Introduced nearly 80 years ago, collision-based ion-activation and dissociation is the most commonly used type of fragmentation commercially available today. In principle, this technique is quite straightforward: apply energy to accelerate the particles of interest until they collide with an inert gas to induce fragmentation. Within these parameters, there are many different sub-categories of the technique. Here we will discuss three collision-based techniques that occur on Thermo Scientific mass spectrometers.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Freedom_to_Fragment_Introduction_The_importance_of_fragmentation_in_mass_spectrometry_1_c8f70d1281.jpg" alt="Thermo Fisher Scientific Freedom to Fragment Introduction" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Freedom_to_Fragment_Introduction_The_importance_of_fragmentation_in_mass_spectrometry_1_c8f70d1281.jpg 245w," sizes="100vw" width="1024" height="512"><h3>Higher-Energy Collisional Dissociation (HCD)</h3><ol><li>Process: HCD is a beam-based technique that occurs in the HCD cell or ion routing multipole, where the ion beam is directed into a potential well. Excited molecules collide with collision gas, causing fragmentation. This gas is typically nitrogen and is fast and efficient, but indiscriminate in technique. To ensure a higher energy collision, the potential energy is dropped (typically from the quadrupole into the collision cell) by many 10s of eV. This ensures the ions have high energy as they enter the cell with nitrogen and collide with enough energy for the fragmentation to occur. In peptides and proteins, HCD favors b- and y-ion formation. [Figure 1]</li><li>Applications: HCD is commonly used for general proteomics and metabolomics.</li><li>Considerations: When using Thermo Scientific mass spectrometers for HCD fragmentation, we generally use normalized collisional energy (NCE) instead of directly putting in the eV of potential well “drop”. The calibration routine determines the optimal voltage for a series of ions in the calibration solution.&nbsp; Then the routine scales these absolute voltages to a “normalized collision energy” value of 30. As such, an NCE value of 30 should work well across a range of m/z values and charge states. To see the actual applied value, one can check the scan header of the spectrum easily in our Thermo Scientific Freestyle software.</li></ol><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Collision_Based_Ion_activation_and_Dissociation_92107a9524.jpg" alt="Thermo Fisher Scientific: Collision-Based Ion-activation and Dissociation: Figure 1: Location of peptide/protein backbone cleavage and its nomenclature. Representative here is a 4-amino acid peptide with side chains labeled R1-4." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Collision_Based_Ion_activation_and_Dissociation_92107a9524.jpg 245w," sizes="100vw" width="1200" height="582"><h3>Collision-Induced Dissociation (CID) (ion trap specific version)</h3><ol><li>Process: CID, as it occurs in Thermo Fisher Scientific’s dual linear ion trap technology, is a resonance-based technique where molecules are excited by a specific frequency.&nbsp; These excited molecules will start running into He molecules at a faster rate.&nbsp; These collisions slowly heat the resonant molecules until they fragment. Once fragmentation occurs, the product ions at new m/z values are no longer excited by the frequency and will cool back down to the center of the trap. In peptides and proteins, CID favors b- and y-ion formation.</li><li>Applications: CID is great for small molecules and peptides and helps fragment oligonucleotides, especially when the q-value is adjusted.&nbsp; It also fragments with higher efficiency, which makes it well-suited for MS3 and higher workflows.</li><li>Considerations: Because CID is resonance-based, there is a compromise outlined in the Matthieu equation. With certain voltages and frequencies applied, only certain m/z values can be trapped. Thus, we have something called the 1/3rd rule. This rule approximates the equation and states that any fragment created that is &lt; 1/3 the m/z of the precursor will not be trapped. This rule makes CID less desirable as a primary fragmentation technique, thus more used as the pinch hitter when needed for alternate fragmentation after HCD is shown inefficient for a specific molecule. Furthermore, CID is a slow heating process.&nbsp;As such, activation/fragmentation takes a few milliseconds, whereas HCD is effectively instantaneous.