<p><strong>In the research article published in ACS <em>Analytical Chemistry</em> journal the international team of researchers from Vrije Universiteit Brussel, University of Salzburg, University of Natural Resources and Life Sciences Vienna, CAP Chromatography Consulting, California, and University of Salzburg presented a comprehensive investigation of the mechanistic understanding of retention and selectivity in hydrophobic interaction chromatography.</strong></p>
<p>This study delves into the mechanisms behind retention and selectivity in hydrophobic interaction chromatography (HIC) for profiling molecular variants of trastuzumab. By evaluating three column chemistries—butyl, alkylamide, and multialkylamide—it highlights the impact of column hydrophobicity, surface area, and the role of chloride ions in enhancing chromatographic selectivity. The multialkylamide column demonstrated improved selectivity due to protein intercalation and steric effects. Furthermore, <a href="https://lcms.labrulez.com/library?instrumentationItems=32"><strong>LC–MS/MS</strong></a> peptide mapping revealed that chloride in the mobile phase facilitated site-specific deamidation and oxidation, offering insights into structural changes impacting trastuzumab&#39;s retention behavior.</p>
<blockquote>
<h4><strong>The original article</strong></h4>
</blockquote>
<blockquote>
<h5><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c04011"><strong>Selectivity and Resolving Power of Hydrophobic Interaction Chromatography Targeting the Separation of Monoclonal Antibody Variants</strong></a></h5>
<p>Raphael Ewonde Ewonde, Katharina Böttinger, Jelle De Vos, Nico Lingg, Alois Jungbauer, Christopher A. Pohl, Christian G. Huber, Gert Desmet, and Sebastiaan Eeltink</p>
<p><em>Analytical Chemistry</em> <strong>2024</strong> <em>96</em> (3), 1121-1128</p>
<p>DOI: 10.1021/acs.analchem.3c04011</p>
<h6>licensed under <a href="https://creativecommons.org/licenses/by/4.0/"><strong>CC-BY 4.0</strong></a></h6>
</blockquote>
<h5>Selected sections from the article follow.</h5>
<h3><strong>Abstract</strong></h3>
<p>This study presents a comprehensive investigation of the mechanistic understanding of retention and selectivity in hydrophobic interaction chromatography. It provides valuable insights into crucial method-development parameters involved in achieving chromatographic resolution for profiling molecular variants of trastuzumab. Retention characteristics have been assessed for three column chemistries, i.e., butyl, alkylamide, and long-stranded multialkylamide ligands, while distinguishing column hydrophobicity and surface area. Salt type and specifically chloride ions proved to be the key driver for improving chromatographic selectivity, and this was attributed to the spatial distribution of ions at the protein surface, which is ion-specific. The effect was notably more pronounced on the multialkylamide column, as proteins intercalated between the multiamide polymer strands, enabling steric effects. Column coupling proved to be an effective approach for maximizing resolution between molecular variants present in the trastuzumab reference sample and trastuzumab variants induced by forced oxidation. Liquid chromatography–mass spectrometry (LC–MS)/MS peptide mapping experiments after fraction collection indicate that the presence of chloride in the mobile phase enables the selectivity of site-specific deamidation (N30) situated at the heavy chain. Moreover, site-specific oxidation of peptides (M₂₅₅, W₄₂₀, and M₄₃₁) was observed for peptides situated at the Fc region close to the CH2–CH3 interface, previously reported to activate unfolding of trastuzumab, increasing the accessible surface area and hence resulting in an increase in chromatographic retention.</p>
<h3><strong>Experimental Section</strong></h3>
<h4><strong>HIC Instrumentation and Conditions</strong></h4>
<p>HIC experiments were conducted using an <a href="https://lcms.labrulez.com/library?manufacturerItems=2&amp;search=Ultimate+3000+bioinert+HPLC"><strong>Ultimate 3000 bioinert HPLC</strong></a> system (Thermo Fisher Scientific, Germering, Germany) composed of a low-pressure gradient pump, a well-plate autosampler enabling inline split-loop injections, a forced-air column oven, and a diode-array UV detector. <a href="https://lcms.labrulez.com/library?manufacturerItems=2&amp;search=Chromeleon"><strong>Chromeleon</strong></a> software (version 7.2.10) was used for system control and data management. The injection volume was set to 5 μL. The temperature of the well-plate sampler was set at 6 °C and the column oven was maintained at 30 °C. A 2.5 μL UV flow cell was used at 210 and 280 nm with a data collection rate of 5 Hz and a response time of 1 s. The columns used in this study were 4.6 mm I.D. × 100 mm packed with 5 μm porous (1000 Å) silica particles functionalized with alkylamide chemistries (MabPac HIC-10 and MabPac HIC-20) or packed with 5 μm nonporous polymer particles functionalized with butyl chemistry (HIC-butyl) obtained from Thermo Fisher Scientific (Sunnyvale). HIC analyses were generally performed in gradient mode by applying inverse salt gradients starting at 2 M (NH4)2SO4 or 4 M NaCl in 50 mM phosphate buffer and decreasing the salt concentration linearly in time. All mobile phases were filtered through a 0.22 μm filter (Millipore, Darmstadt, Germany).</p>
<h4><strong>RP-HPLC-MS/MS Peptide Profiling</strong></h4>
<p>HPLC-MS/MS experiments were performed using an <a href="https://lcms.labrulez.com/library?manufacturerItems=2&amp;search=Ultimate+3000+RSLCnano"><strong>Ultimate 3000 RSLCnano</strong></a> coupled via nano-ESI (NSI) to a <a href="https://lcms.labrulez.com/library?manufacturerItems=2&amp;search=Q+Exactive+Hybrid+Quadrupole-Orbitrap"><strong>Q Exactive Hybrid Quadrupole-Orbitrap</strong></a> mass spectrometer (Thermo Fisher Scientific). Proteins were denatured with 5 mM tris(2-carboxyethyl)phosphine (Sigma-Aldrich) at 60 °C and 900 rpm for 30 min. Disulfides were alkylated using 20 mM iodoacetamide (Sigma-Aldrich) at 22 °C and 750 rpm in darkness for 45 min. Protein subunits were purified using C18 pipet tips (Thermo Fisher Scientific), dried under vacuum (ScanVac, Lynge, Denmark), and digested with trypsin (Promega, enzyme/protein ratio = 1:25) overnight at 37 °C.</p>
<p>Resulting peptides were separated using a 75 μm I.D. × 150 mm <a href="https://lcms.labrulez.com/library?manufacturerItems=2&amp;search=PepMap+Neo"><strong>PepMap Neo</strong></a> column packed with 2 μm C18 particles with 100 Å pores (Thermo Fisher Scientific) with 0.1% FA in H2O (A) and ACN (B) applying the following gradients: 1% B for 5 min, 1–30% B in 40 min, 30–60% B in 10 min, 99% B for 5 min, and 1% B for 20 min at 0.3 μL/min and 50 °C. The spray voltage for the NSI source probe was set at +1.4 kV, a probe heater temperature and capillary temperature at 350 and 250 °C, respectively, and an S-lens RF level at 60. Peptides were analyzed in a data-dependent MS/MS mode. Full scan was operated within a scan range of m/z 400–3000 at a resolution setting of 70,000, with an AGC target of 3e6, and a maximum injection time of 150 ms. Ten data-dependent scans were acquired at a normalized collision energy of 28 with a resolution setting of 17,500, an AGC target of 1e5, a maximum injection time of 150 ms, and a dynamic exclusion of 10 s. MS data were analyzed using Byonic (v. 3.11.3, Protein Metrics Inc., Cupertino). Peptides were quantified using <a href="https://lcms.labrulez.com/library?search=Skyline"><strong>Skyline</strong></a> (v. 20.2).</p>
<h3><strong>Results and Discussion</strong></h3>
<h4><strong>Retention and Selectivity Assessment</strong></h4>
<p>The retention characteristics of a mAb was evaluated on three HIC column chemistries, i.e., a conventional HIC phase based on butyl ligands (HIC-butyl), a bonded phase based on short strands of polymeric alkylamide, and a bonded phase based on long strands of a multialkylamide ligand. <a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c04011#tbl1"><strong>Table 1</strong></a> provides an overview of stationary phase properties.</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Analytical_Chemistry_Anal_Chem_2024_96_3_1121_1128_Table_1_Stationary_Phase_Characteristics_6522dcbf48.jpg" alt="Anal. Chem. 2024, 96, 3, 1121-1128 - Table 1. Stationary Phase Characteristics."/></p>
<p><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c04011#fig1"><strong>Figure 1</strong></a> shows the peak profiles of the trastuzumab reference sample injected on the different columns by applying ammonium sulfate (<a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c04011#fig1"><strong>Figure 1A</strong></a>) and sodium chloride (<a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c04011#fig1"><strong>Figure 1B</strong></a>) salt systems...</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Analytical_Chemistry_Anal_Chem_2024_96_3_1121_1128_Figure_1_Comparison_of_retention_and_selectivity_obtained_on_different_HIC_columns_for_unstressed_trastuzumab_applying_inverse_d12d87b2f4.jpg" alt="Anal. Chem. 2024, 96, 3, 1121-1128: Figure 1. Comparison of retention and selectivity obtained on different HIC columns for unstressed trastuzumab, applying inverse gradients of NH₄(SO₄)₂ from 2 to 0 M (A) and NaCl from 4 to 0 M (B) on a butyl phase (black profile), a bonded phase based on short strands of polymeric amide (green profile), and a covalently attached stationary phase based on a multiamide ligand (red profile). F = 1 mL/min, tG = 10 min, and the column oven was maintained at 30 °C."/></p>
<h4><strong>Optimizing the HIC Resolving Power</strong></h4>
