<p><strong>Per- and polyfluoroalkyl substances (PFAS) have become a major global concern due to their persistence, bioaccumulation, and potential health impacts. With thousands of known PFAS compounds, and new variants continuing to emerge, identifying and quantifying them across complex environmental and biological samples is an ongoing analytical challenge.</strong></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_From_Complexity_to_Clarity_Smarter_PFAS_Identification_Workflows_in_Compound_Discoverer_Software_2_8e83167891.jpg" alt="Thermo Fisher Scientific: From Complexity to Clarity: Smarter PFAS Identification Workflows in Compound Discoverer Software" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_From_Complexity_to_Clarity_Smarter_PFAS_Identification_Workflows_in_Compound_Discoverer_Software_2_8e83167891.jpg 245w," sizes="100vw" width="1024" height="574"></p><h3><strong>Why PFAS analysis matters</strong></h3><p>PFAS are used in everything from firefighting foams to non-stick coatings, yet their chemical stability means they persist in the environment and accumulate in living organisms. Regulators and scientists around the world are racing to better understand their distribution, fate, and toxicity.</p><p>But with tens of thousands of PFAS, many without available reference standards, traditional targeted analysis alone isn’t enough. Analysts increasingly rely on non-targeted analysis (NTA) workflows powered by high-resolution accurate-mass (HRAM) mass spectrometry and advanced software to uncover the full picture.</p><h3><strong>Addressing the challenges of PFAS identification</strong></h3><p>Successful non-targeted PFAS analysis requires overcoming several analytical hurdles:</p><ol><li>Acquiring high-quality MS¹ and MS² data with ultra-high mass resolution and accuracy.</li><li>Detecting low-abundance PFAS hidden within thousands of background compounds.</li><li>Leveraging comprehensive spectral libraries and databases for confident identification.</li><li>Applying data filtering and scoring tools to assign confidence levels to annotations.</li><li>Using visualization and statistical tools to interpret and compare complex datasets.</li></ol><p><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Thermo Scientific Compound Discoverer 3.5 software </strong></a>brings together all the components needed for robust PFAS identification—integrating <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=22&amp;manufacturerItems=3"><strong>HRAM Orbitrap MS</strong></a> data with an expanded suite of PFAS-specific libraries and databases.</p><p><strong>In a single workflow, users can:</strong></p><ul><li>Detect and annotate compounds automatically from LC-MS data.</li><li>Determine possible elemental formulas using isotope pattern and accurate mass information.</li><li>Compare MS² spectra against <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764"><strong>mzCloud</strong></a>, NIST 2023, and <i>in silico</i> PFAS libraries.</li><li>Cross-reference annotations with the EPA PFAS Structure List and the NIST Suspect List of PFAS.</li><li>Use PFAS-specific fragment and neutral loss databases to strengthen identification confidence.</li></ul><p>With these resources combined, the software enables confident annotation of more than<strong> 40,000 PFAS </strong>compounds!</p><h3><strong>New tools for confident, streamlined PFAS identification</strong></h3><p>Compound Discoverer software introduces several new features designed to simplify and accelerate PFAS NTA workflows:</p><ul><li><strong>Apply PFAS Scoring Node:</strong> Automatically calculates PFAS-specific parameters and a new PFAS Score—no R scripting required.</li><li><strong>PFAS Plot:</strong> A visual tool that uses mass-defect metrics to highlight probable PFAS in complex datasets, following methods from Kaufman et al. (2022).</li><li><strong>Expanded suite of libraries and databases:</strong> Combines mzCloud, NIST, <i>in silico</i>, PFAS fragment databases, and a new neutral loss database for greater confidence.</li><li><strong>Advanced data visualization:</strong> Tools like Kendrick Mass Defect and Molecular Network plots reveal homologous PFAS series and related compound families.</li><li><strong>Built-in statistical analysis tools</strong>: Compare PFAS composition between samples using Principal Component Analysis, Differential analysis and Hierarchical Cluster Analysis.</li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_From_Complexity_to_Clarity_Smarter_PFAS_Identification_Workflows_in_Compound_Discoverer_Software_ed32c7f7c1.jpg" alt="Thermo Fisher Scientific From Complexity to Clarity Smarter PFAS Identification Workflows in Compound Discoverer Software" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_From_Complexity_to_Clarity_Smarter_PFAS_Identification_Workflows_in_Compound_Discoverer_Software_ed32c7f7c1.jpg 245w," sizes="100vw" width="800" height="395"></p><h3><strong>From complexity to clarity</strong></h3><p>By uniting Orbitrap HRAM data with the most comprehensive PFAS libraries available, Compound Discoverer 3.5 software streamlines non-targeted PFAS analysis—helping laboratories move from data complexity to confident chemical clarity.</p><p><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5612"><strong>Watch the on-demand webinar</strong></a> to see the full workflow in action and learn how Compound Discoverer software can enhance your PFAS analysis.</p><ul><li><strong>Visit us on&nbsp;</strong><a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/"><strong><u>LinkedIn:</u></strong></a>&nbsp;#PFAS #CompoundDiscoverer #SpectralLibraries</li></ul><blockquote><h5><strong>Zoe Julian</strong></h5><p>Zoe Julian is a Product Marketing Manager for Chromatography and Mass Spectrometry software at Thermo Fisher Scientific. With over 12 years' experience of working with chromatography and mass spectrometry techniques with a background in GC and GC-MS(/MS) organic environmental analysis, she has helped many laboratories and industries improve their workflows through a unique understanding of their challenges. Transitioning to a focus on Chromeleon CDS she has shown customers how software solutions can improve their productivity and support their day-to-day operations.</p></blockquote>