&nbsp;</li></ol>Recent developments in oligonucleotide analysis have shown great strides in using CID for fragmentation of many types, including tRNA, snRNA and digested mRNA. To gain the most impact from these experiments, scientists can adjust the q-value applied within the CID resonance. This is usually set to 0.25; however, for oligonucleotides, lowering that value to 0.2-0.15 can help prevent unwanted fragmentation from occurring and specify backbone cleavage that can be more easily characterized.<h3>Source Induced Dissociation (SID)</h3><ul><li>Process: SID is a collisional-induced activation (and if desired, dissociation) technique that is induced in the source region of mass spectrometers. By applying more voltage in the source region, ions are drawn into the mass spectrometer with more energy. Within the source region, there are still atmospheric inert gases that have been drawn in with the analytes of interest. With the additional energy, collisions with these inert gases can occur. Since SID occurs before any mass analyzer, it applies to all ions that enter the mass spectrometer.</li><li>Applications: SID is most commonly used as a desolvation technique for large native molecules. By applying SID energy in the source, molecules generate vibrational energy, and non-covalent, low-energy bonds will be broken only.</li><li>Analogy: SID could be compared to shaking off an umbrella after coming in from the rain. The jostle doesn’t cause the whole umbrella to fall apart, but it does cause the water droplets to fall off. This is a little like proteins getting desolvated from SID.</li><li>Considerations: SID can be a destructive, dissociative process as well, so if that is not the goal, it is important to monitor the energy applied to the analyte. For example, it has been common practice in top-down proteomics to use a small (10-15 eV) setting for SID to aid in desolvation. However, I have successfully taken pure protein (or well chromatographically separated protein) and applied much higher SID (&gt;50 V) to induce dissociation. The resulting fragmentation pattern can yield surprisingly good results. However, this is not common practice, especially not for coeluting species, as the fragmentation would occur on all proteins eluting.</li></ul>Another consideration for SID is its use in native MS. This is often vital for good detection of native proteins like antibodies. Often, we will employ a stronger SID in these cases, anywhere from 60-120 V, depending on the size and complexity of the protein/protein complex, to ensure proper desolvation and thus detection.<blockquote>Learn more about <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/fragmentation-solutions.html">collisional induced dissociation (CID) and higher energy collisional induced dissociation (HCD)</a>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#CID #HCD #fragmentation</blockquote><section><blockquote><h4>Amanda Lee</h4>Amanda Lee PhD, Product Marketing Manager</blockquote></section>

Collision-Based Ion-activation and Dissociation

Our Library never stops expanding. What are the most recent contributions to LabRulezLCMS Library in the week of 22nd September 2025? Check out new documents from the field of liquid phase, especially HPLC and LC/MS techniques!<blockquote>👉 <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library">SEARCH THE LARGEST REPOSITORY OF DOCUMENTS ABOUT LCMS AND RELATED TECHNIQUES</a></blockquote><blockquote>👉 Need info about different analytical techniques? Peek into <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/library">LabRulezGCMS</a> or <a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/library">LabRulezICPMS</a> libraries.</blockquote>This week we bring you application notes by Agilent Technologies, Shimadzu and Waters Corporation and poster by Thermo Fisher Scientific / HPLC Symposium!<h3>1. Agilent Technologies: Quantitation of N-Nitroso Nebivolol in Nebivolol Tablet Formulation</h3>Using an <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=10&amp;search=6495D+triple+quadrupole">Agilent 6495D triple quadrupole LC/MS system</a><ul><li>Application note</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/an_nebivolol_tablet_formulation_6495_qqq_lc_ms_system_5994_8053en_agilent_e7f21eb12f.pdf">Full PDF for download</a></li></ul>N-Nitroso Nebivolol is a NDSRI of Nebivolol, a beta-1 adrenergic receptor antagonist commonly used in the treatment of hypertension and heart failure. In the carcinogenic potency categorization published by the FDA, N-Nitroso Nebivolol has been categorized as Class 4, indicating the maximum allowable intake limit for the impurity to be 1,500 ng/day. Nebivolol has maximum daily dosage limit of 40&nbsp;mg for adults.Considering a maximum daily dose of 40&nbsp;mg and allowable intake of 1,500&nbsp;ng/day for the nitrosamine impurity in the formulation under study, the specification limit of N-Nitroso Nebivolol has been calculated as 22.5 ng/mL for the 0.6 mg/mL test concentration used during this study.