In the world of biotherapeutics, bigger often means better — at least when it comes to circulation time in the bloodstream. One of the most widely used strategies to extend the half-life of protein drugs is PEGylation: attaching polyethylene glycol (PEG) chains to a therapeutic protein. The added polymer shields the protein, reduces immune clearance, and improves pharmacokinetics.<h4>PEGylation creates a major analytical challenge</h4>PEG is large and polydisperse (a distribution of chain lengths), and when attached to already complex, glycosylated proteins, it creates a molecular puzzle. How many PEGs are attached? Where are they attached? Are there impurities left behind?In this study, <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jproteome.5c00788?goto=supporting-info">Charge Detection Mass Spectrometry and a Glu-C/Lys-C Digestion-Based Data-Dependent Approach Suggest Mono-PEGylation of a Heterogenous Therapeutic Protein</a>, researchers developed a powerful mass spectrometry workflow that answers these questions — using Orbitrap-based charge detection mass spectrometry and a clever bottom-up strategy. The result? A confident determination that the therapeutic protein carries a single ~30 kDa PEG, along with precise mapping of its attachment sites.Let’s break down how they did it.<h3>The analytical problem: pegylation meets glycosylation</h3>The therapeutic protein studied here is already highly heterogeneous:<ul><li>165 amino acids</li><li>3 N-glycosylation sites</li><li>1 O-glycosylation site</li></ul>Add a ~30 kDa polydisperse PEG on top of that, and conventional mass spectrometry quickly runs into trouble:<ul><li>PEG ionizes very efficiently, masking protein charge states</li><li>Charge envelopes overlap</li><li>Intact mass deconvolution becomes difficult</li><li>PEGylated peptides fragment poorly</li></ul>Traditional approaches like post-column triethylamine (TEA) addition or MALDI have limitations, especially when glycosylation adds another layer of complexity.This is where Orbitrap-based Charge Detection Mass Spectrometry (CD-MS) changes the game.<h3>Step 1: Measuring the intact mass with charge detection MS</h3>The <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jproteome.5c00788?goto=supporting-info">team</a> used a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/560">Thermo Scientific Q Exactive UHMR</a> instrument operating in <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/lc-ms-systems/direct-mass-technology.html">Direct Mass Technology mode</a>.Unlike conventional ensemble MS, CD-MS measures:<ul><li>The m/z of each individual ion</li><li>The charge of each ion directly</li></ul>This enables direct mass determination of highly heterogeneous species.<h5>What did they see?</h5>From the data:<ul><li>Non-PEGylated protein (TP): ~28.95 kDa</li><li>PEGylated protein (PEG-TP): ~58.42 kDa</li></ul>That mass shift strongly supports mono-PEGylation — one PEG per protein molecule.Even more impressively, CD-MS revealed:<ul><li>A minor dimer impurity (~3.7%)</li><li>A small free PEGylation reagent (~30.4 kDa), likely residual reagent</li></ul>The mirror plot (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jproteome.5c00788?goto=supporting-info">Figure 2 on page 4</a>) visually highlights this mass shift, clearly separating the TP and PEG-TP populations.<h4>Why CD-MS was critical</h4>Because PEG is polydisperse, it broadens the mass distribution. In conventional ensemble MS, overlapping charge states prevent proper deconvolution. CD-MS bypasses this by assigning charge per ion, enabling:<ul><li>Accurate intact mass measurement</li><li>Impurity detection</li><li>Quantification</li><li>High reproducibility across runs</li></ul>For complex PEGylated biologics, this represents a major analytical advance.<h3>Step 2: Mapping the pegylation sites (bottom-up strategy)</h3>Knowing there’s one PEG is not enough — regulators and developers need to know where it’s attached.The team designed a multi-enzyme digestion workflow:<ul><li>Lys-C digestion</li><li>Glu-C digestion</li><li>Lys-C/Glu-C combination</li><li>PNGase F treatment to remove N-glycans</li></ul>Each digestion generated peptides of different lengths, providing complementary information.But there was still a problem.PEGylated peptides are difficult to fragment because the large PEG dominates ionization and masks peptide signals.