<p>To generate an IgG sample with a substantial amount of oxidized amino acid residues, forced oxidation with hydrogen peroxide was pursued. To optimize the resolution between the resulting antibody variants, the effects of gradient span (Δc), gradient duration (tG), and column length were systematically assessed by injecting the reference standard before and after oxidation. As the determination of the peak width (even at half height) did not result in reliable performance metric, the valley-to-peak ratio (V/P) introduced by Christophe was used to evaluate performance, where V is the height of the valley between the critical peak pair and P is the height of the lowest peak, the lower the V/P, the better the separation. (26) <a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c04011#fig3"><strong>Figure 3A</strong></a> shows the separation of the reference sample (black trace) and the separation of the antibody variant generated after forced oxidation is shown in Figure 3B (red trace) obtained on a 100 mm long column after optimizing Δc (3–0 M) and tG (30 min). When applying only a narrow gradient span from 2 to 0 M, the critical pair elutes close to the column hold-up time and the gradient duration is only utilized to a very small extent, resulting in an increase in V/P and decreasing the resolving power (data not shown). In the next step, the flow rate and gradient duration were systematically varied. Applying Δc of 3–0 M, a flow rate of 1 mL/min in combination with a tG of 30 min yielded a V/P of 0.40. Increasing tG led to a slight decrease in resolving power as the peak width increased linearly with gradient duration. On the other hand, reducing the flow rate to 0.5 mL/min led to an improved separation, yielding a V/P of 0.34. Operating at a lower flow rate results in a decrease in the mass-transfer contribution to the overall peak broadening, surpassing the impact of gradient steepness (tG/t0) on resolving power. To further optimize the separation, the effect of column coupling was assessed. Applying two coupled columns led to a further decrease in V/P, yielding 0.31, see Figure 3C (reference sample) and Figure 3D (trastuzumab after forced oxidation), respectively. Note that tG/t0 was scaled to column length, allowing an unbiased comparison with the performance obtained on one column. While one column displays limited resolution, novel oxidation variants become apparent in the coupled-column experiment.</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Analytical_Chemistry_Anal_Chem_2024_96_3_1121_1128_Figure_3_Separation_of_the_trastuzumab_reference_sample_and_trastuzumab_variants_after_forced_oxidation_on_one_column_A_B_and_f3dc8402cd.jpg" alt="Anal. Chem. 2024, 96, 3, 1121-1128:Figure 3. Separation of the trastuzumab reference sample and trastuzumab variants after forced oxidation on one column (A, B) and two serially coupled columns (C, D). Separations were performed using the multialkylamide stationary phase, applying an inverse gradient of NaCl from 3 to 0 M, F = 0.5 mL/min, tG = 30 min (single column) and tG = 60 min (coupled columns). The fractions that were collected for subsequent RP-HPLC-MS/MS peptide mapping experiments, highlighted by the arrows (C, D)."/></p>
<h3><strong>Conclusions</strong></h3>
<p>We highlight the critical role of phase systems for tuning chromatographic retention and selectivity. To effectively profile molecular mAb variants, a stationary phase chemistry offering complementary interaction modes, such as van der Waals interactions, H-bonding, π–π interactions, and steric interactions, presents abundant opportunities for unparalleled selectivity. In addition, protein–salt interactions can play a key role in achieving high-resolution HIC separation. While (NH4)2SO4 is widely regarded as the gold standard for HIC, chloride ions have been identified as a crucial factor in achieving selectivity, leading to the resolution between distinct molecular antibody variants. Although the linear solvent strength (LSS) plots for mAbs are relatively steep; retention in HIC is not based on an on–off mechanism. Consequently, the increasing column length has a profoundly positive effect on the resolution. This also indicates that the chromatographic performance can likely be further optimized when downscaling the particle diameter and increasing the operating pressure while ensuring protein conformation is not affected. Nonetheless, selectivity mediated by the ligand architecture and salt type should be prioritized during mAb variant analysis. Finally, our study also demonstrated that the site-specific deamidation of trastuzumab lowers the retention time. However, deamidated species can only be separated from the nondeamidated fraction in the presence of chloride ions. Also, site-specific oxidation induces protein unfolding, which, in turn, increases the retention time due to increased hydrophobic residue exposure.</p>


Selectivity and Resolving Power of Hydrophobic Interaction Chromatography Targeting the Separation of Monoclonal Antibody Variants

<p><strong>In the research article recently published in ACS <em>Analytical Chemistry</em> journal the researchers from the Imperial College London, UK, introduced the J-RESRGAN, an adapted and modified generative adversarial network (GAN) for image super-resolution (SR), which was trained specifically for metabolomic J-Resolved spectra to enhance peak resolution.</strong></p>
<p>J-Resolved (J-Res) NMR spectroscopy is vital for metabolomics research, but it often requires a trade-off between high-resolution but time-intensive experiments and quicker low-resolution experiments prone to peak overlap. To address this, J-RESRGAN, a modified generative adversarial network (GAN), was developed to enhance the resolution of J-Res spectra using deep learning. By training the model on simulated high-resolution spectra and introducing a novel symmetric loss function, J-RESRGAN significantly improved peak resolution across a variety of sample types. The model demonstrated enhanced resolution in over 80% of peak pairs in experimental data, offering quick, accessible improvements for existing datasets. J-RESRGAN, openly accessible on GitHub, presents a promising approach for advancing precision in NMR-based metabolomics.</p>
<blockquote>
<h4><strong>The original article</strong></h4>
</blockquote>
<blockquote>
<h5><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00563"><strong>Resolution Enhancement of Metabolomic J-Res NMR Spectra Using Deep Learning</strong></a></h5>
<p>Yan Yan, Michael T. Judge, Toby Athersuch, Yuchen Xiang, Zhaolu Liu, Beatriz Jiménez, and Timothy M. D. Ebbels</p>
<p><em>Analytical Chemistry</em> <strong>2024</strong> <em>96</em> (29), 11707-11715</p>
<p>DOI: 10.1021/acs.analchem.4c00563</p>
<h6>licensed under <a href="https://creativecommons.org/licenses/by/4.0/"><strong>CC-BY 4.0</strong></a></h6>
</blockquote>
<h3><strong>Abstract</strong></h3>
<p>J-Resolved (J-Res) nuclear magnetic resonance (NMR) spectroscopy is pivotal in NMR-based metabolomics, but practitioners face a choice between time-consuming high-resolution (HR) experiments or shorter low-resolution (LR) experiments which exhibit significant peak overlap. Deep learning neural networks have been successfully used in many fields to enhance quality of natural images, especially with regard to resolution, and therefore offer the prospect of improving two-dimensional (2D) NMR data. Here, we introduce the J-RESRGAN, an adapted and modified generative adversarial network (GAN) for image super-resolution (SR), which we trained specifically for metabolomic J-Res spectra to enhance peak resolution. A novel symmetric loss function was introduced, exploiting the inherent vertical symmetry of J-Res NMR spectra. Model training used simulated high-resolution J-Res spectra of complex mixtures, with corresponding low-resolution spectra generated via blurring and down-sampling. Evaluation of peak pair resolvability on J-RESRGAN demonstrated remarkable improvement in resolution across a variety of samples. In simulated plasma data, 100% of peak pairs exhibited enhanced resolution in super-resolution spectra compared to their low-resolution counterparts. Similarly, enhanced resolution was observed in 80.8–100% of peak pairs in experimental plasma, 85.0–96.7% in urine, 94.4–98.9% in full fat milk, and 82.6–91.7% in orange juice. J-RESRGAN is not sample type, spectrometer or field strength dependent and improvements on previously acquired data can be seen in seconds on a standard desktop computer. We believe this demonstrates the promise of deep learning methods to enhance NMR metabolomic data, and in particular, the power of J-RESRGAN to elucidate overlapping peaks, advancing precision in a wide variety of NMR-based metabolomics studies. The model, J-RESRGAN, is openly accessible for download on GitHub at <a href="https://github.com/yanyan5420/J-RESRGAN"><strong>https://github.com/yanyan5420/J-RESRGAN.</strong></a></p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Analytical_Chemistry_Anal_Chem_2024_96_29_11707_11715_Figure_6_Examples_of_peak_pairs_from_experimental_data_For_each_individual_panel_the_upper_row_displays_the_2_D_HR_LR_and_SR_c002ecf982.jpg" alt="Anal. Chem. 2024, 96, 29, 11707-11715: Figure 6. Examples of peak pairs from experimental data. For each individual panel, the upper row displays the 2D HR, LR, and SR spectra respectively; the subsequent row depicts the 1D profiles along the red dashed line; blue─HR, red─LR, and green─SR. Plots (a, b) display two examples of peak pairs aligned along the F1 axis, demonstrating the recovery to doublets in the SR spectra from the singlets observed in LR spectra."/></p>


Resolution Enhancement of Metabolomic J-Res NMR Spectra Using Deep Learning

<p><strong>Our Library never stops expanding. What are the most recent contributions to LabRulezGCMS Library in the week of 19th August 2024? Check out new documents from the field of the gas phase, especially GC and GC/MS techniques!</strong></p>