From Complexity to Clarity: Smarter PFAS Identification Workflows in Compound Discoverer Software

<h3><strong>Two Dimensions, One Solution: Advancing Oligonucleotide Analysis with 2D-LC</strong></h3><h4><strong>Why Consider 2D-LC for Oligonucleotide Analysis?</strong></h4><p>In oligonucleotide analytics, achieving reliable and precise results is not optional—it is fundamental. These biomolecules are inherently complex, often containing truncated sequences, structural variants, and a wide range of impurities. Such complexity frequently exceeds the separation capabilities of conventional one-dimensional liquid chromatography (1D-LC). As a result, critical components may coelute or remain unresolved, limiting analytical confidence.</p><p><strong>Two-dimensional liquid chromatography (2D-LC) </strong>offers a powerful alternative by significantly enhancing separation performance. By combining two complementary separation mechanisms, 2D-LC improves resolution, sensitivity, and overall analytical reliability. This enables a much deeper understanding of oligonucleotide samples and their compositional intricacies.</p><blockquote><h4><strong>Previous parts from the Oligos Made Easy</strong> <strong>series</strong></h4><ul><li><strong>Part 1: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6808"><strong>Overview</strong></a></li><li><strong>Part 2: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6846"><strong>AEX</strong></a></li><li><strong>Part 3: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6880"><strong>IP-RP</strong></a></li><li><strong>Part 4: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6912"><strong>HILIC</strong></a></li><li><strong>Part 5: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6944"><strong>SEC</strong></a></li><li><strong>Part 6: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6982"><strong>Column Navigator</strong></a></li><li><strong>Part 7: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/7012"><strong>Large Scale AEX</strong></a></li><li><strong>Part 8: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/7045"><strong>Sepapure oliGO</strong></a></li></ul></blockquote><h4><strong>Moving Beyond the Limits of 1D-LC</strong></h4><p>For many years, 1D-LC has served as a standard tool for biopharmaceutical characterization. However, its inherent limitations become apparent when dealing with highly complex mixtures. The selectivity of a single chromatographic dimension is restricted, and the lack of orthogonality in retention mechanisms often results in insufficient separation. As sample complexity increases, the resolving power of 1D-LC becomes inadequate.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_1_2_D_LC_Principle_Graphic_by_KNAUER_43e04d32a2.jpg" alt="KNAUER: Figure 1 - 2D-LC Principle (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_1_2_D_LC_Principle_Graphic_by_KNAUER_43e04d32a2.jpg 245w," sizes="100vw" width="1291" height="391"></p><p>Two-dimensional LC addresses these limitations by coupling two chromatographic separations, which can be either similar or fundamentally different. Each dimension targets different physicochemical properties of analytes, enabling the resolution of compounds that would otherwise overlap. In essence, 2D-LC introduces an additional level of separation capacity, allowing analysts to disentangle coeluting species that remain unresolved in a single dimension.</p><p>An important practical consideration is that the overall analysis time is governed by the second dimension. Because fractions from the first dimension must be processed sequentially, the second dimension must operate rapidly and efficiently. High-speed separations in the second dimension are therefore essential to maintain system performance and data quality.</p><h4><strong>Architecture of a 2D-LC System</strong></h4><p>At its core, a 2D-LC system relies on precise coordination between its components. The <strong>setup typically consists</strong> of <strong>two chromatographic columns</strong>, <strong>two pumping systems</strong>, and a <strong>switching valve</strong> that enables fraction transfer between dimensions. The sample is introduced through an autosampler and first separated on the primary column. Fractions of interest are then transferred into a loop via a switching valve and subsequently introduced into the second column for further separation.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_2_2_D_LC_System_Configuration_Example_Graphic_by_KNAUER_f5747adf3a.jpg" alt="KNAUER: Figure 2 -  2D LC System Configuration Example (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_2_2_D_LC_System_Configuration_Example_Graphic_by_KNAUER_f5747adf3a.jpg 245w," sizes="100vw" width="859" height="517"></p><p>The <strong>valve plays a crucial role</strong> in this process, acting as the interface between both chromatographic dimensions. Its function is to alternately <strong>collect fractions from the first dimension and inject them into the second dimension</strong> under high-pressure conditions. Various valve configurations can be employed, including ten-port or eight-port valves with dual-loop arrangements, or synchronized six-port valves. Regardless of configuration, the underlying principle remains the same: <strong>while one loop is being filled, the other is being flushed into the second dimension</strong>.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_3_Schematic_figure_of_ten_port_left_and_eight_port_valve_right_2_position_setup_for_2_D_LC_Graphic_by_KNAUER_9209661ea8.jpg" alt="KNAUER: Figure 3 - Schematic figure of ten-port (left) and eight-port valve (right) 2-position setup for 2D-LC (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_3_Schematic_figure_of_ten_port_left_and_eight_port_valve_right_2_position_setup_for_2_D_LC_Graphic_by_KNAUER_9209661ea8.jpg 245w," sizes="100vw" width="1287" height="406"></p><p>This alternating process requires <strong>precise timing</strong>. The second-dimension separation must be completed before the next fraction is ready for transfer. Consequently, synchronization between flow rates, loop volumes, and switching intervals is essential for maintaining chromatographic integrity.