&nbsp;This application note demonstrates a highly specific, sensitive, and reproducible method for the quantitation of N-Nitroso Nebivolol in a 20 mg Nebivolol tablet formulation. The method uses a 1290 Infinity II LC coupled to a 6495D triple quadrupole LC/MS/MS. The multiple reaction monitoring (MRM) conditions and ion source parameters were automatically optimized using the optimizer tool available with MassHunter Acquisition software to maximize the sensitivity of the target analyte. The API peaks were diverted to waste with the help of an integrated, software-controlled diverter valve during quantitation of the&nbsp;impurity.<h4>Experimental</h4><h5>Equipment&nbsp;</h5>The analysis was performed on a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=10&amp;search=1290+Infinity+II+LC">1290 Infinity II LC system</a> coupled to a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=10&amp;search=6495D+triple+quadrupole">6495D triple quadrupole LC/MS/ MS</a>. The LC system was equipped with the following&nbsp;modules: – Agilent 1290 Infinity II high-speed pump (G7120A) – Agilent 1290 Infinity II multisampler (G7167B) – Agilent 1290 Infinity II multicolumn thermostat (G7116B) – Agilent 1290 Infinity II diode array detector (G7117A)<h4>Conclusion&nbsp;</h4>A highly sensitive and robust MRM method was developed for the quantitation of N-Nitroso Nebivolol in 20&nbsp;mg Nebivolol tablet formulation using an Agilent 6495D triple quadrupole LC/MS system. The chromatographic method developed provided good separation between the analyte and the API. The method showed LOD and LOQ of 2 and 5 pg/mL, respectively. The minimum signal-to-noise ratio at the LOQ level was found to be more than 50:1 (Peak to Peak). The calibration curve from 5 pg/mL to 50&nbsp;ng/mL was found to be linear, with 1/x weighting. R and R2 values were 0.999 and 0.997, respectively. Spike recovery analysis showed the efficiency of sample extraction with a recovery percentage of 116.8% in API, 108.3% in placebo, and 111.8% in tablet formulation at the spiking level of 200 pg/mL. The method was found to be highly reproducible at the LOQ level, while the %RSD value for the area response of seven replicate injections was approximately 3.1%.<h3>2. Shimadzu: Efficient Method Development for Synthetic Peptide and Related Impurities</h3><ul><li>Application note</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/an_01_00780_en_4d0aa014ea.pdf">Full PDF for download</a></li></ul><h5>User Benefits</h5><ul><li>LabSolutions MD improves the efficiency of the entire workflow for method development of synthetic peptide and impurities.&nbsp;</li><li>Screening for multiple mobile phases and columns can be automated using mobile phase and column switching valves.&nbsp;</li><li>Molecular weights of peptides and related impurities can be estimated and accurately tracked with LCMS-2050, a single quadrupole mass spectrometer.</li></ul>Peptide therapeutics, characterized by specific amino acid sequences crucial to their function, can be synthesized chemically, similar to small molecule drugs. The production of synthetic peptides involves multiple steps, including deprotection, activation, coupling, and the cleavage of the final sequence from the solid support. Impurities, such as those resulting from premature chain termination or missing amino acids, can affect the safety and efficacy of the final product. Therefore, these impurities must be separated by liquid chromatography (LC). In LC analysis, selecting the appropriate mobile phase and column across a wide range of combinations is critical for achieving optimal separation, as it significantly impacts the separation. However, since the separation pattern varies depending on the peptide chain lengths, amino acid compositions, and presence of modifications, optimizing separation for each peptide sequence is time-intensive. This study describes how to efficiently find the best separation conditions for peptides and related impurities utilizing LabSolutions MD, a dedicated software for supporting method development, through both screening and optimization phases.