<h3>The clever trick: high source CID</h3>They applied high in-source collision-induced dissociation (~90 eV) to partially strip PEG chains before MS/MS.This generated truncated PEG forms (PEG1–PEG50 variants), allowing:<ul><li>Precursor isolation</li><li>Efficient HCD fragmentation</li><li>Identification of diagnostic fragment ions</li></ul><a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jproteome.5c00788?goto=supporting-info">Figure 4 (page 7)</a> dramatically shows how high source CID transforms a messy PEG-dominated spectrum into clean multiply charged peptide precursors ready for sequencing.<h3>The result: three pegylation sites identified</h3>Using DDA and software-assisted analysis (<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1837">Biopharma Finder</a>), the study confidently identified PEGylation at:<ul><li>K52 (major site)</li><li>K45</li><li>N-terminal A1</li></ul>K52 — The dominant site K52 was consistently observed across all digestion strategies. Fragment maps showed strong diagnostic ions carrying truncated PEGs (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jproteome.5c00788?goto=supporting-info">Figures 5–7</a>). Multiple truncations (PEG22–PEG29 and beyond) were observed, confirming robust assignment.K45 — A secondary site K45 was confirmed in the combined Lys-C/Glu-C digestion (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jproteome.5c00788?goto=supporting-info">Figure 8</a>), where shorter peptides improved fragmentation and site localization.N-Terminal A1 — also modified Unexpectedly, PEGylation was also identified at the N-terminus (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jproteome.5c00788?goto=supporting-info">Figure 9</a>), with highly accurate fragment ion mass measurements supporting this assignment.The evidence suggests that:<ul><li>K52 and A1 are the most frequently occupied sites</li><li>K45 is less populated</li></ul><h3>Why this matters for biopharma</h3>PEGylated therapeutics must demonstrate:<ul><li>Batch-to-batch consistency</li><li>Controlled PEGylation stoichiometry</li><li>Clear impurity profiles</li><li>Verified modification sites</li></ul>This workflow delivers:<ul><li>Intact mass confirmation under native condition</li><li>Quantification of impurities</li><li>Confident site localization</li><li>High reproducibility</li><li>Software-assisted interpretation</li></ul>Importantly, it requires minimal sample — a key advantage in early development.<h3>The bigger picture: a blueprint for complex biologics</h3>The combination of:<ul><li>Orbitrap-based Charge Detection MS</li><li>Native intact mass analysis</li><li>Multi-enzyme digestion</li><li>High source CID optimization</li><li>Advanced data processing</li></ul>creates a seamless, comprehensive characterization strategy.Since pharma companies have been adding PEGylated modalities to their pipelines, the importance of this study will continue to shine. Furthermore, PEGylation and other polymer conjugations continue to evolve, and the analytical workflows must keep pace. This study demonstrates how modern mass spectrometry — particularly single-ion charge detection — can tackle extreme molecular heterogeneity with confidence.For PEGylated therapeutics, the mass spectrometer doesn’t just weigh molecules. It tells the full molecular story.<blockquote><h4>Reference:</h4><a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jproteome.5c00788?goto=supporting-info">Charge Detection Mass Spectrometry and a Glu-C/Lys-C Digestion-Based Data-Dependent Approach Suggest Mono-PEGylation of a Heterogenous Therapeutic Protein</a>Zoltan Szabo, Shero Lao, Katie S. Peterson, Kristina Srzentič, Kyle P. Bowen, Amanda E. Lee, Michael W. Senko, Dietmar Reusch, Steffen Lippold, and Markus HabergerJournal of Proteome Research Article ASAPDOI: 10.1021/acs.jproteome.5c00788</blockquote>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#PEGylation #Pharmacuetical #teamMassSpec #therapeutics

Cracking the Code of PEGylated Proteins: How Advanced Mass Spectrometry Reveals What’s Really Attached

Pipetting Made Easy – Part 1: Best Practice Guide