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_4_Schematic_figure_KNAUER_eight_port_2_position_valve_for_2_D_LC_Graphic_by_KNAUER_f9a5f06f5f.jpg" alt="KNAUER: Figure 4 - Schematic figure KNAUER eight-port 2 position valve for 2D-LC (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_4_Schematic_figure_KNAUER_eight_port_2_position_valve_for_2_D_LC_Graphic_by_KNAUER_f9a5f06f5f.jpg 245w," sizes="100vw" width="756" height="391"></p><h4><strong>Applying 2D-LC to Oligonucleotide Analysis</strong></h4><p>In oligonucleotide workflows, 2D-LC combines two complementary separation strategies to address sample complexity. The <strong>first dimension</strong> is typically used for <strong>bulk separation</strong> based on properties such as <strong>size, charge, or polarity</strong>. Techniques such as <strong>size-exclusion chromatography</strong> (SEC), <strong>anion-exchange chromatography</strong> (AEX), <strong>ion-pair reversed-phase chromatography </strong>(IP-RP), <strong>hydrophilic interaction chromatography</strong> (HILIC), or <strong>mixed-mode chromatography</strong> (MMC) are commonly applied. This step reduces sample complexity and can also serve as an online desalting stage, removing salts and buffer components that could interfere with downstream detection, particularly when mass spectrometry is used.</p><p>Following this initial separation, selected fractions are transferred to the second dimension. This transfer can be performed either selectively or comprehensively, depending on the analytical goal. The second dimension is typically optimized for high-resolution separation, allowing detailed characterization of closely related species such as truncated oligonucleotides, sequence variants, or chemically modified impurities. When coupled with mass spectrometry, this setup enables accurate identification and sequencing.</p><p>A <strong>key advantage of 2D-LC</strong> lies in the <strong>flexibility of combining different stationary phases and mobile phase</strong> conditions.&nbsp;</p><p>Numerous separation combinations are possible, including:</p><ul><li>SEC×AEX</li><li>HILIC×IP-RP</li><li>IEC×IP-RP</li><li>IP-RP×IP-RP</li><li>AEX×HIC</li><li>MMC×SEC,</li><li>and even chiral×RP systems.&nbsp;</li></ul><p>This adaptability allows tailored workflows for specific analytical challenges.</p><h4><strong>Heart-Cutting vs. Comprehensive 2D-LC</strong></h4><p>When implementing 2D-LC, two primary transfer strategies are commonly used: <strong>heart-cutting</strong> and <strong>comprehensive transfer</strong>. Each approach offers distinct advantages depending on the analytical objective.</p><p><strong>Heart-cutting 2D-LC</strong> focuses on selected regions of interest from the first dimension. Only specific peaks or time windows are transferred to the second dimension for further analysis. This approach allows extended separation time and higher resolution in the second dimension, making it particularly suitable for targeted investigations of known critical compounds. However, because only selected fractions are analyzed, unexpected impurities outside the selected region may remain undetected.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_5_2_D_LC_Single_Heart_Cut_Principle_Graphic_by_KNAUER_b1b400784b.jpg" alt="KNAUER: Figure 5 - 2D-LC Single Heart-Cut Principle (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_5_2_D_LC_Single_Heart_Cut_Principle_Graphic_by_KNAUER_b1b400784b.jpg 245w," sizes="100vw" width="1276" height="319"></p><p>In contrast, <strong>comprehensive 2D-LC</strong> transfers the entire eluate from the first dimension into the second dimension in a continuous manner. This approach provides a complete and detailed representation of the sample, making it ideal for research and development, impurity profiling, and regulatory applications. While more demanding in terms of speed and system performance, comprehensive 2D-LC ensures full sample coverage.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_6_Full_Comprehensive_2_D_LC_Principle_Graphic_by_KNAUER_e13da63ef1.jpg" alt="KNAUER: Figure 6 - Full Comprehensive  2D-LC Principle (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_6_Full_Comprehensive_2_D_LC_Principle_Graphic_by_KNAUER_e13da63ef1.jpg 245w," sizes="100vw" width="1327" height="292"></p><p>In practice, <strong>hybrid approaches may also be employed</strong>, combining targeted heart-cutting with broader comprehensive analysis to balance resolution and coverage.</p><h4><strong>Practical Considerations for Method Development</strong></h4><p>Successful implementation of 2D-LC for oligonucleotide analysis requires careful method design.&nbsp;</p><h5><strong>1. Column selection</strong>&nbsp;</h5><p>It is a critical starting point, as the combination of stationary phases must provide sufficient orthogonality while maintaining compatibility between mobile phases. Typically, the first dimension is optimized for general separation of oligonucleotide size or class, while the second dimension focuses on sequence-specific resolution and compatibility with mass spectrometry.</p><h5><strong>2. Mobile phase selection&nbsp;</strong></h5><p>Differences in pH and organic modifiers can significantly influence separation behavior, but incompatibility between dimensions can compromise performance. Therefore, mobile phases must be designed as a coordinated system. The use of volatile buffers, such as ammonium acetate, is often preferred for MS-based detection.</p><h5><strong>3. Instrumentation&nbsp;</strong></h5><p>The switching valve must operate reliably under high pressure, with precise timing to ensure accurate fraction transfer. Loop volumes must be carefully selected to avoid overfilling, as excessive loading can lead to sample loss and distortion due to flow profile effects. As a general guideline, loops should not be filled beyond approximately 70% of their capacity.</p><h5><strong>4. Method development&nbsp;</strong></h5><p>Typically begins with optimization of the second dimension, as it dictates overall system timing. Fast separations using short columns and steep gradients are often required to maintain sufficient sampling frequency. Once the second dimension is established, the first dimension can be adjusted to achieve optimal resolution and compatibility.</p><h4><strong>Final Remarks</strong></h4><p>Two-dimensional liquid chromatography represents a powerful advancement in oligonucleotide analysis, enabling the resolution of complex mixtures that exceed the capabilities of conventional 1D approaches. By combining orthogonal separation mechanisms, 2D-LC reveals structural details and impurity profiles that would otherwise remain hidden.</p><p>However, achieving optimal performance requires careful balancing of multiple factors, including column chemistry, mobile phase compatibility, system timing, and data acquisition. When properly implemented, 2D-LC provides a robust and highly informative platform for modern oligonucleotide characterization.</p><blockquote><ul><li>If you're planning to set up or optimize your oligonucleotide workflow, feel free to contact us at <a href="sales@knauer.net"><strong>sales@knauer.net</strong></a>. Stay tuned for more exciting insights into the Oligonucleotide world in our “<strong>Oligos Made Easy</strong>” series.</li><li>For more in-depth discussion or questions, reach out to the author at <a href="kindler@knauer.net"><strong>kindler@knauer.net</strong></a></li></ul></blockquote>