<h4>Experimental</h4><ul><li>LC System: <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=1&amp;search=Nexera+X3">Nexera X3</a> (Method Scouting System)</li><li>MS System: <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=1&amp;search=LCMS-2050">LCMS-2050</a></li></ul><h4>Automated Peak Tracking by LCMS-2050&nbsp;</h4>LC chromatograms obtained with a gradient time of 5 min, flow rate of 0.6 mL/min, and initial concentration of 5 % and 15 %, along with molecular weights for FLP and impurities, are shown in Fig. 18. The UV spectra for each impurity are displayed in Fig. 19. The similarity between UV spectra of Met(O2), p.A1del, p.A1_E2del, p.A1_K3del, and p.A1_D5del is greater than 0.99, suggesting that peak tracking based on UV spectra would be challenging. In contrast, LabSolutions MD enables peak tracking based on molecular weights acquired by LCMS-2050, facilitating accurate identification of compounds with similar UV spectra (Fig. 18). The estimated molecular weights for each compound show small mass errors compared to the theoretical values (Table 3), which can be used to confirm the molecular weights of known compounds as well as to approximate the molecular weights of unknown impurities.<h4>Conclusion</h4>The separation patterns of synthetic peptides vary depending on mobile phase composition, column type, and various LC parameters, such as gradient conditions, column oven temperature, and flow rate. Separation behavior can also differ based on peptide structure, including length, amino acid composition, and the presence of modifications. Therefore, it is necessary to optimize the separation for each peptide sequence individually. However, optimizing analytical conditions through numerous analyses and data processing can be time-consuming. LabSolutions MD automates the entire workflow, including generating analysis schedules, preparing mobile phases, and processing the data, thanks to functionalities such as automated peak tracking, ranking of chromatograms, and design space visualization. This article introduced a case where the optimal separation conditions for synthetic peptides were efficiently identified through screening and optimization phases. LabSolutions MD also offers fully automated gradient optimization by AI algorithm to meet user-defined criteria. For more details, please refer to the application news, “Automatic Optimization of Gradient Conditions by AI Algorithm on Synthetic Peptide and Impurities: 01-00814”.<h3>3. Thermo Fisher Scientific / HPLC Symposium: Sensitive cationic lipids impurities analysis with quantitation by charged aerosol detection and simultaneous mass confirmation by MS</h3><ul><li>Poster</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/po_sensitive_cationic_lipids_impurities_analysis_quantitation_po_en_3dacf61554.pdf">Full PDF for download</a></li></ul>Cationic lipid is a critical component in lipid nanoparticle formulations for delivering nucleic acids such as mRNA, siRNA, antisense oligonucleotides etc. [2] Cationic lipids are amphiphilic molecules that possess a hydrophilic region, a hydrophobic region, and a linker structure connecting the two. [1] Charged aerosol detector (CAD) and evaporative light scattering detectors (ELSD) are preferred for characterizing lipid nanoparticle components, with CAD being the better choice for impurity quantification due to its higher sensitivity [3]. In a previous study, an inverse gradient method was developed to quantify impurities in cationic lipids raw materials.[1] To demonstrate the inverse gradient method on CAD HP, the same cationic lipids -- R-DOTAP, DLin-KC2- DMA and ALC-0315 -- were measured to this experiment as in Application note 003384 [1]. New diverter valve and software features were showcased, along with method’s sensitivity and repeatability.<h4>Materials and methods</h4>Using the inverse gradient method from Application note 003384 [1], to demonstrate impurity analysis in cationic lipids on the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2176">Thermo Scientific Vanquish Charged Aerosol Detector HP (CAD HP)</a> integrated in the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/743">Thermo Scientific Vanquish Flex Inverse Gradient UHPLC System</a>, with parallel mass confirmation by the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/413">Thermo Scientific ISQ EM Single Quadrupole Mass Spectrometer</a>.&nbsp;Methods: The workflow uses a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/743">Vanquish Flex Inverse Gradient LC system</a> with Vanquish CAD HP and <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1970">Thermo Scientific Hypersil GOLD C8 column</a>.<h5>Data Analysis&nbsp;</h5><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/76">Thermo Scientific Chromeleon Chromatography Data System (CDS)</a> 7.2.10 was used for data acquisition and analysis.<h4>Conclusions&nbsp;</h4>The CAD HP integrates perfectly into the Vanquish Inverse Gradient LC system and offers high sensitivity and excellent repeatability for quantitative cationic lipid impurity analysis, while the ISQ EM MS provides straightforward mass confirmation with high repeatability, all under compliance-ready conditions.