Our Library never stops expanding. What are the most recent contributions to LabRulezLCMS Library in the week of 20th July 2026? 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 posters by Agilent Technologies / ASMS, Shimadzu / ASMS, Thermo Fisher Scientific / HPLC Symposium and Waters Corporation / ASMS and technical note by KNAUER!<h3>1. Agilent Technologies / ASMS: Comprehensive characterization of oligonucleotides and related impurities using advanced LC/Q-TOF analytical workflows</h3><ul><li>Poster</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/po_oligonucleotide_lc_q_tof_mp_536_asms_2026_en_agilent_b896ffee63.pdf">Full PDF for download</a></li></ul>Therapeutic oligonucleotides are synthetic, short nucleic acid sequences designed to modulate gene expression by targeting RNA or DNA with high sequence specificity. However, their inherent structural heterogeneity makes impurity profiling essential, as during GMP manufacturing, impurities like phosphorothioate to phosphodiester, 5′ and 3′ truncations or extensions, depurination, and abasic species can directly impact both product safety and efficacy. Antisense oligonucleotides (ASO) like Nusinersen (7127.171 g/mol) are indicated for the treatment of spinal muscular atrophy (SMA). Their closely related variants coelute with the main peak, complicating their characterization in conventional one-dimensional LC/MS workflows. To address this challenge, a 2D LC/MS strategy was implemented using the Agilent 1290 Infinity III Bio LC system with multiple heart cutting, coupled to the 6545XT AdvanceBio LC/Q-TOF and MassHunter BioConfirm software. The first-dimension separation uses an ion pairing buffer-based method to achieve higher chromatographic peak resolution, while the second dimension provides MS compatible desalting, enabling enhanced mass spectrometric sensitivity and improved detection of low-level impurities.&nbsp;<h4>Instrumentation</h4>1290 Infinity III Bio 2D-LC &amp; <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=10&amp;search=6545XT">6545XT Q-TOF</a> includes:&nbsp;<ul><li>1290 Infinity III Bio Flexible Pump (G7131A)&nbsp;</li><li>1290 Infinity III Bio High-Speed Pump (G7132A)&nbsp;</li><li>1290 Infinity III Bio Multisampler (G7137A)&nbsp;</li><li>1290 Infinity III Multicolumn Thermostat (G7116B)&nbsp;</li><li>1290 Infinity III Variable Wavelength Detector (G7114B)&nbsp;</li><li>1290 Infinity III Diode Array Detector (G7117B)&nbsp;</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=10&amp;search=2D-LC">2D-LC System</a> with MHC set up</li></ul><h4>Conclusions</h4><ul><li>A 2D-LC/MS workflow enabled effective separation and identification of coeluting impurities.&nbsp;</li><li>HiRes sampling with multi-injection improved resolution and throughput while preserving 1D separation for MScompatible desalting.&nbsp;</li><li>6545XT AdvanceBio LC/Q-TOF delivered accurate mass and MS/MS data for low-abundance impurity detection.&nbsp;</li><li>MassHunter BioConfirm software enabled automated sequence confirmation and impurity identification.&nbsp;</li><li>This integrated platform offers a robust solution for oligonucleotide characterization in therapeutic development.</li></ul><h3>2. KNAUER: Smart Monitoring &amp; Optimization Solutions for SMB Processes: In-Line and Off-Line Tools for SMB Systems</h3><ul><li>Technical note</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/VTN_0048_knauer_in_line_and_off_line_tools_for_smb_systems_50a5f1c1cf.pdf">Full PDF for download</a></li></ul>In liquid chromatography, the purification of target compounds is classically carried out using single column batch chromatography. More efficient approaches include semi – continuous systems with two to three columns and continuous multicolumn systems. The most widely used of the latter is the simulated moving bed (SMB) chromatography which enables the continuous separation of binary or pseudo-binary mixtures. SMB purification is used in various areas such as petrochemical, pharmaceutical or food industry for the production of fine chemicals in different quantities and purities ranging from gram to tons per day. SMB systems vary significantly in size from small lab scale systems operating columns with 8 mm inner diameter (ID) to industrial systems operating columns of onemeter ID or larger.Ideally, an SMB process is developed in a smaller lab scale system to reduce solvent and sample consumption compared to development at production scale. Once the separation parameters are established, the SMB process allows for accurate up scaling from lab to production scale. During method development but also production, different tools can be used to monitor and control the process which can be distinguished between in-line and off-line measures. The most crucial parameter, in addition to measuring the pressure, is monitoring the flow rates of the pumps, outlets and/or zones accurately with additional flowmeters. Normally, SMB systems are not equipped with detectors, but UV or RI detectors can be integrated to monitor process stability.