Oligos Made Easy - Part 9: 2D-LC

News from LabRulezLCMS Library - Week 14, 2026

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Bioanalytic Individual LC-MS/MS training

We are ready to prepare customized LC-MS/MS training for the needs of participants.

<h4><strong>BASIC INFORMATION</strong></h4><ul><li>TITLE: <strong>Customized LC-MS/MS Training</strong></li><li>CATEGORY: <strong>LC-MS/MS training</strong></li><li>LOCATION: <strong>Lodz, PL</strong> or other</li><li>TRAINING TIME: <strong>1-5 days</strong> or more</li><li>NUMBER OF PARTICIPANTS: <strong>4-8 people</strong></li><li>EQUIPMENT:<strong> SCIEX QTRAP/QTOF LC-MS/MS</strong></li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Bioanalytic_Bioanalytic_Individual_LC_MS_MS_training_8a73408c56.jpg" alt="Bioanalytic: Bioanalytic Individual LC-MS-MS training." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Bioanalytic_Bioanalytic_Individual_LC_MS_MS_training_8a73408c56.jpg 245w," sizes="100vw" width="1536" height="930"></p><h4><strong>TRAINING DESCRIPTION</strong></h4><p>Customized LC-MS/MS training we are ready to prepare for the needs of participants, discussing:</p><ul><li>theoretical basics of chromatography, mass spectrometry,</li><li>practical operation of the LC-MS/MS system,</li><li>qualitative and quantitative analysis,</li><li>DDA &amp; DIA screening methods,</li><li>“omics” analyses,</li><li>validation of analytical methods,</li><li>solving basic methodological and technical problems,</li><li>software,</li><li>calibration,</li><li>“tips&amp;tricks”,</li><li>etc...</li></ul><p>We offer training for both novices starting the fascinating adventure of LC-MS/MS analytics, as well as for those who are LC-MS/MS users and are interested in expanding and consolidating their knowledge.</p><h4><strong>Framework training program</strong></h4><ul><li>individual LC-MS/MS training is developed according to the customer's demand</li><li>conducting theoretical and/or practical training at the customer's workplace</li><li>carrying out theoretical and/or practical training in a laboratory in Lodz</li></ul>