<h3>4. Waters Corporation: Quantitative Analysis of Four Long-Chain Lysophosphatidylcholines (LPCs) in Dried Blood Spot using Liquid Chromatography Tandem Mass Spectrometry for Clinical Research</h3><ul><li>Application note</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/720008826_en_dc154872b6.pdf">Full PDF for download</a></li></ul><h5>Benefits</h5><ul><li>Good chromatographic resolution of all forms</li><li>Short extraction time compared to traditional methods for lipid extraction</li><li>Short analysis injection-to-injection 7 minutes</li></ul>Historically, very long chain fatty acids have been quantified using direct transesterification and gas chromatography methods which involve time-consuming and labor-intensive sample preparation and analysis. Consequently, simpler LC-MS/MS methods have been reported for the measurement of long-chain LPCs (LPCs generic chemical structure, Figure 1) in DBS. Interferences have been reported using positive ESI, thus researchers have developed methodologies utilizing negative ESI to circumvent isobaric interferences when there is lack of chromatographic resolution. Here a UHPLC-MS/MS method is described using acetate adducts for the reliable analysis of four long-chain LPCs in DBS for clinical research.&nbsp;A UHPLC-MS/MS method for quantifying a panel of LPCs (C20:0, C22:0, C24:0, and C26:0-LPCs) was developed. The mobile phase composition consisted of a mixture of water, acetonitrile, and isopropanol with 5 mM ammonium acetate as a modifier. The DBS sample extraction used a working solution prepared with the deuterated LPC internal standards in methanol. The method was developed with an ACQUITY UPLC I-Class PLUS System (Fixed Loop) using an ACQUITY Premier CSH C18 Column, which provided baseline resolution of endogenous isobaric interferences for the saturated forms of the targeted LPCs. The detector was a Xevo TQ-S micro Mass Spectrometer operated in negative ESI mode. This methodology resulted in a total analysis time (injection-to-injection) of 7 minutes.<h5>LC Conditions&nbsp;</h5><ul><li>LC system: <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/199">ACQUITY UPLC I-Class PLUS FL&nbsp;</a></li><li>System Detection: <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/209">Xevo TQ-S micro Mass Spectrometer&nbsp;</a></li><li>Plate: Waters 96-well Sample Collection Plate, 350 µL&nbsp;</li><li>Column(s): <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1952">ACQUITY Premier CSH C18 Column</a>, 2.1 mm x 50 mm, 1.7 µm (p/n: 186009460)</li></ul><h5>MS Conditions&nbsp;</h5><ul><li>MS system: Xevo TQ-S micro Mass Spectrometer</li></ul><h5>Data Management&nbsp;</h5><ul><li>MS software: <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/635">MassLynx™ v4.2 Software SCN 1045&nbsp;</a></li><li>Informatics: TargetLynx™ XS v4.2 Software SCN1045 and QUAN Review</li></ul><h4>Results and Discussion&nbsp;</h4>During method development, different types of column chemistry, mobile phase composition, and ESI polarity modes were assessed to optimize chromatographic peak shape, analytical sensitivity and manage interferences. In positive mode, ammonium formate favored the formation of m/z 184 and m/z 104 as daughter ions for all the LPCs. The m/z 184 ion lacks specificity because most phospholipids share this moiety, so the ion m/z 104 was selected as quantifier. Having evaluated conditions in positive mode for the analysis of the four saturated LPCs, it was observed that some existing interferences were not only affecting the parent masses of the analytes but their corresponding internal standard parent ion masses too. Hence, negative ionization using ammonium acetate as modifier was assessed for the detection of LPCs. Acetate adducts [M+CH3COO]- were the most abundant parent ion masses, generated under these conditions for each LPC. The acyl-chain product ions generated in negative ionization reduce the detection of interferences coming from other phosphocholine headgroups. The latter detection conditions were used for the validation of the method presented herein.<h4>Conclusion&nbsp;</h4>An LC-MS/MS clinical research method for measuring C20:0, C22:0, C24:0, and C26:0 LPCs with the ACQUITY UPLC I-Class PLUS FL System, and the Xevo TQ-S micro Mass Spectrometer that:<ul><li>Demonstrates good linearity, with no significant carryover, or matrix effects</li><li>Offers good precision with a total reproducibility and repeatability ≤10% CV</li><li>Offers reliability in the identification of LPCs from interfering isobaric compounds Provides good selectivity and analytical sensitivity in negative mode and is relatively fast as approximately 220 samples can be analyzed in 24 hours</li></ul>