<blockquote>
<h4>👉 <a href="https://gcms.labrulez.com/library"><strong>SEARCH THE LARGEST REPOSITORY OF DOCUMENTS ABOUT GCMS AND RELATED TECHNIQUES</strong></a></h4>
</blockquote>
<blockquote>
<p><strong>👉 Need info about different analytical techniques?</strong> Peek into <a href="https://lcms.labrulez.com/library"><strong>LabRulezLCMS</strong></a> or <a href="https://icpms.labrulez.com/library"><strong>LabRulezICPMS</strong></a> libraries.</p>
</blockquote>
<p>This week we bring to you a posters from <a href="https://gcms.labrulez.com/events/568"><strong>ASMS 2024</strong></a> by <strong>LECO</strong>, <strong>Agilent Technologies</strong>,  <strong>Shimadzu</strong>, and <strong>Thermo Fisher Scientific</strong>!</p>
<h4><strong>1. LECO: <a href="https://gcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/NIST_LIBRARY_MATCH_QUALITY_HRT_MMS_CF_ASMS_24_LPSS_320_90d3c6e8c9.pdf">Evaluation of the NIST Library Matching Quality of Mass Spectra Generated by the GC-HR-TOFMS with Multi-Mode Ionization Source</a></strong></h4>
<ul>
<li>poster / <a href="https://gcms.labrulez.com/companies/296"><strong>ASMS 2024</strong></a></li>
</ul>
<p><strong>Introduction:</strong> Comparison of electron ionization spectra against standardized libraries is a staple approach to compound identification in non-targeted GC-MS analysis. High-quality matches are central to the pace of, and confidence in, such analyses. Recent developments in gas chromatography high resolution mass spectrometry have progressed non-targeted analysis applications to a wide variety of studies. However, modern ion-optical design principles which allow gains in sensitivity and resolving power may inadvertently alter fragmentation patterns, which may in turn affect the reliability of automated comparisons against standard libraries. Thus, thorough evaluation and validation of the high-quality spectra matching to the standard libraries, like NIST, is necessary for comprehensive assessment of the promised benefits of new technologies.</p>
<p><strong>Conclusions:</strong> This multi-mode ionization source, as assessed using these 207 diverse analytes, generates fragmentation patterns which align very well with the NIST spectral library. Across all analytes in standard solutions, the mean library match score was 935 and the standard deviation for this value was 24.2. Mean match scores were agreeable regardless of moieties present. Percent differences for MRPS #2 spiked into a Pu’er Tea and MRPS #8 spiked into a dietary supplement were - 3.75 % and -1.44 %, illustrating how the system can easily maintain spectral confidence even in complex matrices. Overall, this study suggests the electron ionization mode of this multimode ion source, in combination with its high-resolution time of flight mass analyzer, yields spectra in excellent agreement with the quadruple dominated NIST library.</p>
<h4><strong>2. Agilent Technologies: <a href="https://gcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/po_7000d_mrm_fast_analysis_enviro_compounds_asms_2024_thp360_en_agilent_d338929001.pdf">Fast Analysis of 140 Environmental Compounds by GC/MS/MS</a></strong></h4>
<ul>
<li>poster / <a href="https://gcms.labrulez.com/companies/296"><strong>ASMS 2024</strong></a></li>
</ul>
<p><strong>Introduction:</strong> Pesticides, polycyclic aromatic hydrocarbons (PAHs), and polychlorinated biphenyls (PCBs) are persistent environmental pollutants with the potential for bioaccumulation.¹ Previously, these compound classes have been analyzed using gas chromatography with an electron capture detector (GC-ECD), but this requires full chromatographic separation of all analytes for confident chemical identification. With a triple quadrupole detector (QQQ), analysis time significantly drops due to mass identification eliminating the need to chromatographically separate all components. Further, multiple reaction monitoring (MRM) mode on the QQQ provides a higher confidence in peak identification than analysis by scan or selected ion monitoring (SIM) mode. Combining chromatographic separation and MS/MS analysis is especially useful for PAHs and PCBs where multiple analytes may have the same m/z value.</p>
<p><strong>Conclusions:</strong> Transitioning methods from GC-ECD to GC/MS/MS is highly beneficial.</p>
<p>By running in MRM mode, we enable the following:</p>
<ul>
<li>Significant time-savings</li>
<li>Increased confidence in hits</li>
<li>Sample quantification remains the same</li>
</ul>
<h4><strong>3. Shimadzu: <a href="https://gcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/Th_P364_Novel_High_Sensitivity_Detector_for_GCMS_adcdac36c4.pdf">Novel High Sensitivity Detector for GC/MS</a></strong></h4>
<ul>
<li>poster / <a href="https://gcms.labrulez.com/companies/296"><strong>ASMS 2024</strong></a></li>
</ul>
<p><strong>Overview</strong></p>
<ul>
<li>We have developed a novel high sensitivity detector which has a simple structure to achieve high ion transmission and eliminate neutral molecules simultaneously.</li>
<li>Signal to noise ratio (S/N) was 1.5 times higher than that with a conventional detector.</li>
</ul>
<p><strong>Introduction:</strong> </p>
<p>In GC/MS, numerous neutral molecules originated from carrier gas pass through quadrupole mass filter without being removed, and thereby they are finally transferred to ion detector. When they enter the detector, they may cause noise in the detecting signal. For this problem, some detector structures have already been proposed to remove these neutral molecules. However, they have complex structures and the room for improvement of ion transmission. In this study, we have developed the new high sensitivity detector which has a simple structure to achieve high ion transmission and to eliminate neutral molecules simultaneously.</p>
<p><strong>Conclusions:</strong></p>
<ul>
<li>We have developed the new high sensitivity detector and achieved the high ion transmission and removal of neutral molecules simultaneously.</li>
<li>Signal intensity was increased by 1.2 times and noise was reduced by about 20%, S/N was 1.5 times higher than that with the conventional detector.</li>
<li>This noise reduction effect will be larger in the high flow analysis. In addition, this detector is promising to extend the lifetime of the detector due to less contamination from neutral particles in the conversion dynode and electron multiplier.</li>
</ul>
<h4><strong>4. Thermo Fisher Scientific: <a href="https://gcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/po_142_utilizing_hydrogen_pesticides_food_gc_ms_po142_asms2024_en_7ed0951b93.pdf">Utilizing hydrogen carrier gas for sensitive analysis of pesticides in food using gas chromatography mass spectrometry</a></strong></h4>
<ul>
<li>poster / <a href="https://gcms.labrulez.com/companies/296"><strong>ASMS 2024</strong></a></li>
</ul>
<h5><strong>Abstract</strong></h5>
<p><strong>Purpose:</strong> To demonstrate the performance of the Thermo Scientifc HeSaverH2Safer kit for iConnect split-splitless (SSL) injection module for trace analysis of pesticides using H2 as a carrier gas as a safe and sustainable solution for laboratory operations </p>
<p><strong>Methods:</strong> In this study, hydrogen was used as a carrier gas for GC-MS/MS analysis of trace levels of pesticides in food. The GC was fitted with a new hydrogen safer split/splitless injector, with chromatographic separation performed on a TG-5 SIL MS (30 m × 0.25 mm, 0.25 μm) capillary GC column. The chromatographic conditions applied ensured critical pair separation was achieved. The GC-MS/MS system was equipped with an advanced electron ionization (AEI) source to increase sensitivity for analyte detection. Quantification and assessment of critical regulatory requirements, such as linearity and sensitivity, were performed in a single software.</p>
<h5><strong>Conclusions</strong></h5>
<ul>
<li>The use of the HeSaver-H2Safer technology allows for a safe and compliant use of hydrogen as an alternative carrier gas in GC/GC-MS applications without the need to install a hydrogen sensor and removes any risk of unwanted reactions with the sample in the hot SSL injector.</li>
<li>When used with hydrogen, the limited carrier gas consumption offered by the HeSaverH2Safer mode permits a very controlled system demand for hydrogen, making this solution ideal for laboratories working with hydrogen generators.</li>
<li>Migrating the GC-MS/MS method from helium to hydrogen requires an adaptation of method parameters to address (i.e., retention time shift and different fragmentation patterns).</li>
<li>97% of pesticides in baby food and 98% in honey showed a linear response in the concentration range 0.005–0.500 mg/kg and the relative standard deviation for N=5 repeats of each sample type at 0.01 mg/kg was equal or lower than 10% for 98% of the evaluated compounds.</li>
</ul>


News from LabRulezGCMS Library - Week 34, 2024

<p><strong>Our Library never stops expanding. What are the most recent contributions to LabRulezLCMS Library in the week of 19th August 2024? Check out new documents from the field of liquid phase, especially HPLC and LC/MS techniques!</strong></p>
<blockquote>
<h4>👉 <a href="https://lcms.labrulez.com/library"><strong>SEARCH THE LARGEST REPOSITORY OF DOCUMENTS ABOUT LCMS AND RELATED TECHNIQUES</strong></a></h4>
</blockquote>
<blockquote>
<p><strong>👉 Need info about different analytical techniques?</strong> Peek into <a href="https://gcms.labrulez.com/library"><strong>LabRulezGCMS</strong></a> or <a href="https://icpms.labrulez.com/library"><strong>LabRulezICPMS</strong></a> libraries.</p>
</blockquote>
<p>This week we bring to you posters from <a href="https://gcms.labrulez.com/events/568"><strong>ASMS 2024</strong></a> by <strong>Agilent Technologies</strong>, <strong>Shimadzu</strong>, <strong>Thermo Fisher Scientific,</strong> and <strong>Waters Corporation</strong>!</p>