Bioanalytic Basic LC-MS/MS training

Basic LC-MS/MS training covers the theoretical basics of mass spectrometry and familiarization with the basic operation of the instrument.

<h4><strong>BASIC INFORMATION</strong></h4><ul><li>TITLE: <strong>Basic LC-MS/MS training</strong></li><li>CATEGORY: <strong>LC-MS/MS training</strong></li><li>LOCATION: <strong>Lodz, PL</strong></li><li>TRAINING TIME: <strong>3 days</strong></li><li>NUMBER OF PARTICIPANTS: <strong>up to 5 people</strong></li><li>EQUIPMENT:<strong> SCIEX QTRAP </strong><span class="ts-pf-details-content"><strong>&amp; </strong></span><strong>QTOF LC-MS/MS</strong></li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Bioanalytic_Bioanalytic_Basic_LC_MS_MS_training_fb1382a55b.jpg" alt="Bioanalytic: Bioanalytic Basic LC-MS-MS training." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Bioanalytic_Bioanalytic_Basic_LC_MS_MS_training_fb1382a55b.jpg 205w," sizes="100vw" width="1293" height="987"></p><h4><strong>TRAINING DESCRIPTION</strong></h4><p>Basic LC-MS/MS training covers the theoretical basics of mass spectrometry and familiarization with the basic operation of the instrument. Basic LC-MS/MS training is primarily aimed at those who are new to LC-MS/MS equipment or who wish to become familiar with this analytical technique. During the training, the following will be presented:</p><ul><li>principles of developing and optimizing quantitative and qualitative methods on low (triple quadrupole, QTRAP) and high resolution (QTOF) instruments,</li><li>basic functionality of the software,</li><li>procedures and objectives of instrument calibration,</li><li>principles of maintaining the cleanliness of mass spectrometer operation.</li></ul><h5><strong>Basic LC-MS/MS training - the program</strong></h5><p><span style="font-size:20px;"><strong>Day I</strong></span></p><p><strong>Theoretical classes:</strong></p><ul><li>Introduction to LC</li><li>Introduction to mass spectrometry (basics)</li><li>Quantitative analysis.</li></ul><p><strong>Practical part:</strong></p><p>QTRAP:</p><ul><li>QTRAP scanning modes on the instrument - Q1, , MS2, MRM, demonstration and discussion on the example of a selected pesticide of the fragmentation spectrum and its fragmentation pathway.</li><li>MRM pair formation (manual, semi-automatic, automatic).</li><li>optimization of ion source parameters -T-conector</li><li>explanation of the main parameters related to LC (column selection, gradient vs isocrat, autosampler)</li><li>LC-MS/MS method setup and optimization</li></ul><p>QTOF:</p><ul><li>manual and automatic optimization of MRM<sup>HR</sup></li><li>ion source and LC parameters (transfer from method developed above)</li></ul><p>Sequence of quantitative analysis on both instruments.</p><p><span style="font-size:20px;"><strong>Day II</strong></span></p><p><strong>Quantitative analysis:</strong></p><ul><li>data processing and analysis,</li><li>reporting - Sciex OS (QTRAP, QTOF).</li><li>Discussion of types of integration algorithms (MQ4, autopeak) and integration parameters.</li><li>independent selection of integration parameters and plotting of master curves.</li><li>independent data analysis and generation of analysis report.</li></ul><p><strong>Qualitative analysis:</strong></p><ul><li>Theoretical introduction - introduction to qualitative analysis:</li><li>qwadrupole modes (Prec/NL),</li><li>trap modes (EMS, EPI, MS3),</li><li>QTOF modes (TOF MS, TOF MS/MS).</li><li>mixed methods,</li><li>targeted vs. untargeted analysis,</li><li>DDA (IDA) - discussion of method development,</li></ul><p><strong>Practical part:</strong></p><ul><li>creation of qualitative methods on QTRAP (Prec-IDA, MRM-IDA), other parameters (LC, ion source) as the previous day,</li><li>LightSight - discussion of operation, creation of MRM-IDA multimethod for selected pesticide and analysis of samples (night).</li><li>QTOF - creation of IDA method, other parameters (LC, ion source) as the previous day.</li></ul><p>Sequence of qualitative analysis overnight.</p><p><span style="font-size:20px;"><strong>Day III</strong></span></p><p><strong>Qualitative data analysis:</strong></p><p>QTRAP:</p><ul><li>Discussion of Prec-IDA, MRM-IDA results - what we see in different types of MS and MS/MS scans. Manual review of data and via IDA Explorer (SciexOS).</li><li>Analysis of results in LightSight, comparison with Prec-IDA, for example - advantages/disadvantages</li></ul><p>QTOF:</p><ul><li>search for potentially present compounds in the sample,</li><li>manual comparison of blank vs. test sample,</li><li>manual by XIC extraction (by sum formula),</li><li>Formula finder - derivation of sum formula on TOF MS data and verification of fragmentation on TOF MS/MS data</li><li>search in IDA Explorer mode - application of filters: similarity, isotopic distribution, mass defect,</li><li>database searching,</li><li>Molecule Profiler - demonstration of software capabilities on selected pesticide example,</li></ul><p><strong>Instrument calibration:</strong></p><ul><li>resolution, mass-to-charge ratio, intensity,</li><li>Q1 and Q3, LIT (MS and MS/MS), TOF MS and TOF-MS/MS</li><li>Automation vs. manual calibration,</li></ul><p><strong>LC-MS/MS application examples</strong></p><p><strong>Summary</strong></p><p><strong>Discussion</strong></p>