News from LabRulezLCMS Library - Week 39, 2025

<h5>Why compromise between performance and price when you can have both?</h5>With Thermo Scientific factory-certified, pre-owned <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=5&amp;manufacturerItems=3">mass spectrometers</a>, you can access legendary LC-MS technology—trusted around the world—at a fraction of the cost of buying new. Our refurb program delivers the quality, precision, and reliability you expect from Thermo Fisher Scientific, while helping you stay within budget and on top of your analytical goals.<h3>Factory-Certified for confidence</h3>Every certified pre-owned system goes through a rigorous factory reconditioning process. From updated hardware and software to comprehensive performance testing, each instrument is restored to meet the same high standards as our new products.<h4>What’s included?</h4>When you choose a certified LC-MS system, you get more than just an instrument—you get the complete Thermo Scientific experience:<ul><li>Full 1-year factory warranty for peace of mind</li><li>29-point inspection checklist, re-certification, and final quality testing</li><li>Software and hardware updates to current revisions</li><li>Re-certification using only genuine Thermo Scientific factory parts</li><li>Professional installation by Unity Lab Services field engineers</li><li>Optional training and application support to get you up and running fast</li></ul><h4>What gets replaced?</h4>Our reconditioning process is comprehensive. These critical components are replaced on every system:<ul><li>All hoses</li><li>Probes</li><li>Ion sources</li><li>Ion transfer tube</li><li>Multiplier</li><li>Mechanical pumps</li><li>Acquisition PC and software</li><li>PCBs (when required for revision)</li></ul><h3>Maximize uptime with expert support</h3>Behind every certified system is a global team of Thermo Fisher specialists committed to helping your lab succeed. Support doesn’t stop after installation:<ul><li>Flexible service contract options through Unity Lab Services</li><li>Guaranteed response times for select contracts</li><li>Financing solutions to meet your budget</li><li>System qualifications and validations</li><li>Technology refresh solutions to keep you ahead of the curve</li></ul><h3>A smarter, more sustainable choice</h3>Investing in a factory-certified pre-owned system isn’t just cost-effective—it’s a sustainable solution that extends the life of high-performance equipment and reduces waste. You get the data quality and instrument reliability your work depends on, while making an environmentally conscious choice.<h3>More ways to access Thermo Scientific excellence—affordably</h3>We understand that every lab’s financial situation is different. That’s why Thermo Fisher offers multiple paths to help you acquire the right mass spectrometry solution, when you need it.<h4>1. <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/mass-spectrometer-price-affordability-programs/factory-certified-refurbished-mass-spectrometers.html">Factory-certified refurbished systems</a></h4>Already covered above, this option gives you fully reconditioned, factory-tested LC-MS instruments at a lower price point—without compromising performance or support.View our brochure for a comprehensive overview.<h4>2. <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/mass-spectrometer-price-affordability-programs/mass-spectrometer-trade-upgrade.html">Trade-in and trade-up</a>: Turn your old into increased productivity</h4>Already own a system—Thermo Fisher or otherwise? Trade it in and upgrade to a newer model with greater capabilities and sensitivity.How it works:<ul><li>Receive a discount on your next system based on the residual value of your current instrument</li><li>Avoid the hassle of selling or decommissioning your old system</li><li>Transition with minimal downtime and disruption</li></ul>Why labs choose this path:<ul><li>Keeps productivity high while moving to new technology</li><li>Eases the financial burden of upgrading</li><li>Helps labs stay competitive with improved system performance</li></ul><h4>3. Personalized equipment <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/products-and-services/services/financial-leasing-services.html">financing &amp; leasing options</a></h4>If upfront capital is limited, our tailored financing and leasing plans offer flexibility that aligns with your lab’s budget and growth plans.<h5>Ready to get started?</h5><ul><li><a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/mass-spectrometer-price-affordability-programs.html">Explore our certified systems, trade-in opportunities, and financing solutions.</a></li></ul>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#affordabiliy #LCMS #sustainability #productivity<blockquote><h5>Ema Ruzic</h5>Vertical Marketing Manager, Chromatography and Mass Spectrometry Division (CMD)</blockquote>

