proteins.  </p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">What types of sample can be analyzed using the TMTcalibrator workflow?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>In biomarker discovery studies TMTcalibrator requires two types of sample;</p> <ul> <li>The peripheral fluid (CSF, Plasma) in which you want to look for disease associated biomarkers</li> <li>A calibrant sample (tissue or cells) that is associated to the pathophysiology of the disease</li> </ul> <p>In validation studies, synthetic or recombinant peptides can also be used as the calibrant sample.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">Can synthetic or recombinant peptides be used as the calibrant in a TMTcalibrator study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Yes, synthetic or recombinant peptides can be used when using TMTcalibrator for validation studies or as an absolute qualification method.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">What is the recommended amount of starting material per sample for a TMTcalibrator study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>TMTcalibrator usually requires around 50 – 100 micrograms of protein from each fluid sample and around 800 micrograms of protein for the calibration sample. If combining TMTcalibrator with phosphopeptide enrichment we require approximately 10 times this amount for both fluids and the calibrant.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">What type of mass spectrometry is used for a TMTcalibrator study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>For TMTcalibrator we typically use LC-MS/MS (MS2) running on UHPLC-Orbitrap Fusion Tribrid, ThermoScientific.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">Can enrichment or immunoprecipitation be incorporated into a TMTcalibrator study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Yes. We have successfully combined TMTcalibrator with metal affinity enrichment of phosphopeptides. In principle any enrichment method can be followed, though careful consideration must be given when using immunoprecipitation methods. Please contact us discuss your specific requirements.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">Is it possible to incorporate an include list into the mass spectrometry method for TMTcalibrator?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>It is possible to add an include list to any of our mass spectrometry methods however for TMTcalibrator an include list would not normally be required. This is because the calibrator trigger provides excellent protein coverage without the need to run include list that can reduce the total number of peptides and proteins identified.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">How many proteins are identified in a TMTcalibrator study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>TMTcalibrator typical performance stats;</p> <ul> <li>Approx 500,000 data points, 50,000 peptides, 4,000 proteins.</li> </ul> <p>The peptides and proteins that are identified in TMTcalibrator originate from three groups;</p> <ul> <li>Fluid proteins</li> <li>Tissue proteins</li> <li>Tissues proteins that have filtered into the fluid.</li> </ul> <p>It is the proteins within this final group that are the best candidate fluid biomarkers of disease.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">What is the sensitivity of the TMTcalibrator workflow?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Sensitivity of TMTcalibrator will vary from peptide to peptide and is influenced by the efficiency of trypsin digestion of the parent protein and the ease of ionisation of the TMT-labelled peptide relative to other peptides eluting at the same time. We have been able to detect peptides from proteins known to be at concentrations of around 100 pg/ml in CSF and similar low abundance targets in plasma such as myelin basic protein, neurogranin and PDGF receptor alpha.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">What does the TMTcalibrator data output look like?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>The standard data output of TMTcalibrator is QuantSheet, a Microsoft Excel file. We can also provide other formats such as .CSV or .txt on request. Please discuss specific requirements with our sales team.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="14" data-tag=""> <h2 class="u-redlineLeftSm">What additional bioinformatics and data interpretation packages are available for a TMTcalibrator study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmtcalibrator-workflow">TMTcalibrator</a> tissue-enhanced fluid proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><ul> <li>PS offers its TMTcalibrator customers a bioinformatics and data interpretation consultancy service.</li> <li>This service is designed to enable our TMTcalibrator customers to unlock the valuable insight contained within their data.