<h4><strong>1. Agilent Technologies: <a href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/po_6475_spe_pfas_semiconductor_asms_2024_wp496_en_agilent_cf6e3f6528.pdf">Quantitative Analysis of Legacy &amp; Emerging PFAS in Semiconductor Lubricant using Triple Quadrupole LC/MS</a></strong></h4>
<ul>
<li>poster / <a href="https://gcms.labrulez.com/companies/296"><strong>ASMS 2024</strong></a></li>
</ul>
<p><strong>Introduction:</strong> Per- and polyfluoroalkyl substances (PFAS) are known to play an important role in the semiconductor industry. For example, PFAS-containing lubricants used in manufacturing processes mainly include perfluoropolyether (PFPE), polytetrafluoroethylene (PTFE) and others that are believed to be of very low toxicity.¹ With environmental regulations &amp; manufacturing restrictions continuing to expand in their scope, the semiconductor industry is facing the challenge of sustainability.² Reliable workflows are needed to ensure effective monitoring and control of PFAS in upstream processes. This study established a workflow based on solid phase extraction (SPE) and LC/MS/MS for analyzing over 100 PFAS from semiconductor lubricant matrix. </p>
<p><strong>Conclusions:</strong></p>
<ul>
<li>A reliable workflow for quantitation of trace levels of PFAS in semiconductor lubricant, based on SPE cleanup and LC/MS/MS was developed.</li>
<li>The Agilent Bond Elut PFAS WAX cartridge offered selective and effective extraction for matrix cleanup and preconcentration of PFAS analytes in lubricant.</li>
<li>The workflow performance confirmed the applicability of the Agilent PFAS MRM Database and eMethod, for quantitation of PFAS using the Agilent 6475 LC/TQ system.</li>
<li>This workflow enables a ready-to-use protocol for lubricant suppliers and semiconductor manufactures to monitor trace levels of critical PFAS in lubricants.</li>
</ul>
<h4><strong>2. Shimadzu: <a href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/MP_220_Identification_of_Double_Bond_Position_in_Cyclic_Ester_using_OAD_TOF_system_5918fdc1f4.pdf">Identification of Double Bond Position in Cyclic Ester using OAD TOF system</a></strong></h4>
<ul>
<li>poster / <a href="https://gcms.labrulez.com/companies/296"><strong>ASMS 2024</strong></a></li>
</ul>
<h5><strong>Overview</strong></h5>
<p>Oxygen Attachment Dissociation (OAD) (x1 000 000) is a novel method for fragmentation providing additional fragmentation to CID on the LCMS 9050 To enhance identification of cyclic ester(lactone) which is one of the aromatic ingredients OAD-MS/MS has been applied to provide double bond specific dissociation enabling C=C position assignments.</p>
<p><strong>Introduction:</strong> Lactones Lactones, which are aromatic aromatic ingredients find wide applications in perfumes detergents, and foods The aroma is derived from a combination of various compounds rather than single compound The presence of different types and amounts of impurities in these compounds whether synthesized or purified from natural products can result in distinct aromas To accurately evaluate the aroma it is crucial to identify the precise structural information of the compound including impurities However when the compound has a stable cyclic structure such as lactone direct access to the double bond position within the ring by the neutral radical generated through OAD becomes challenging. In this study, various lactones were hydrolyzed to convert the cyclic ester into a hydroxycarboxylic acid, enabling the identification of the double bond position.</p>
<h5><strong>Conclusions:</strong></h5>
<ul>
<li>Hydrolyzation combined with OAD MS/MS was worked to identify C=C bond positions of cyclic ester.</li>
<li>It was suggested that there are several isomers of Lactone B other than the position of the C=C bond.</li>
<li>OAD-MS/MS can distinguish isomers that cannot be identified by CID.</li>
</ul>
<h4><strong>3. Waters Corporation: <a href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/2024_asms_stevens_pahs_micro_plastic_bf33e7cfcd.pdf">ANALYSIS OF HIGH MASS POLYCYCLIC AROMATIC HYDROCARBONS (PAHS) EXTRACTED FROM MICROPLASTICS SPILLED IN THE MARINE ENVIRONMENT</a></strong></h4>
<ul>
<li>poster / <a href="https://gcms.labrulez.com/companies/296"><strong>ASMS 2024</strong></a></li>
</ul>
<p><strong>INTRODUCTION</strong></p>
<p>In 2021 the container ship M/V X-Press Pearl  caught fire and later sank off the coast of Sri  Lanka. Over 1600 tons of polyethylene pellets,  aka nurdles, were aboard the ship along with 25  tons of nitric acid which began to leak and is  suspected to be the cause of the fire that lead to  the sinking. To add to the witches brew of  ingredients in this fire were fertilizers and  explosives being transported and flame  retardants deployed to douse the fire. When  combined with abundant, naturally-occurring  compounds found in the marine environment,  the need arises to characterize the composition  of intact, burned, and broken pieces of the  spilled plastic later collected from kilometers of  Sri Lankan beaches¹.</p>
<p>Determining the distribution and abundance of  PAHs in the samples is important for  characterizing the source of the microplastics  (MPs) and in selecting appropriate handling,  disposal and/or recycling methods. Both  traditional and advanced GC/MS methods such  as 2D GC are suitable for the determination of  PAHs up to 302 Da which is useful for such  purposes as the differentiation of pyrogenic  versus petrogenic inputs2. However, the toxicity  characteristics of samples has demonstrated  poor correlation with low mass (&lt;302 Da) PAHs  in past studies3. For that reason this work was  aimed at investigating the routine analysis of  higher mass PAHs in the range of 314 to 424 Da  to provide access to additional analytes that  may better correlate with toxicity as well as to  provide the possibility of additional source  markers.</p>
<p><strong>CONCLUSIONS</strong></p>
<ul>
<li>Analysis of an expanded range of high  molecular weight PAHs in unfractionated  extracts of MPs was achieved using a  standard GC-APCI QqQ configuration combined  with  asimple,  generic  METHODS  microextraction</li>
<li>Charge transfer, atmospheric pressure  chemical ionization facilitated the  implementation of a class-specific MRM  acquisition scheme</li>
<li>Only minor modification to the GC method  used for lower mass PAHs is required</li>
<li>Nitrogen carrier gas achieved elution of  HWM PAHs with symmetric, narrow peaks  through the use of flow programming</li>
<li>Further investigation of HMW PAHs for  potential source markers and toxic  compounds is enabled with this approach</li>
</ul>
<h4><strong>4. Thermo Fisher Scientific: <a href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/po_carbon_nitrogen_isotopomer_orbitrap_stellar_ms_hybrid_po_en_0e1e253794.pdf">Carbon and Nitrogen Positional Isotopomer Determination in Metabolites using Orbitrap IQ-X and Stellar MS - a novel hybrid nominal mass instrument</a></strong></h4>
<ul>
<li>poster / <a href="https://gcms.labrulez.com/companies/296"><strong>ASMS 2024</strong></a></li>
</ul>
<h5><strong>Abstract</strong></h5>
<p><strong>Purpose:</strong> Development of a targeted MS²/MS³ approach for the determination of positional isotopomers.</p>
<p><strong>Methods:</strong> Initial data acquired on Thermo Scientific Orbitrap IQ-X Tribrid Mass Spectrometer was used for the structural annotation. A targeted MSn based assay utilizing the above data to get the structural information of the metabolites was developed on a novel hybrid nominal mass instrument.</p>
<p><strong>Results:</strong> A targeted MS²/MS³ method was established for the determination of positional isotopomers in Adenosine Monophosphate (AMP). The method was used for evaluation of the effect of hypoxia on cellular metabolism in an in-vitro model.</p>
<h5><strong>Conclusions</strong></h5>
<ul>
<li>A workflow for targeted stable isotope analysis of isotopomer is described.</li>
<li>The use of product scans with MSn and alternate fragmentation can give positional information of label using nominal mass resolution instrument.</li>
</ul>


News from LabRulezLCMS Library - Week 34, 2024

<p><strong>Our Library never stops expanding. What are the most recent contributions to LabRulezICPMS Library in week 34, 2024? Check out new documents from the field of spectroscopy, especially ICP/MS techniques!</strong></p>
<blockquote>
<h4>👉 <a href="https://icpms.labrulez.com/library"><strong>SEARCH THE LARGEST REPOSITORY OF DOCUMENTS ABOUT ICPMS AND RELATED TECHNIQUES</strong></a></h4>
</blockquote>
<blockquote>
<p><strong>👉 Need info about different analytical techniques?</strong> Peek into <a href="https://lcms.labrulez.com/library"><strong>LabRulezLCMS</strong></a> or <a href="https://gcms.labrulez.com/library"><strong>LabRulezGCMS</strong></a> libraries.</p>
</blockquote>
<p>This week we bring to you a poster from <a href="https://gcms.labrulez.com/events/568"><strong>ASMS 2024</strong></a> by <strong>Agilent Technologies</strong>, applications by <strong>Shimadzu</strong> and <strong>Thermo Fisher Scientific</strong>, and technical note by <strong>Metrohm</strong>!</p>
<h4><strong>1. Agilent Technologies: <a href="https://icpms.labrulez.com/labrulez-bucket-strapi-h3hsga3/po_7850_icpms_elemental_impurities_oligo_asms_2024_mp131_en_agilent_e8292cc884.pdf">Analysis of Elemental Impurities in Synthetic Oligonucleotides by ICP-MS In compliance with USP &lt;232&gt;/&lt;233&gt; and ICH Q3D(R2)/Q2(R1)</a></strong></h4>
<ul>
<li>poster / <a href="https://gcms.labrulez.com/companies/296"><strong>ASMS 2024</strong></a></li>
</ul>