Bioanalytic Quantitative LC-MS/MS analysis training

The goal of the training is to introduce users to the procedures and capabilities of the LC-MS/MS system and software to achieve sensitivity, selectivity, precision and reproducibility in quantitative analysis.

<h4><strong>BASIC INFORMATION</strong></h4><ul><li>TITLE: <strong>Quantitative LC-MS/MS analysis training</strong></li><li>CATEGORY: <strong>LC-MS/MS training</strong></li><li>LOCATION: <strong>Lodz, PL</strong></li><li>TRAINING TIME: <strong>3 days</strong></li><li>NUMBER OF PARTICIPANTS: <strong>up to 5 people</strong></li><li>EQUIPMENT:<strong> SCIEX QTRAP LC-MS/MS</strong></li></ul><figure class="image"><img style="aspect-ratio:1200/675;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Bioanalytic_Bioanalytic_Quantitative_LC_MS_MS_analysis_training_d13b5d8127.jpg" alt="Bioanalytic: Bioanalytic Quantitative LC-MS-MS analysis training." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Bioanalytic_Bioanalytic_Quantitative_LC_MS_MS_analysis_training_d13b5d8127.jpg 245w," sizes="100vw" width="1200" height="675"></figure><h4><strong>TRAINING DESCRIPTION</strong></h4><p>Quantitative LC-MS/MS analysis - the training is designed for laboratory personnel using LC-MS/MS systems for quantitative analysis. The following topics are covered during the training:</p><ul><li>Triple quadrupole spectrometer calibration</li><li>MRM pair formation and optimization</li><li>Optimization of ion source parameters</li><li>Optimization of chromatographic parameters</li><li>Sample preparation using the example of blood drawn on <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1283"><strong>Mitra®</strong></a> samplers (VAMS)</li><li>Matrix effect, internal standards (ISTD), matrix curves</li><li>Validation of the quantitative method</li><li>Reporting of results</li></ul><p>The goal of the training is to introduce users to the procedures and capabilities of the LC-MS/MS system and software to achieve sensitivity, selectivity, precision and reproducibility in quantitative analysis while covering the widest possible linear range of concentrations.</p><h3><strong>Training program</strong></h3><h4><span style="font-size:20px;"><strong>Day I</strong></span></h4><h5><strong>Theoretical part:</strong></h5><p>Triple quadrupole structure, ionization, MRM and sMRM scanning, chromatography, multimethods</p><h5><strong>Practical part:</strong></h5><ul><li>Q1/Q3 calibration (10 Da/s), MS/MS - resolution, m/z, intensity.</li><li>MRM pair formation and optimization (manual, semi-automatic, automatic).</li><li>Ion source optimization - T-concector and FIA</li><li>Gradient vs isocrat, dosing, column selection, temperature selection, other important parameters</li><li>Establishment and optimization of LC-MS/MS method.</li><li>How to take care of MS cleanliness - ionization time programming, multi-way valve, cleaning of ion source and instrument front end</li></ul><p>Sample preparation in pure solvent (standard curve, QC, solvent, solvent+ISTD, test samples), overnight analysis sequence.</p><h4><span style="font-size:20px;"><strong>Day II</strong></span></h4><h5><strong>Practical part - preparation of whole blood samples (Mitra®):</strong></h5><ul><li>Preparation of matrix standard curves</li><li>Preparation of quality control (QC) samples in three concentrations</li><li>Preparation of blank samples (without ISTD and with ISTD).</li><li>Preparation of samples for recovery determination (“pre-spiked” and “post-spiked”)</li><li>Preparation of test samples</li></ul><h5><strong>Theoretical part:</strong></h5><ul><li>Samples in the matrix - discussion of the matrix effect and ways to level it.</li><li>Optimization of sample preparation method and LC-MS/MS method</li></ul><h5><strong>Practical part:</strong></h5><ul><li>Sample extraction from Mitra® samplers for LC-MS/MS analysis.</li><li>Sequence of analysis of prepared samples overnight</li></ul><h4><span style="font-size:20px;"><strong>Day III</strong></span></h4><h5><strong>Theoretical part:</strong></h5><ul><li>Validation of the quantitative LC-MS/MS method</li></ul><h5><strong>Practical part:</strong></h5><ul><li>Software - data integration algorithms, signal smoothing, weighing.</li><li>Matrix curves vs curves in solvent, influence of ISTD (Sciex OS).</li><li>Method validation - validation criteria, determination of LOD, LLOQ, ULOQ, linearity, working range of the method, repeatability, recovery.</li><li>Preparation of summary validation reports</li><li>Reporting of results from test samples - report vs export of data to Excel.</li><li>Summary and discussion.</li></ul>