</li> <li>As a consultancy service the details and outputs are discussed with our customers on a case by case basis, to meet the needs of the customer and are typically charged at a daily rate. Please contact us for further details.</li> </ul></div> </div> <div class="u-margBottom5 js-filterItem" data-category="24" data-tag=""> <h2 class="u-redlineLeftSm">What types of sample can be analyzed using the TMT-MS3 workflow?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms3-workflow">TMT-MS3</a> quantitative proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>While all samples types, across all therapeutic areas can be analyzed in a TMT-MS3 study we particularly recommend it for plasma biomarker discovery and other highly complex samples where quantitative accuracy is the most important factor.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="24" data-tag=""> <h2 class="u-redlineLeftSm">How many samples can be analyzed in a TMT-MS3 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms3-workflow">TMT-MS3</a> quantitative proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Sample multiplexing in TMT-MS3 studies is achieved using TMT-11 and TMT-18 plex tags. When sample numbers exceed 11 or 18 samples, one of the channel is used as a pooled reference bridging channel, such that, for example each TMT 18-plex set contains 17 study samples plus the reference sample.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="24" data-tag=""> <h2 class="u-redlineLeftSm">What is the recommended amount of starting material per sample for a TMT-MS3 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms3-workflow">TMT-MS3</a> quantitative proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>The standard TMT labelling protocol requires a minimum of 100 µg total protein per sample. We also request a minimum of 50µg total protein for sample quality control to assess the suitability of samples for analysis.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="24" data-tag=""> <h2 class="u-redlineLeftSm">Can enrichment or immunoprecipitation be incorporated into a TMT-MS3 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms3-workflow">TMT-MS3</a> quantitative proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Yes, TMT based workflows are compatible with a wide range of proteomic techniques. Please contact us discuss your specific requirements. If you are specifically interested in phosphopeptide (or other PTM's) enrichment please see our SysQuant workflow.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="24" data-tag=""> <h2 class="u-redlineLeftSm">What type of mass spectrometry is used for a TMT-MS3 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms3-workflow">TMT-MS3</a> quantitative proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>TMT-MS3 studies are run on either a UHPLC-Orbitrap Fusion Tribrid or a UHPLC-Orbitrap Exploris 480, both from ThermoScientific. Please contact us discuss your specific requirements.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="24" data-tag=""> <h2 class="u-redlineLeftSm">Is it possible to incorporate an include list into the mass spectrometry method for a TMT-MS3 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms3-workflow">TMT-MS3</a> quantitative proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Yes, it is possible to add an include list to the mass spectrometry method in TMT-MS3 studies. Please contact us discuss your specific requirements.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="24" data-tag=""> <h2 class="u-redlineLeftSm">What does the TMT-MS3 data output look like?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms3-workflow">TMT-MS3</a> quantitative proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>The standard data output of TMT-MS3 is QuantSheet, a Microsoft Excel file. We can also provide other formats such as .CSV or .txt on request. Please contact us to discuss your specific requirements.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="24" data-tag=""> <h2 class="u-redlineLeftSm">What additional bioinformatics and data interpretation packages are available for a TMT-MS3 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms3-workflow">TMT-MS3</a> quantitative proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><ul> <li>PS offers its TMT-MS3 customers a bioinformatics and data interpretation consultancy service.</li> <li>This service is designed to enable our TMT®MS3 customers to unlock the valuable insight contained within their data.</li> <li>As a consultancy service the details and outputs are discussed with our customers on a case by case basis, to meet the needs of the customer and are typically charged at a daily rate.  Please contact us for further details.</li> </ul></div> </div> <div class="u-margBottom5 js-filterItem" data-category="26" data-tag=""> <h2 class="u-redlineLeftSm">What is SRM?