<p><strong>Introduction:</strong> Synthetic oligonucleotides are short chains (oligomers) of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) molecules. They are used in applications such as polymerase chain reaction (PCR) tests, DNA sequencing and novel therapeutic products.</p>
<p>The synthesis of oligonucleotides involves a four-step cyclic process followed by multi-step downstream purification. This manufacturing process as well as environment, packaging, and container closure systems can be potential sources of contamination leading to inorganic impurities formation.</p>
<p>To control and monitor product safety, permitted daily exposure (PDE) limits of 24 elements are defined in ICH guideline Q3D(R2)1 and USP chapter &lt;232&gt;2. ICH Q2(R1)3 and USP&lt;233&gt; 4 describe analytical measurement requirements and procedures for the measurement of those elemental impurities. Although oligonucleotide products have not been included in those regulatory guidelines yet, the industry common practice is to follow those guidelines.</p>
<p>In this study, an analytical workflow (Figure1) was developed in accordance with the ICH/USP guidelinesfor the analysis of elemental impurities in an oligonucleotide sample using an Agilent 7850 ICP-MS. Data was acquired to evaluate the accuracy, specificity, reproducibility, and ruggedness of the method.</p>
<p><strong>Conclusion:</strong> The study has demonstrated the suitability of the Agilent 7850 ICP-MS for the identification and quantification of 24 elements in a synthetic oligonucleotide sample in compliance with existing USP and ICH guidelines. Instrument and method performance requirements for stability, detectability, precision, specificity, ruggedness, accuracy, and spike recovery were all achieved per the criteria given in USP &lt;232&gt;/&lt;233&gt; and ICH Q3D(R2)/Q2(R1).</p>
<p>As the development and use of oligonucleotides in therapeutic applications continue to advance, the elemental impurities analysis of oligonucleotides using 7850 ICP-MS can safeguard the product quality and safety.</p>
<h4><strong>2. Metrohm: <a href="https://icpms.labrulez.com/labrulez-bucket-strapi-h3hsga3/Metrohm_OMNIS_NIRS_An_efficiency_boost_for_your_706048fea4.pdf">OMNIS NIRS: An efficiency boost for your laboratory</a></strong></h4>
<ul>
<li>Technical note</li>
</ul>
<h5><strong>Routine lab analysis – simplified with OMNIS NIRS</strong></h5>
<p>Near-infrared spectroscopy (NIRS) is an analytical technique used to determine multiple parameters in samples quickly without requiring any chemicals. Determinations can be performed in liquids, pastes, and solids with this non-destructive method.</p>
<p>Many industries benefit from using NIRS in their laboratory workflows. Time and cost savings are two of the most convincing arguments for adopting NIRS in the laboratory. It is also easy to use, even for non-technical operators.</p>
<p>This White Paper discusses the concept and benefits of NIR spectroscopy, supplemented with the use of the Metrohm NIR solution, OMNIS NIRS, in several real-life laboratory application examples. Applications from the petrochemical, food and beverage, semiconductor, and pharmaceutical industries are used to demonstrate the unique functionalities of OMNIS NIRS in different situations.</p>
<p><strong>SUMMARY:</strong> With OMNIS NIRS, users get a flexible, modular analytical solution which is suitable for many industries. Unique functionalities include:</p>
<ul>
<li>automatic model development (OMD)</li>
<li>a high measurement speed</li>
<li>the possibility to recognize sample insertion and removal</li>
<li>sophisticated temperature control</li>
<li>the ability to combine different analytical technologies from a single manufacturer—even in an automated system</li>
</ul>
<p>Boost the efficiency of your laboratory with OMNIS NIRS.</p>
<h4><strong>3. Shimadzu: <a href="https://icpms.labrulez.com/labrulez-bucket-strapi-h3hsga3/an_01_00712_en_f0d3971af4.pdf">Analysis of Metal Elements in Culture Medium Using ICPMS-2050</a></strong></h4>
<ul>
<li>Application</li>
</ul>
<p><strong>User Benefits</strong></p>
<ul>
<li>Analysis of both trace and high-concentration elements is possible in culture media.</li>
<li>Culture media can be analyzed with simple dilution-only pretreatment using the ICPMS-2050.</li>
<li>The elements in the culture medium can be analyzed reliably and accurately over a long period.</li>
</ul>
<p><strong>Introduction:</strong> A culture medium usually contains elements spanning a wide range of concentrations, from trace (Co, Cu, Se, etc.) to several thousand ppm (Na). Elementsin the medium are important in cell cultures because they are taken up by the cells and contribute to enzyme activity and redox reactions. On the other hand, it has been pointed out that unexpected contamination from raw materials and equipment in the culture media manufacturing process may cause differences in element concentrations among batches. Therefore, it is important to know the element concentration profiles in the culture medium to achieve a homogeneous cell culture. </p>
<p>ICP-MS issuitable for this purpose because it can analyze multiple elements with high sensitivity and has a wide dynamic range. In this Application News, an ICPMS-2050 was used to analyze both trace and high-concentration elements in a culture medium by dilution-only pretreatment. Furthermore, the spike recovery and long-term stability in the culture medium were evaluated using the ICPMS-2050 to confirm that there was no effect on the analytical value due to dilution-only pretreatment.</p>
<p><strong>Summary:</strong> In this Application News, the ICPMS-2050 was used to analyze trace and high-concentration elements in a culture medium using dilution-only pretreatment. Good spike recoveries were obtained for all the measured elements, verifying that the culture medium can be accurately analyzed with dilution-only pretreatment. In addition, the results of CCV and internal standard recoveries showed good long-term stability.</p>
<h4><strong>4. Thermo Fisher Scientific: <a href="https://icpms.labrulez.com/labrulez-bucket-strapi-h3hsga3/an_002821_tea_icap_ms_icap_tqe_industrial_an002821_em_en_b60acdccc6.pdf">Analysis of process water from hydrogen fuel cells using triple quadrupole inductively coupled plasma mass spectrometry (ICP-MS)</a></strong></h4>
<ul>
<li>Application</li>
</ul>
<p><strong>Keywords:</strong> Fluorine, fuel cell, high resolution, ICP-MS, KED, PEM, process water, triple quadrupole, TQ-O2 mode</p>
<p><strong>Goal:</strong> To demonstrate the analysis of process water from hydrogen fuel cells for inorganic trace contaminants with high sensitivity and accuracy using triple quadrupole ICP-MS</p>
<p><strong>Conclusions:</strong> The iCAP TQe ICP-MS was employed to analyze 53 elements including fluorine in process water derived from hydrogen fuel cells. Among the analytes, several critical interferences can cause unexpected bias, and these were investigated closely for effective and complete removal by means of selective collision / reaction cell reactions with oxygen. This study also included the development of a method for the analysis of fluorine, generally only possible in an indirect measurement. This analytical method was rigorously tested, and the results obtained clearly demonstrate the fowling analytical advantages:</p>
<ul>
<li>The iCAP TQe ICP-MS operated in TQ-O2 and He KED modes allowed the analysis of 53 elements in relevant sample matrices over a wide concentration range. For minor elements, the method was tested over 4 orders of magnitude (from 0.01 to 100 µg·L-1), whereas major elements were tested between 1 to 100 µg·L⁻¹.</li>
<li>Using a high throughput analysis approach, with a new autosampler equipped with a Step Ahead feature for minimizing total analysis time, all elements relevant for the development of hydrogen fuel cell technology could be measured accurately with low detection limits.</li>
<li>The use of TQ-O₂ mode provided advanced performance for eliminating the polyatomic interferences of phosphorus, sulfur, silver, and cadmium in the simulated hydrogen fuel cell process water. This covered both polyatomic interferences as well as overlaps created by intense signals from isotopes of elements present in high concentrations.</li>
<li>he iCAP TQe ICP-MS offers the flexibility to choose high resolution for the Q1 and Q3 quadrupoles, enabling complete elimination of polyatomic interference and isobaric interferences.</li>
<li>The feasibility of fluorine analysis was demonstrated using an indirect method after complexation with barium. The iCAP TQe ICP-MS showed accurate and precise determination of fluorine as proven by the spike recovery tests performed.</li>
<li>Excellent stability performance was obtained with the iCAP TQe ICP-MS together with excellent CCV and spike recovery results over a 3-hour run without internal standard correction. This provides the advantage of avoiding potential contamination from addition of the internal standard solution.</li>
</ul>


News from LabRulezICPMS - Library Week 34, 2024

<p><strong>In the research article published in ACS <em>Analytical Chemistry</em> journal the researchers from the University of Leicester, UK, and Leicester NIHR Biomedical Research Center developed a new approach to comprehensive two-dimensional gas chromatography data processing by streamlining the integration of free and proprietary tools within a single platform, enhancing the workflow for researchers.</strong></p>