Bioanalytic QTRAP vs QTOF Quality analysis training

The training includes a presentation of the basic differences in application and a comparison of the capabilities of QTRAP and QTOF instruments in qualitative analysis.

<h4><strong>BASIC INFORMATION</strong></h4><ul><li>TITLE: <strong>QTRAP vs QTOF Quality analysis training</strong></li><li>CATEGORY: <strong>LC-MS/MS training</strong></li><li>LOCATION: <strong>Lodz, PL</strong></li><li>TRAINING TIME: <strong>3 days</strong></li><li>NUMBER OF PARTICIPANTS: <strong>up to 5 people</strong></li><li>EQUIPMENT:<strong> SCIEX QTRAP </strong><span class="ts-pf-details-content"><strong>&amp; </strong></span><strong>QTOF LC-MS/MS</strong></li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Bioanalytic_Bioanalytic_QTRAP_vs_QTOF_Quality_analysis_training_18ca66163f.jpg" alt="Bioanalytic: Bioanalytic QTRAP vs QTOF Quality analysis training." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Bioanalytic_Bioanalytic_QTRAP_vs_QTOF_Quality_analysis_training_18ca66163f.jpg 221w," sizes="100vw" width="1000" height="707"></p><h4><strong>TRAINING COURSE DESCRIPTION</strong></h4><p><strong>QTRAP vs QTOF qualitative analysis</strong> - the training is aimed at people who perform analyses related to substance identification or metabolite search in their research work. The training includes a presentation of the basic differences in application and a comparison of the capabilities of QTRAP and QTOF instruments in qualitative analysis. In addition to the theoretical session, participants will undergo a course in the development and optimization of <strong>DDA (IDA)</strong> (QTRAP &amp; QTOF) and <strong>DIA (SWATH) </strong>(QTOF) methods. Analysis and comparison of results will be conducted using <a target="_blank" rel="noopener noreferrer" href="https://sciex.com/products/software/sciex-os-software">SciexOS</a>, <a target="_blank" rel="noopener noreferrer" href="https://sciex.com/products/software/markerview-software">MarkerView</a>, <a target="_blank" rel="noopener noreferrer" href="https://sciex.com/products/software/lightsight-software">LightSight</a> and <a target="_blank" rel="noopener noreferrer" href="https://sciex.com/products/software/molecule-profiler-software">MoleculeProfiler</a> software.</p><h5><strong>Training program</strong></h5><h4><span style="font-size:20px;"><strong>Day I</strong></span></h4><h5><strong>Theoretical part</strong></h5><ul><li>Principle of operation of MS/MS systems</li><li>Differences and capabilities of QTRAP and QTOF</li><li>Comparison of typical analytical procedures and their application</li><li>DDA (IDA) vs DIA (SWATH) methodology.</li><li>Supporting software - LightSight, Molecule Profiler, ACD Labs, MarkerView</li><li>General principles of compound fragmentation</li></ul><h4><span style="font-size:20px;"><strong>Day II</strong></span></h4><p><strong>Objective - to develop methods to search for metabolites of a known substance.</strong></p><h5><strong>QTRAP</strong></h5><ul><li>Development of IDA screening methods (pMRM, Prec/NL, EMS)</li><li>Optimization of LC-MS/MS IDA method</li><li>Data acquisition</li></ul><h5><strong>QTOF</strong></h5><ul><li>Development and optimization of LC-MS/MS IDA and SWATH methods</li><li>Data acquisition</li></ul><h4><span style="font-size:20px;"><strong>Day III</strong></span></h4><p><strong>Objective - identification and profiling of metabolites of a known substance</strong></p><h5><strong>QTRAP data analysis</strong></h5><ul><li>Manual search and identification</li><li>LightSight, MarkerView</li></ul><h5><strong>QTOF data analysis</strong></h5><ul><li>Search and data analysis methods</li><li>Manual search and identification</li><li>IDA vs SWATH</li><li>Automated search and identification - SciexOS, databases</li><li>Molecule Profiler, MarkerView</li></ul><p>Summary and discussion<br>&nbsp;</p>