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/srm">SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Selective Reaction Monitoring (SRM) is a targeted mass spectrometry assay format that enables absolute biomarker quantitation.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="26" data-tag=""> <h2 class="u-redlineLeftSm">Why should I choose a SRM assay over a TMT-SRM assay for candidate biomarker validation?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/srm">SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>We recommend a classical SRM assay for:</p> <ul> <li>Absolute biomarker quantitation</li> <li>A bespoke list of candidates generated from the literature a biomarker discovery project that did not use TMT</li> <li>A bespoke list of post-translational modifications on particular protein(s)</li> <li>Customers looking to obtain specific measurements of endogenous as well as transgene proteins in pre-clinical models.</li> </ul></div> </div> <div class="u-margBottom5 js-filterItem" data-category="26" data-tag=""> <h2 class="u-redlineLeftSm">Why should I choose a SRM assay over an antibody based method for candidate biomarker validation?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/srm">SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>SRM is particularly suited to the measurement of candidates that do not have commercially available antibodies especially post-translational modifications, protein isoforms and species specific proteins.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="26" data-tag=""> <h2 class="u-redlineLeftSm">How many proteins can be included in a SRM Assay?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/srm">SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>SRM assays are typically developed for between 5 to 50 biomarker candidates.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="26" data-tag=""> <h2 class="u-redlineLeftSm">What are the stages of SRM Assay Development?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/srm">SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>There are six stages in the SRM Assay Development process:</p> <ul> <li>Phase 1 - Selection of proteotypic peptides</li> <li>Phase 2 - Ordering AQUA peptides (if required)</li> <li>Phase 3 - SRM assay development and validation</li> <li>Phase 4 - Optimization of sample preparation (if required)</li> <li>Phase 5 - Biomarker qualification in small cohort</li> <li>Phase 6 - Biomarker validation in larger cohort</li> </ul></div> </div> <div class="u-margBottom5 js-filterItem" data-category="26" data-tag=""> <h2 class="u-redlineLeftSm">What types of sample can be analyzed using a SRM assay?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/srm">SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>All sample types including cell and tissue lysates and body fluids such as CSF and plasma across all therapeutic areas can be analyzed in a SRM Assay.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="26" data-tag=""> <h2 class="u-redlineLeftSm">What performance characteristics are defined during TMT-SRM assay development?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/srm">SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>LOD, LOQ, precision and linear working range.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="26" data-tag=""> <h2 class="u-redlineLeftSm">What type of mass spectrometry is used for a SRM study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/srm">SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>SRM Assays are developed and ran on a UHPLC-TSQ Vantage Triple Stage Quadrupole LC/MS Mass Spectrometer from ThermoScientific.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="26" data-tag=""> <h2 class="u-redlineLeftSm">What does the SRM data output look like?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/srm">SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Quantitative values for each analyte are provided normally in a simple spreadsheet format.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="26" data-tag=""> <h2 class="u-redlineLeftSm">What additional bioinformatics and data interpretation packages are available for a SRM study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/srm">SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><ul> <li>PS offers its SRM customers a biostatistics consultancy service.</li> <li>As a consultancy service the details and outputs are discussed with our customers on a case by case basis, to meet the needs of the customer and are typically charged at a daily rate. Please contact us for further details.</li> </ul></div> </div> <div class="u-margBottom5 js-filterItem" data-category="28" data-tag=""> <h2 class="u-redlineLeftSm">What is TMT-SRM?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-srm">TMT-SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>TMT-SRM is a targeted mass spectrometry assay format that enables the rapid validation of biomarker candidates.