<p>Comprehensive two-dimensional gas chromatography (GC×GC) is an advanced analytical method used for detailed chemical analysis, but it produces complex datasets that are difficult to manage. A new approach has been developed using an underutilized interface in commercial software to streamline the integration of free and proprietary tools within a single platform, enhancing the workflow for researchers. This integrated system was tested on a large-scale GC×GC metabolomics dataset, employing unique algorithms to significantly reduce variations in retention times, demonstrating improved data accuracy and processing efficiency. The interface not only facilitates workflow automation but also enhances the connectivity among various chemometric tools, paving the way for better integration with broader data management systems.</p>
<blockquote>
<h4><strong>The original article</strong></h4>
</blockquote>
<blockquote>
<h5><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.0c02844"><strong>Automating and Extending Comprehensive Two-Dimensional Gas Chromatography Data Processing by Interfacing Open-Source and Commercial Software</strong></a></h5>
<p>Michael J. Wilde, Bo Zhao, Rebecca L. Cordell, Wadah Ibrahim, Amisha Singapuri, Neil J. Greening, Chris E. Brightling, Salman Siddiqui, Paul S. Monks, and Robert C. Free</p>
<p><em>Analytical Chemistry</em> <strong>2020</strong> <em>92</em> (20), 13953-13960</p>
<p>DOI: 10.1021/acs.analchem.0c02844</p>
<h6>licensed under <a href="https://creativecommons.org/licenses/by/4.0/"><strong>CC-BY 4.0</strong></a></h6>
</blockquote>
<h3><strong>Abstract</strong></h3>
<p>Comprehensive two-dimensional gas chromatography (GC×GC) is a powerful analytical tool for both nontargeted and targeted analyses. However, there is a need for more integrated workflows for processing and managing the resultant high-complexity datasets. End-to-end workflows for processing GC×GC data are challenging and often require multiple tools or software to process a single dataset. We describe a new approach, which uses an existing underutilized interface within commercial software to integrate free and open-source/external scripts and tools, tailoring the workflow to the needs of the individual researcher within a single software environment. To demonstrate the concept, the interface was successfully used to complete a first-pass alignment on a large-scale GC×GC metabolomics dataset. The analysis was performed by interfacing bespoke and published external algorithms within a commercial software environment to automatically correct the variation in retention times captured by a routine reference standard. Variation in 1tR and 2tR was reduced on average from 8 and 16% CV prealignment to less than 1 and 2% post alignment, respectively. The interface enables automation and creation of new functions and increases the interconnectivity between chemometric tools, providing a window for integrating data-processing software with larger informatics-based data management platforms.</p>
<h3><strong>Introduction</strong></h3>
<p>Advanced analytical technologies are revealing new chemical complexities in our environment (e.g., wastewaters and air quality), our bodies (e.g., metabolome and microbiome), and our food and commodities (e.g., packaging, materials, and petrochemicals). Comprehensive two-dimensional gas chromatography (GC×GC) is a technique that (theoretically) affords unparalleled separation of volatile and semivolatile matrices, providing a powerful analytical tool for both nontargeted and targeted analyses. (1−3) The increased peak capacity and separation of individual compounds within complex mixtures can benefit studies focused on biomarker discovery and signature profiling, such as global metabolomics. (4−7) Targeted methods for screening, such as biomonitoring persistent organic pollutants, benefit from less-extensive sample preparations and increased confidence in chemical assignment. (8,9)</p>
<p>Much work has been done to advance the hardware to make the technique more accessible and affordable and reach new chromatographic optima. (1,10,11) However, the complexity of the resultant datasets makes it difficult to automate, reproduce, and share data and data workflows. Increased adoption of GC×GC for routine analyses and for larger scale discovery analysis is at risk from the lagging development of more integrated platforms for data processing, management, and storage.</p>
<p>Commercially available pieces of software for processing GC×GC data (coupled to both univariate, e.g., flame ionization detectors, and multivariate detectors, e.g., mass spectrometric detectors, herein described collectively as “GC×GC” data) are powerful. They have high functionality and advanced graphical user interfaces (GUIs) (<a href="https://pubs.acs.org/doi/suppl/10.1021/acs.analchem.0c02844/suppl_file/ac0c02844_si_001.pdf"><strong>Table S1</strong></a>). However, despite efforts to make the software user friendly (e.g., by introducing guided workflows), users can require extensive periods of learning (with one or two dedicated experienced users per group). They are also expensive and often instrument-specific, restricting analysts to one type of software, and the data output may be incompatible with other software or require time-consuming export steps.</p>
<p>Furthermore, commercial or original equipment manufacturer (OEM) software for processing GC×GC data is not flexible enough for the different workflows that exist within the various applications of GC×GC. Although it is not economically viable for vendors to create custom functions on an individual basis, researchers need tools that maintain a level of flexibility to meet the demands of different projects and experimental designs. The locked-down nature of proprietary systems, although some are scriptable, makes it difficult to embed them in custom data-processing pipelines.</p>
<p>For instance, the processing of chromatographic data for the generation of a peak table (i.e., data matrix), including baseline correction, peak detection, and the critical step of alignment, is often only one part of a wider workflow (<a href="https://pubs.acs.org/doi/10.1021/acs.analchem.0c02844#fig1"><strong>Figure 1</strong></a>). These steps can be preceded by sample collection and quality control steps, followed by multivariate analysis and compound identification, finally uploading the data to a data management platform or repository (<a href="https://pubs.acs.org/doi/10.1021/acs.analchem.0c02844#fig1"><strong>Figure 1</strong></a>).</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Analytical_Chemistry_Anal_Chem_2020_92_20_13953_13960_Figure_1_Flow_diagram_depicting_the_complexity_and_layers_of_GC_GC_data_processing_within_a_wider_data_workflow_b5508ce959.jpg" alt="Analytical Chemistry - Anal. Chem. 2020, 92, 20, 13953-13960 - Figure 1. Flow diagram depicting the complexity and layers of GC×GC data processing within a wider data workflow (preprocessing includes steps such as baseline correction and signal smoothing. Postprocessing includes steps such as feature extraction/peak detection. Data reduction can include application of multivariate analysis and machine learning techniques)."/></p>
<p>Several chemometric methods using free and open-source software (FOSS) or bespoke tools and scripts have been developed for processing GC×GC data (<a href="https://pubs.acs.org/doi/suppl/10.1021/acs.analchem.0c02844/suppl_file/ac0c02844_si_001.pdf"><strong>Table S1</strong></a>). (12) Such tools overcome issues of accessibility and cost; they are often compatible with multiple file types for wider adoption; and the open-source programming language allows modification by the user.</p>
<p>Nonetheless, poor-quality supporting documentation can make it very time-consuming to determine how to use functions owing to a lack of user-friendly GUIs. They can also be a niche for certain application areas or address one task or specific part of a workflow, for example, an algorithm for performing alignment or peak detection. These tools are a great resource, which enhance the analyst’s tool kit; however, this only increases the complexity of the task faced by the analysts in choosing the optimum workflow for their data. This means that the user might have to swap between multiple software to process a single dataset. In addition, they are often specific to one programming language (unless produced as libraries with wrappers in different languages); they all are not readily accessible (i.e., published as “in-house”), and although the package or script may be made freely available, the environment/platform may not be freely available.</p>
<p>Consequently, analysts report unique combinations of both commercial software and FOSS. The powerful core functions of commercial software are used as a foundation (acquiring and converting raw data files at minimum) and then expanded on using external FOSS alongside manual editing to produce a data workflow. (4,5,13−19) This is done in discrete laborious steps, which are difficult to report and reproduce.</p>
<p>Herein, we provide the primary description for interfacing open-source and commercial software for processing GC×GC data. The objectives were to demonstrate the use of an underused interface that exists within commercial software (i) for automating steps, which were not previously possible within the software GUI, (ii) for creating new functions, (iii) for integrating open-source and bespoke code with commercial software functions, and (iv) to highlight its future potential for increasing interconnectivity between chemometric tools.</p>
<p>To keep the proof of concept simple, the command-line interface was used in a popular piece of software for GC×GC data processing. We illustrate its use for automating the alignment of a metabolomics dataset as an example to provide analysts with the knowledge needed to accelerate and automate their own workflows. The new method makes it possible to combine the powerful functionality of commercial software and the flexibility of FOSS to produce a custom data workflow within a single software environment, tailoring the commercial software and workflow to the needs of the individual researcher.</p>