Bioanalytic QTOF quantitative and qualitative analysis training

The purpose of the training is to introduce users to the capabilities of the LC-HR-MS/MS (QTOF) system in quantitative and qualitative analysis.

<h4><strong>BASIC INFORMATION</strong></h4><ul><li>TITLE:&nbsp;<strong> QTOF quantitative and qualitative analysis training</strong></li><li>CATEGORY: <strong>LC-MS/MS training</strong></li><li>LOCATION: <strong>Lodz, PL</strong></li><li>TRAINING TIME: <strong>3 days</strong></li><li>NUMBER OF PARTICIPANTS: <strong>up to 5 people</strong></li><li>EQUIPMENT:<strong> SCIEX</strong><span class="ts-pf-details-content"><strong> </strong></span><strong>QTOF LC-MS/MS</strong></li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Bioanalytic_Bioanalytic_QTOF_quantitative_and_qualitative_analysis_training_af1620ae8c.jpg" alt="Bioanalytic: Bioanalytic QTOF quantitative and qualitative analysis training." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Bioanalytic_Bioanalytic_QTOF_quantitative_and_qualitative_analysis_training_af1620ae8c.jpg 221w," sizes="100vw" width="1000" height="707"></p><h4><strong>TRAINING COURSE DESCRIPTION</strong></h4><p><strong>Qualitative and quantitative analysis of QTOF</strong> - the training is designed for laboratory personnel using <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?instrumentationItems=30&amp;mainauthorItems=55"><strong>high-resolution (HR) LC-MS/MS</strong></a> systems for qualitative and quantitative analysis. The following topics are covered during the training:</p><ul><li><strong>QTOF spectrometer calibration</strong></li><li><strong>Targeted and untargeted methods</strong></li><li><strong>Quantitative analysis (TOF MS, MRMhr)</strong></li><li><strong>Qualitative and quantitative analysis - DDA (IDA) vs DIA (SWATH) methodology</strong></li><li><strong>Software and its use in high-resolution data analysis</strong></li><li><strong>Reporting of results</strong></li></ul><p>The purpose of the training is to introduce users to the capabilities of the LC-HR-MS/MS (QTOF) system in quantitative and qualitative analysis. To point out the advantages of high resolution in identifying or confirming the presence of substances in a sample and also the strengths of modern QTOF systems in parallel quantitative analysis.</p><h3><strong>Training program</strong></h3><h4><span style="font-size:20px;"><strong>Day I</strong></span></h4><h5><strong>Theoretical part</strong></h5><ul><li>The principle of operation and capabilities of the QTOF system</li><li>Comparison of typical analytical procedures and their application</li><li>Targeted and quantitative analysis (TOF MS vs MRMhr)</li><li>DDA (IDA) vs DIA (SWATH) methodology.</li><li>Supporting software - Molecule Profiler, ACD Labs, MarkerView</li><li>General principles of compound fragmentation</li></ul><h4><span style="font-size:20px;"><strong>Day II</strong></span></h4><p><strong>Objective</strong> - to develop methods for quantitative analysis, confirmation or search for metabolites of a known substance, general characterization of the sample.</p><h5><strong>Practical part:</strong></h5><ul><li>Creation and optimization of the MRMhr targeted method</li><li>Creation and optimization of a non-targeted method IDA</li><li>Creation and optimization of the non-targeted method SWATH</li><li>Data acquisition (overnight)</li></ul><h4><span style="font-size:20px;"><strong>Day III</strong></span></h4><p><strong>Objective</strong> - quantitative analysis, confirmation of the presence or identification of metabolites of a known substance, general characterization of the sample (identification of compounds present in the sample), profiling.</p><h5><strong>Practical part:</strong></h5><ul><li>Quantitative analysis - TOF MS vs MRMhr</li><li>Methods for searching and analyzing data</li><li>IDA vs SWATH data</li><li>Manual search and identification</li><li>Automated search and identification - SciexOS, databases</li><li>Molecule Profiler, MarkerView</li><li>Summary and discussion</li></ul>

Products from category Trainings focused on LC/MS/MS distributed by Bioanalytic - page 1

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