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="28" data-tag=""> <h2 class="u-redlineLeftSm">Why should I choose a TMT-SRM assay over a SRM assay for candidate biomarker validation?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-srm">TMT-SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>TMT-SRM is particularly suited to candidates identified in TMT discovery workflows (<a class="u-linkSubtle" href="/services/sysquant-workflow" title="SysQuant®">SysQuant</a> , <a class="u-linkSubtle" href="/services/tmtcalibrator-workflow" title="TMTcalibrator™ Workflow">TMTcalibrator</a>, <a class="u-linkSubtle" href="/services/tmt-ms2-workflow" title="TMT®MS2 Workflow">TMT-MS2</a>, <a class="u-linkSubtle" href="/services/tmt-ms3-workflow" title="TMT®MS3 Workflow">TMT-MS3</a>) providing a faster and less expensive approach to biomarker validation than classical SRM.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="28" data-tag=""> <h2 class="u-redlineLeftSm">Why should I choose a TMT-SRM assay over an antibody based method for candidate biomarker validation?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-srm">TMT-SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Development of a TMT-SRM assay offers a bespoke approach to validate your candidates in one single assay without the need to purchase multiple antibodies for Western Blotting or ELISA kits.TMT-SRM is particularly suited to the validation of proteins and post-translational modifications that do not have commercially available antibodies.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="28" data-tag=""> <h2 class="u-redlineLeftSm">How many proteins can be included in a TMT-SRM Assay?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-srm">TMT-SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>TMT®SRM assays are typically developed for between 5 and 50 biomarker candidates.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="28" data-tag=""> <h2 class="u-redlineLeftSm">What are the stages of TMT-SRM Assay Development?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-srm">TMT-SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>There are four stages in the TMT-SRM Assay Development process:</p> <ul> <li>Phase 1 - Selection of proteotypic peptides</li> <li>Phase 2 - TMT-SRM assay development and validation</li> <li>Phase 3 - Biomarker qualification in small cohort</li> <li>Phase 4 - Biomarker validation in larger cohort</li> </ul></div> </div> <div class="u-margBottom5 js-filterItem" data-category="28" data-tag=""> <h2 class="u-redlineLeftSm">What types of sample can be analysed using a TMT-SRM assay?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-srm">TMT-SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>All sample types including cell and tissue lysates and body fluids such as CSF and plasma across all therapeutic areas can be analyzed in a TMT-SRM Assay.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="28" data-tag=""> <h2 class="u-redlineLeftSm">What performance characteristics are defined during TMT-SRM assay development?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-srm">TMT-SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>LOD, LOQ, precision and linear working range.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="28" data-tag=""> <h2 class="u-redlineLeftSm">What type of mass spectrometry is used for a TMT-SRM study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-srm">TMT-SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>TMT-SRM Assays are developed and ran on a UHPLC-TSQ Vantage Triple Stage Quadrupole LC/MS Mass Spectrometer from Thermo Scientific.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="28" data-tag=""> <h2 class="u-redlineLeftSm">What does the TMT-SRM data output look like?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-srm">TMT-SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Quantitative values for each analyte are provided normally in a simple spreadsheet format.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="28" data-tag=""> <h2 class="u-redlineLeftSm">What additional bioinformatics and data interpretation packages are available for a TMT-SRM study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-srm">TMT-SRM</a> Assay Development </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><ul> <li>PS offers its TMT-SRM customers a biostatistics consultancy service.</li> <li>As a consultancy service the details and outputs are discussed with our customers on a case by case basis, to meet the needs of the customer and are typically charged at a daily rate. Please contact us for further details.</li> </ul></div> </div> <div class="u-margBottom5 js-filterItem" data-category="31" data-tag=""> <h2 class="u-redlineLeftSm">What is TMT-MS2?