<h3><strong>Experimental Details</strong></h3>
<p>Analysis by <a href="https://gcms.labrulez.com/library?instrumentationItems=2&amp;mainauthorItems=10&amp;manufacturerItems=1"><strong>GC×GC</strong></a> was conducted as described previously using an <a href="https://gcms.labrulez.com/library?manufacturerItems=1&amp;search=Agilent+7890A"><strong>Agilent 7890A</strong></a> gas chromatogram, fitted with a <a href="G3486A"><strong>G3486A</strong></a> CFT flow modulator. (20) The instrument was coupled to a <a href="https://gcms.labrulez.com/library?mainauthorItems=6&amp;manufacturerItems=7&amp;search=Markes+TD-100xr"><strong>TD-100xr</strong></a> thermal desorption autosampler (Markes International Ltd, Llantrisant, UK). Sample tubes were placed in trays, typically six sample tubes per tray along with a tube loaded with the n-alkane and aromatic mixture and in every four trays another tube loaded with a reference indoor air mixture. (20)</p>
<p>Exhaled <a href="https://gcms.labrulez.com/webinars?search=VOCs"><strong>volatile organic compounds</strong></a> (VOCs) were collected from breath using the ReCIVA device (Owlstone Medical, Cambridge, UK) within a prospective real-world observational study involving adults presenting with self-reported acute breathlessness. (20,21) Written informed consent was obtained from all participants. The study protocol was approved by the National Research Ethics Service Committee East Midlands (REC number: 16/LO/1747) IRAS 198921.</p>
<p>Data were acquired in <a href="https://gcms.labrulez.com/library?instrumentationItems=22&amp;mainauthorItems=10&amp;manufacturerItems=1&amp;search=MassHunter+GC%E2%80%93MS"><strong>MassHunter GC–MS</strong></a> Acquisition B.07.04.2260 (Agilent Technologies Ltd, Stockport, UK) and the data were processed using the command-line interface within the GC Image v2.8 suite (GC Image, LLC. Lincoln, NE, US). Step-by-step examples of the data analysis are described in further detail. The files used in the exemplar methods have been made available with supporting documentation via a repository at <a href="https://github.com/rcfgroup/gc-automation"><strong>https://github.com/rcfgroup/gc-automation</strong></a>.</p>
<p>...</p>
<h3><strong>Conclusions</strong></h3>
<p>GC×GC workflows are challenging and often cannot be done in a single software environment. Through the use of an interface, such as the command line, users have the ability to create more powerful and flexible workflows by being able to mold commercial software with their own and others’ scripts and tools developed in FOSS.</p>
<p>The successful interface of open-source and commercial software for processing GC×GC data has been demonstrated. Advantages of the method include the automation of multisoftware steps within a single software environment and the addition of new functionalities within commercial software using open-source scripts. Applications include the development of more user-friendly tools; automated batch processing tailored for and by the individual researcher; the sharing of reproducible workflows; and the integration of data-processing tools and workflows with data standardization platforms (e.g., ISA), repositories, and sample collection platforms (e.g., LabPipe) (45) for the seamless collection, analysis, and processing of high-fidelity datasets.</p>


Automating and Extending Comprehensive Two-Dimensional Gas Chromatography Data Processing by Interfacing Open-Source and Commercial Software

<p><strong>In the research article published in ACS <em>Analytical Chemistry</em> journal the researchers from the University of Geneva, Switzerland, and Waters Corporation took a deep dive into understanding the retention mechanism of oligonucleotides (ONs), evaluation of the applicability of the linear solvent strength (LSS) retention model, and exploration of the potential of ultra-short columns.</strong></p>
<p>Ion-pairing reversed-phase liquid chromatography (<a href="https://lcms.labrulez.com/webinars?search=IP-RP"><strong>IP-RPLC</strong></a>) serves as a key method for characterizing oligonucleotides and their impurities. This study delved into understanding the retention mechanisms of oligonucleotides, validating the linear solvent strength (LSS) retention model for molecules ranging from 3 to 30 kDa, and confirmed the model&#39;s ability to predict retention times accurately. It introduced the use of ultra-short 5 mm columns which facilitated rapid separations of oligonucleotide mixtures in just 30 seconds without compromising separation efficiency. Despite oligonucleotides displaying &quot;on-off&quot; elution patterns similar to smaller proteins, the effectiveness of these shorter columns suggests no further gains in selectivity or efficiency from using longer columns. This finding sets the stage for future research on more complex oligonucleotide formulations using this accelerated method.</p>
<blockquote>
<h4><strong>The original article</strong></h4>
</blockquote>
<blockquote>
<h5><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c01934"><strong>High-Throughput Chromatographic Separation of Oligonucleotides: A Proof of Concept Using Ultra-Short Columns</strong></a></h5>
<p>Honorine Lardeux, Szabolcs Fekete, Matthew Lauber, Valentina D’Atri, and Davy Guillarme</p>
<p><em>Analytical Chemistry</em> <strong>2023</strong> <em>95</em> (27), 10448-10456</p>
<p>DOI: 10.1021/acs.analchem.3c01934</p>
<h6>licensed under <a href="https://creativecommons.org/licenses/by/4.0/"><strong>CC-BY 4.0</strong></a></h6>
</blockquote>
<h5>Selected sections from the article follow.</h5>
<h3><strong>Abstract</strong></h3>
<p>Ion-pairing reversed-phase liquid chromatography (IP-RPLC) is the reference separation technique for characterizing oligonucleotides (ONs) and their related impurities. The aim of this study was to better understand the retention mechanism of ONs, evaluate the applicability of the linear solvent strength (LSS) retention model, and explore the potential of ultra-short columns having a length of only 5 mm for the separation of model ONs. First, the validity of the LSS model was evaluated for ONs having sizes comprised between 3 and 30 kDa, and the accuracy of retention time predictions was assessed. It was found that ONs in IP-RPLC conditions follow an “on–off” elution behavior, despite a molecular weight lower than that of proteins. For most linear gradient separation conditions, a column length between 5 and 35 mm was found to be appropriate. Ultra-short columns of only 5 mm were therefore explored to speed up separations by considering the impact of the instrumentation on the efficiency. Interestingly, the impacts of injection volume and post-column connection tubing on peak capacity were found to be negligible. Finally, it was demonstrated that longer columns would not improve selectivity or separation efficiency, but baseline separation of three model ONs mixtures was enabled in as little as 30 s on the 5 mm column. This proof-of-concept work paves the way for future investigations using more complex therapeutic ONs and their related impurities.</p>
<p>...</p>
<h3><strong>Experimental Section</strong></h3>
<h4><strong>Chemicals and Samples</strong></h4>
<p>Water was obtained from a Milli-Q water purification system from Millipore (Bedford, MA). LC-MS grade methanol (MeOH) was purchased from Thermo Fisher Scientific (Reinach, Switzerland). Oligonucleotides were purchased from Eurogentec (Seraing, Switzerland) and Integrated DNA Technologies (IDT, Leuven, Belgium). 1,1,1,3,3,3-Hexafluoro-2-propanol (HFIP, ≥99%), triethylamine (TEA, ≥99.5%), and RNase-free water were purchased from Sigma-Aldrich (Buchs, Switzerland).</p>
<h4><strong>Sample and Mobile Phase Preparation</strong></h4>
<p>100 μM oligonucleotide aliquots were initially prepared by reconstituting lyophilized material in the appropriate volume of RNase-free water and stored at −20 °C.</p>
<p>Equimolar oligonucleotide mixtures were prepared by mixing aliquots and diluting the products to 5 μM in RNase-free water prior to the IP-RPLC analysis (if not stated otherwise). Sample mixtures used to illustrate the retention of oligonucleotides were (first part of the study) the following: dT10–40 (a mixture of seven poly-deoxythymidylic (dT) acids of 10-, 15-, 20-, 25-, 30-, 35-, and 40-mer) and dT40–100 (a mixture of four poly-dT acids of 40-, 60-, 80-, and 100-mer). For the second part of the study, dT40–100, 4 dT (a mixture of four poly-dT acids of 10-, 20-, 30-, and 40-mer), and 4 PS (a mixture of four 20-mer poly-dT acids with 0, 6, 9, and 19 phosphorothioate modifications that replace the phosphodiester linkages) were used.</p>
<p>Mobile phase A was 14 mM TEA in water, containing 100, 160, or 400 mM HFIP, pH 8.2, 8.1, or 7.8, respectively. Mobile phase B was a mixture of 50:50 mobile phase A and methanol.</p>
<h4><strong>Chromatographic System, Columns, and Software</strong></h4>
<p>All chromatographic separations were performed on a Waters <a href="https://lcms.labrulez.com/library?mainauthorItems=5&amp;manufacturerItems=5&amp;search=ACQUITY+UPLC+I-Class"><strong>ACQUITY UPLC I-Class</strong></a> System (Milford, MA) equipped with a binary solvent delivery pump, an autosampler with a flow-through-needle (FTN), and a UV detector with a 0.5 μL UV flow cell. The overall extra-column volume was measured as 5.6 μL from the injection seat of the autosampler to the detector cell, while the offset time was equal to 0.87 s. These values were found after plotting system residence time vs reciprocal flow rate (1/F) for various experiments conducted at several flow rates in the absence of a column (zero-dead volume union). Waters <a href="https://lcms.labrulez.com/library?from=2020&amp;mainauthorItems=5&amp;manufacturerItems=5&amp;to=2024&amp;search=ACQUITY+UPLC+BEH"><strong>ACQUITY UPLC BEH</strong></a> C18 1.7 μm Column, 5 mm × 2.1 mm, 130 Å <a href="https://lcms.labrulez.com/library?from=2020&amp;mainauthorItems=5&amp;manufacturerItems=5&amp;to=2024&amp;search=VanGuard+Pre-column"><strong>VanGuard Pre-column</strong></a> was used in this study. Commercial 50 mm and 150 mm × 2.1 mm columns (Waters ACQUITY Premier Oligonucleotide BEH C18 1.7 μm, 130 Å Column) were also used. Data acquisition and instrument control were performed by <a href="https://lcms.labrulez.com/library?mainauthorItems=5&amp;manufacturerItems=5&amp;search=Empower"><strong>Empower</strong></a> 3 Software (Waters). The freely available Excel Spreadsheet developed by Guillarme et al. was used to derive LSS parameters and predict retention times. (23,24)</p>