&nbsp;A standard off-line tool is used to analyse samples taken for one switch or cycle at the raffinate and extract outlets. The resulting chromatograms are used to check, if the separation is working. Further, samples can be taken during the process allowing the depiction of concentration profiles in the different zones. These tools will be described in more detail in the following sections.<h4>MATERIAL AND METHODS</h4><ul><li>AZURA Lab SMB system: SMB, biocompatible, 30 ml/min zone1, 4 ml/min feed, 10 – 130 bar&nbsp;</li><li>AZURA Lab SMB system: SMB, stainless steel, 30 ml/min zone1, 4 ml/min feed, 10 – 130 bar&nbsp;</li><li>AZURA Pilot SMB system, standard: SMB, stainless steel, 250 ml/min zone1, 40 ml/min feed, 2 – 100 bar&nbsp;</li><li>AZURA Pilot SMB system, high flow: SMB, stainless steel, 400 ml/min zone1, 100 ml/min feed, 2 – 60 bar</li><li>Refractive index detector: <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2429">AZURA® RID2.1L HighFlow detector</a> 100 ml/min&nbsp;</li><li>UV detector: <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2428">AZURA®UVD 2.1S detector</a>, w/o flow cell</li><li>UV detector: AZURA®UVD2.1S UV detector, fiber optics w/o flow cell</li></ul><h4>CONCLUSION&nbsp;</h4>SMB is a continuous separation process that can run for several hours or days without interruption. Therefore, it is important to monitor the process and to be able to adapt to changes during the run. Different tools are available that can be used for process monitoring and method development. These tools can be divided into two main categories: in-line and off-line tools. In-line tools monitor parameters such as pressure and flow rate directly during the run, whereas off-line tools take a sample, which is then analyzed by an HPLC system. The tools described can be added to the KNAUER SMB systems depending on the customer’s needs. The more parameters that are measured, the better the process can be monitored. This is especially helpful during SMB method development.<h3>3. Shimadzu / ASMS: Accelerating drug screening in forensic hair analysis by applying high-speed polarity switching in HR LC-MS/MS</h3><ul><li>Poster</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/TP_180_Accelerating_drug_screening_in_forensic_hair_analysis_by_applying_high_speed_polarity_switching_in_HR_LC_MSMS_168f8cc0b2.pdf">Full PDF for download</a></li></ul>In 2023, the Society of Hair Testing (SoHT) published updated consensus guidelines for the forensic analysis of drugs of abuse in hair, defining recommended targets across eight major drug classes: opiates, cocaine, amphetamines, cannabinoids, opioids, methadone, buprenorphine, and ketamine. Legal drivers, accepted use cases, and degree of prescription differ between US and Europe but in both jurisdictions, mass spectrometry is widely applied to support legally defensible conclusions. The challenge for any drug testing in hair samples, whether it is in forensic and safeguarding contexts, workplace testing or a judicial setting is the need to develop methods capable of detecting expanded search panels with the increased prevalence of new psychoactive substances (NPS) and non-medical prescription drug use. The approach applied in this work considered a LC/QTOF analysis using DDAMS/MS with rapid polarity switching with a novel data processing application, Insight Profiler. The software was designed to support a single click approach to automate data processing of complex data sets in non-targeted analysis from feature detection to compound identification.