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms2-workflow">TMT-MS2</a> Broadest Coverage Workflow </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>TMT-MS2 is our standard quantitative proteomics workflow for the analysis of cells and tissues when phosphopeptide enrichment is not required. The workflow combines the multiplexing power of tandem mass tags (TMT), with state-of-the-art mass spectrometry (MS) and bioinformatics to provide the broadest and deepest analysis of the proteome with excellent precision.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="31" data-tag=""> <h2 class="u-redlineLeftSm">What types of sample can be analyzed using the TMT-MS2 workflow?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms2-workflow">TMT-MS2</a> Broadest Coverage Workflow </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>While all samples types, across all therapeutic areas can be analysed in a TMT-MS2 study we particularly recommend it for the analysis of cell and tissue lysates, in applications that require the broadest coverage of the proteome.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="31" data-tag=""> <h2 class="u-redlineLeftSm">Why should I choose a TMT-MS2 study over a TMT-MS3 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms2-workflow">TMT-MS2</a> Broadest Coverage Workflow </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>In highly complex samples such as plasma quantitation using MS2 can become comprised. To overcome this a further round of fragmentation MS3 is applied. Whilst using MS3 is slower and so reduces total proteome coverage, the gain in quantitative accuracy can reveal biomarkers that would have otherwise been missed. </p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="31" data-tag=""> <h2 class="u-redlineLeftSm">How many samples can be analyzed in a TMT庐MS2 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms2-workflow">TMT-MS2</a> Broadest Coverage Workflow </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Sample multiplexing in TMT-MS2 studies is achieved using either TMT-11 and TMTpro-18plex. When sample numbers exceed 18 samples, one of the channels is used as a pooled reference bridging channel, such that each TM1-18plex set contains 17 study samples plus the reference sample. </p> <p><strong> </strong></p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="31" data-tag=""> <h2 class="u-redlineLeftSm">What is the recommended amount of starting material per sample for a TMT-MS2 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms2-workflow">TMT-MS2</a> Broadest Coverage Workflow </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>The standard TMT labelling protocol requires a minimum of 100 µg total protein per sample. We also request a minimum of 50 µg total protein for sample quality control to assess the suitability of samples for analysis. </p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="" data-tag=""> <h2 class="u-redlineLeftSm">Can enrichment or immunoprecipitation be incorporated into a TMT-MS2 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Yes, TMT workflows are compatible with a wide range of proteomic techniques. Please contact us discuss your specific requirements. If you are specifically interested in phosphopeptide enrichment please see our SysQuant workflow.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="" data-tag=""> <h2 class="u-redlineLeftSm">What type of mass spectrometry is used for a TMT-MS2 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>TMT-MS2 studies are run on either a UHPLC-Orbitrap Fusion Tribrid or a UHPLC-Orbitrap Exploris 480, both from ThermoScientific. Please contact us discuss your specific requirements. </p> <p> </p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="31" data-tag=""> <h2 class="u-redlineLeftSm">Is it possible to incorporate an include list into the mass spectrometry method for a TMT-MS2 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms2-workflow">TMT-MS2</a> Broadest Coverage Workflow </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>Yes, it is possible to add an include list to the mass spectrometry method in TMT-MS2 studies. Please contact us discuss your specific requirements.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="31" data-tag=""> <h2 class="u-redlineLeftSm">What does the TMT-MS2 data output look like?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms2-workflow">TMT-MS2</a> Broadest Coverage Workflow </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>The standard data output of TMT-MS2 is QuantSheet, a Microsoft Excel file. We can also provide other formats such as .CSV or .txt on request. Please discuss specific requirements with our sales team.</p></div> </div> <div class="u-margBottom5 js-filterItem" data-category="31" data-tag=""> <h2 class="u-redlineLeftSm">What additional bioinformatics and data interpretation packages are available for a TMT-MS2 study?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms2-workflow">TMT-MS2</a> Broadest Coverage Workflow </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><ul> <li>PS offers its TMT-MS2 customers a bioinformatics and data interpretation consultancy service.