Unlock High-Performance LC-MS with Factory-Certified Systems from Thermo Fisher Scientific

This is the second part of a multi-part Library blog series. For additional information, see blog <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6709">Part 1- Generating Quantitative Methods Automatically From Spectral Library Data </a>and stay tuned for more blogs on our website.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_58afeccc3e.jpg" alt="Thermo Fisher Scientific: Identification of Substructures in Unknowns Through MSn Data." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_58afeccc3e.jpg 216w," sizes="100vw" width="1024" height="740">While identification of unknowns remains a significant challenge, it has become easier over the years with the growth of large MSn spectral libraries. These libraries, such as <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764">mzCloud</a>, can provide substructure data on unknowns.&nbsp; Such information can help us to elucidate the structure of compounds that would previously remain unknown.Substructure identification such as this takes advantage of the fact that a structure will always create the same fragments under a given set of fragmentation conditions regardless of if that structure was from MS1 or an MSn level of fragmentation.&nbsp; While no library will ever contain fragmentation data on all possible chemicals, what we need with this approach is enough breadth of coverage in the various substructures commonly occurring to “build up” larger molecules.&nbsp; What that means is we can take the MSn data on many structurally diverse molecules and use it to identify substructures in our unknown.As an example of using MSn data in this fashion, figure 1 shows the query MSn spectra for an unknown and two of the library hits.&nbsp; The hits are from MSn spectra of two known compounds and the precursor of the specific MSn fragment spectra is shown.&nbsp; Both hits from the library provide a similar structure – an aromatic benzyne linked to either an amide or linked to a carbonyl and amine group.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_2_010011961a.jpg" alt="Thermo Fisher Scientific: Identification of Substructures in Unknowns Through MSn Data: Figure 1: The MS3 spectra of the unknown (A) and two matching fragment spectra from the library search along with the precursors of those spectra (B)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_2_010011961a.jpg 245w," sizes="100vw" width="1024" height="288">While in this example, the specific orientation could not be determined, we have at least a very good starting point in our structure determination by knowing at least one piece of our unknown.&nbsp; Further searches with other MSn spectra from our molecule may uncover other substructures bringing us close to a final identification.&nbsp; In fact, the unknown in this case was isoproturon (Figure 2) which indeed has the substructure indicated from the search.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_3_72dbd5fcef.jpg" alt="Thermo Fisher Scientific: Identification of Substructures in Unknowns Through MSn Data: Figure 2: Structure of Isoproturon." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_3_72dbd5fcef.jpg 245w," sizes="100vw" width="1024" height="578">By utilizing a large library of MSn reference data and acquiring the same MSn query data on our unknowns, we can begin to build up a picture based on substructures we identify.&nbsp; Visit <a target="_blank" rel="noopener noreferrer" href="https://www.mzcloud.org/">mzCloud </a>to see the breadth of MSn fragmentation spectra on a diverse range of chemicals that can be used for such an approach.<ul><li>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#mzCloud #MassSpectralLibraries</li></ul><blockquote><h5>Tim Stratton</h5>Tim is a University of Minnesota graduate with over a decade of experience in pharmaceutical analysis and research, specializing in structure elucidation and interpretation of fragmentation. After roles at Solvay Pharmaceuticals and Abbott Laboratories spanning regulated analysis, method validation, and drug metabolism/pharmacokinetics, Tim joined Thermo Fisher Scientific. Over the past decade, he has focused on supporting hardware and software development, as well as building high-resolution, accurate mass spectral libraries to advance unknown identification in research.</blockquote>

Identification of Substructures in Unknowns Through MSn Data

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