<h4><strong>Apparatus and Methodology</strong></h4>
<p>Sample volumes of 1 μL were injected using linear gradients (for all separations). The column temperature was set at 60 °C unless stated otherwise. Various semi-empirical models are used in LC to describe the relationship between experimentally observed retention times and mobile phase composition or gradient conditions. In this study, the following model was considered...</p>
<h3><strong>Results and Discussion</strong></h3>
<h4><strong>Retention Properties of Oligonucleotides</strong></h4>
<p>Several studies have reported the elution behavior of ONs in IP-RPLC in the presence of various ion-pairing reagents and using different stationary phases. (25−27) Efforts were mainly focused on (1) improving the chromatographic resolution (selectivity and peak capacity) of ONs or (2) improving the LC-MS sensitivity. (25) Relative retention indices and retention time calibration of homo-oligonucleotides in IP-RPLC have been published, (28) but absolute dimensionless measures of retention (like the S parameter of the LSS model) have not been reported yet, at least to the best of our knowledge. In this study, we focus our attention especially on the sensitivity of solute retention to mobile phase composition (S parameter), as this determines the required (effective) column length. We also discuss the log k0 parameter that corresponds to the extrapolated value of k for φ = 0. Here, the change in mobile phase composition was approximated by the change of organic modifier composition (methanol), while neglecting the effect of the small change in additive concentration. (29) It has also been reported that IP-RPLC separations of ONs benefit from shallow gradients, as they elute in relatively sharp peaks, despite the shallow gradient applied. (25) This may indicate that the retention of the solute is very sensitive to the eluent composition (on–off-like behavior). In practice, 50–150 mm long columns are often used for the IP-RPLC analysis of ONs, which is not necessary if the on–off behavior is valid.</p>
<p>...</p>
<h4><strong>Illustration of the On–Off Mechanism of Oligonucleotides</strong></h4>
<p>In general, IP-RPLC acts as a mixed-mode chromatographic mode combining hydrophobic and electrostatic (ionic) retention mechanisms. However, if the ion-pairing reagent concentration is sufficiently high, elution is mainly driven by hydrophobic interactions occurring between the stationary phase ligands and the hydrophobic part (i.e., alkyl chain) of the ion-pairing reagent molecules.</p>
<p><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c01934#fig2"><strong>Figure 2</strong></a>A shows plots of the log retention factor as a function of mobile phase composition (φ) for ATP, dT20, dT100, and a monoclonal antibody (mAb) as a reference. The figure was constructed on the basis of data obtained with the 100 mM HFIP mobile phase, resulting in the highest S values. It clearly illustrates that dT20 already shows an on–off behavior (very steep curve, S = 60). For the dT100, we observed a 2.5 times higher S value (S = 264) compared with an intact mAb (S typically ranges between 100 and 150). The higher S values observed with ONs are probably due to the differences in molecular shape and specific surface available for interaction with the stationary phase (helical straight shape versus Y-shape).</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Analytical_Chemistry_Anal_Chem_2023_95_27_10448_10456_Figure_2_Logarithmic_solute_retention_factor_d0e09e3597.jpg" alt="Analytical Chemistry 2023, 95 (27), 10448-10456 - Figure 2. Logarithmic solute retention factor (A) and relative migration velocity (u/u0) (B) as a function of the volume fraction of the organic mobile phase φ for ATP (black, MW = 0.5 kDa; S = 13), dT20 (green, MW = 6 kDa; S = 60), dT100 (red, MW = 30 kDa; S = 264), and an intact mAb (blue, MW = 150 kDa, S = ∼116)."/></p>
<p><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c01934#fig2"><strong>Figure 2</strong></a>B shows the relative migration velocity as a function of mobile phase composition. Such a plot illustrates the transition between fully adsorbed (“on”) and fully released (“off”) states. The value of S = 264 (and the log k0 = 45.2) means that up to a mobile phase composition of φ = 0.164, the migration velocity of the dT100 is practically zero (bound at the column inlet, its velocity is less than 1% of the interstitial mobile phase velocity), whereas from φ = 0.179, it moves at a velocity greater than 99% of the mobile phase velocity, indicating that the solute is fully desorbed from the column. The transition range between the adsorbed and desorbed states therefore corresponds to a Δφ range of only 1.5% (0.179–0.164). The transition range for the dT20 is somewhat wider, namely, 6.5% of Δφ. This transition typically occurs between 3 and 4% Δφ for an intact mAb in RPLC mode. For the small ATP molecule, we observed a transition range of 31.4% Δφ (from φ = 0.116–0.430).</p>
<p><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c01934#fig3"><strong>Figure 3</strong></a> shows a plot of the column length (Leff) required to effectively retain dT20 and dT100 (at least at ke = 0.5, which is a common practice for small molecule separations) as a function of gradient time and flow rate.</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Analytical_Chemistry_Anal_Chem_2023_95_27_10448_10456_Figure_3_Color_coded_surface_plot_of_the_column_length_Leff_required_to_retain_d_T20_and_d_T100_with_ke_0_5_7271adf747.jpg" alt="Analytical Chemistry 2023, 95 (27), 10448-10456 - Figure 3. Color-coded surface plot of the column length (Leff) required to retain dT20 and dT100 with ke = 0.5, as a function of gradient time and flow rate (dc = 2.1 mm ID, ε = 0.68, and Δφ = 0.2)."/></p>
<p>...</p>
<h3><strong>Conclusions</strong></h3>
<p>The goal of this proof-of-concept work was to evaluate if ultra-short columns can be used in IP-RPLC for the analysis of model oligonucleotides in gradient elution mode.</p>
<p>First, the validity of the LSS model was evaluated, and the accuracy of retention time predictions was assessed. It was found that ONs in IP-RPLC conditions follow the on–off elution behavior and that for most linear gradient separation conditions an effective column length between 5 and 35 mm was sufficient to obtain the best selectivity and separation efficiency. Therefore, the applicability of ultra-short columns was explored to speed up ON separations. In this regard, the extra-column band broadening induced by the instrumentation was carefully evaluated. Interestingly, the impact of injection volume and post-column connection tubing on peak capacity were found to be negligible. Next, the impact of column length on apparent efficiency was also monitored. First, column length was varied (150, 50, and 5 mm), while flow rate and gradient time were kept constant. Then, various gradient times and flow rates were tested on the three column lengths. In all cases, the on–off retention mechanism of ONs was confirmed. In addition, 5 mm column proved to be an advantageous choice to (i) increase the overall resolution achievable in gradient mode and (ii) perform ultra-fast separations with reasonable kinetic performance.</p>
<p>Optimized ultra-fast separations were therefore developed on the 5 mm column by using a flow rate of 1 mL/min and a gradient time of 1 min. Three model oligonucleotide mixtures including small, large, and PS-modified ONs were analyzed, and a remarkable resolution was especially obtained for the separation of the small ONs mixture. The separations were subsequently pushed to their limits at a higher flow rate (1.75 mL/min) and temperature (90 °C against the previous 60 °C), enabling baseline separation of all of the mixtures in as little as 30 s.</p>
<p>For the first time, a comprehensive study on the demonstration of the applicability of the LSS model to model oligonucleotides’ IP-RPLC separations in gradient elution mode was performed. The understanding of the ONs retention behavior enabled the evaluation of ultra-short columns and the selection of a 5 mm column to boost the ONs baseline separations in less than 1 min. These findings represent the first proof of concept for achieving ONs high-throughput analysis and pave the way for further investigation using more complex therapeutic oligonucleotides.</p>
<p>Interestingly, there are two possible reasons for using ultra-short columns for ONs: (i) achieving ultra-fast separation (1 min or less), while maintaining a reasonable efficiency, provided that the flow rate is sufficiently high and (ii) increasing the overall resolution achievable in gradient mode (corresponding to Pmin) within a reasonable analysis time (few minutes). The second aspect has not yet been explored but will be investigated in an upcoming work.</p>


High-Throughput Chromatographic Separation of Oligonucleotides: A Proof of Concept Using Ultra-Short Columns

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