</li> <li>This service is designed to enable our TMT-MS2 customers to unlock the valuable insight contained within their data.</li> <li>As a consultancy service the details and outputs are discussed with our customers on a case by case basis, to meet the needs of the customer and are typically charged at a daily rate.</li> </ul></div> </div> <div class="u-margBottom5 js-filterItem" data-category="24" data-tag=""> <h2 class="u-redlineLeftSm">What is TMT-MS3?</h2> <div class="Grid Grid--fit u-darkerText u-margBottom2"> <div class="Grid-cell u-sizeAuto">Product: </div> <div class="Grid-cell u-md-sizeFull"> <span class="u-textNoWrap"><a href="/services/tmt-ms3-workflow">TMT-MS3</a> quantitative proteomics </span> </div> </div> <div class="ShadeContent u-margBottom2 u-padRight5"><p>TMT-MS3 is our standard workflow for plasma biomarker discovery and other highly complex samples where quantitative accuracy is the most important factor. The workflow combines the multiplexing power of tandem mass tags (TMT), with state of the art mass spectrometry (MS), MS3 fragmentation & bioinformatics to provide the most accurate quantitative results while retaining good coverage.</p></div> </div> </div> </div> </div> </div> <div class="DisplayBanner DisplayBanner--blueGradient u-colorWhite"> <div class="DisplayBanner-overlay" style="background-image: url('https://files.aptuitivcdn.com/JxEdylMPMz-1515/theme/custom/images/hero-overlay.1654711795.png')"></div> <div class="Container"> <div class="Content u-padBottom4"> <div class="u-textCenter u-margTop3 u-margBottom5"> <img src="https://files.aptuitivcdn.com/JxEdylMPMz-1515/theme/custom/images/logo-white-alt.1654711795.svg" width="90px" height="auto"> <h2 class="u-largeText u-margTop3 u-margBottom4">Measuring Proteins for Better Medicines</h2> <a class="Button Button--secondary" href="#">learn more</a> </div> </div> </div> </div> </main> <footer class="Footer"> <div class="Footer-upper"> <div class="Container"> <div class="Grid Grid--fit Grid--alignMiddle"> <div class="Grid-cell u-sizeAuto u-lg-hide"> <a href="/" title="Back to home page"> <img class="Footer-logo" src="https://files.aptuitivcdn.com/JxEdylMPMz-1515/theme/custom/images/logo-white.1654711795.svg" alt="Proteome Sciences"> </a> </div> <div class="Grid-cell u-lg-sizeFull u-lg-textCenter"> <ul class="FooterNav"> <li class="FooterNav-item is-first"> <a href="/about" class="is-first FooterNav-link">About Us</a> </li> <li class="FooterNav-item"> <a href="/services" class="FooterNav-link">Proteomic Services</a> </li> <li class="FooterNav-item"> <a href="/news" class="FooterNav-link">News</a> </li> <li class="FooterNav-item"> <a href="/investors" class="FooterNav-link">Investors</a> </li> <li class="FooterNav-item"> <a href="/contact" class="FooterNav-link">Contact</a> </li> <li class="FooterNav-item is-last"> <a href="/privacy-notice" class="is-last FooterNav-link">Privacy Notice</a> </li> </ul> </div> <div class="Grid-cell u-sizeAuto u-lg-size1of2 u-textRight u-lg-textCenter u-sm-sizeFull u-sm-margBottom4"> <img src="https://files.aptuitivcdn.com/JxEdylMPMz-1515/images/ISO-9001-2.2015.jpg" height="125" width="150" alt="DQS Quality Management" class="Footer-badge"> <a href="https://twitter.com/ProteomeScience" title="Follow us on Twitter" class="Footer-iconLink" target="_blank" rel="noopenner noreferrer"> <svg class="Footer-icon Icon" role="img" alt="Twitter" aria-labelledby="iconTitle-rezmJx" focusable="false"><title id="iconTitle-rezmJx">Twitter</title><use xlink:href="#icon-twitter" /></svg></a> <a href="https://www.linkedin.com/company/proteome-sciences-plc" title="Follow us on LinkedIn" class="Footer-iconLink" target="_blank" rel="noopenner noreferrer"> <svg class="Footer-icon Icon" role="img" alt="LinkedIn" aria-labelledby="iconTitle-HpZDQ2" focusable="false"><title id="iconTitle-HpZDQ2">LinkedIn</title><use xlink:href="#icon-linkedin" /></svg></a> </div> </div> </div> </div> <div class="Container u-spaced1 u-gutters1"> <div class="Grid Grid--fit Grid--alignMiddle"> <div class="Grid-cell u-sizeAuto u-md-size1of2 u-md-textCenter u-sm-sizeFull u-sm-margBottom1 u-darkerText">Copyright © Proteome Sciences 2024</div> <div class="Grid-cell u-md-size1of2 u-md-textCenter u-sm-sizeFull u-darkerText"></div> <div class="Grid-cell u-sizeAuto u-md-sizeFull u-md-textCenter"> <div class="Footer-credit u-inlineBlock"> <a href="https://www.aptuitiv.com" target="_blank" class="Footer-link Footer-creditLink">Site Design By Aptuitiv</a>-<a href="https://www.branchcms.com" target="_blank" class="Footer-link Footer-creditLink">Powered by BranchCMS</a> </div> </div> </div> </div> </footer> <script> tarteaucitron.services.recaptchav3 = { "key": "recaptchav3", "type": "analytic", "name": "reCAPTCHA", "needConsent": true, "cookies": ['_GRECAPTCHA', 'AEC'], "js": function () { "use strict"; 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Frequently Asked Questions - Proteome Sciences