<h4>Materials and Methods</h4><h5>Reversed phase LC Separation: <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=1&amp;search=Nexera+X2">Nexera X2&nbsp;</a></h5><ul><li>Shim-pack Velox Biphenyl (100 x 2.1 mm, 2.7 µm) column; column temp. 40 ºC, flow rate: 0.3 mL/min, 17 min total analysis time. Methanol:water gradient with 2 mM ammonium formate and 0.002% formic acid&nbsp;</li></ul><h5>High resolution QTOF analysis: <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=1&amp;search=LCMS-9050">LCMS-9050&nbsp;</a></h5><ul><li>MS scan m/z 100-1000, 100 msec scan time. Polarity switching time 800 msec.&nbsp;</li><li>MS/MS DDA: 4 scans in positive ion mode (m/z 40-1000, 33 msec), 2 scans in negative ion mode (m/z 40-1050, 33 msec) CE 5-55V (1.998 sec total cycle time).</li></ul><h5>Data processing</h5><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=1&amp;search=Insight+Profiler">Insight Profiler</a>, feature detection threshold set to low, compound identification search lists included NIST, HighResNPS, Shimadzu Forensic Toxicology database.<h4>Conclusions&nbsp;</h4><ul><li>The targeted DDA-MS/MS polarity switching approach successfully identified a significant number of unknown compounds in the samples not routinely targeted by triple quadrupole analysis.&nbsp;</li><li>The method using DDA-MS/MS was easily configured to support an expanded DoA target panel to meet the needs of forensic toxicology screening.&nbsp;</li><li>Non-targeted analysis using Insight Profiler accelerated data analysis by aligning identified compounds from the same hair donor showing direction of change for pharmaceutical and illicit compounds detected.</li></ul><h3>4. Thermo Fisher Scientific / HPLC Symposium: Enhancing semi-volatile analyte detection in HPLC-CAD using temperature coupling mode for optimized evaporation control</h3><ul><li>Poster</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/po_004766_hplc_vanquish_cad_fatty_acid_quantification_po004766_na_en_4a0868c2cb.pdf">Full PDF for download</a></li></ul>Polysorbates are widely used in biopharmaceutical formulations but can degrade or contain FAs impurities that must be accurately measured to ensure product quality and safety. Charged Aerosol Detection is commonly used for FA analysis, though its performance depends strongly on EvapT. Higher EvapT improves S/N ratios but can reduce sensitivity for semi-volatile compounds like FAs, while lower EvapT has the opposite effect. The <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2176">Thermo Scientific Vanquish Charged Aerosol Detector P</a> series introduces a Temperature Coupling Mode that links EvapT with the charging detection module (CDM) temperature, overcoming limitations of earlier systems with fixed CDM temperature of 40 ºC. This coupling improves response and measurement reliability for semi-volatile species, enabling better optimization of FA analysis1.<h4>Conclusions&nbsp;</h4><ul><li>Advanced temperature control in CAD improved method sensitivity up to ~47% for semi-volatile fatty acids.&nbsp;</li><li>The best overall S/N was achieved at 25.0 °C EvapT with Temperature Coupling Mode enabled.&nbsp;</li><li>The optimized CAD approach supports more sensitive FA impurities and degradants quantification in pharmaceutical and biopharmaceutical formulations.</li></ul><h3>5. Waters Corporation / ASMS: High mass and spatial resolution MS imaging of soft fruit sample cross-sections using desorption electrospray ionization (DESI)</h3><ul><li>Poster</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/720009492_282619e388.pdf">Full PDF for download</a></li></ul><div><div><section><div><div><div><div><div><div>This poster demonstrates the use of desorption electrospray ionization mass spectrometry imaging (DESI MSI) for visualizing the spatial distribution of metabolites in high-water-content soft fruits, specifically strawberries and raspberries. The authors developed a simple direct-transfer workflow to overcome the challenges associated with imaging delicate fruit tissues and compared three transfer substrates: plain glass microscope slides, nitrocellulose membranes, and Hamamatsu Poropare plates. The goal was to determine which surface best preserves metabolite localization while enabling high-quality mass spectrometry imaging.Fresh fruit cross-sections were transferred to each substrate by direct contact for 10 seconds before analysis using a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?mainauthorItems=5&amp;search=DESI+XS">Waters DESI XS ion source</a> coupled to a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2433">Waters Xevo™ MRT P10 high-resolution mass spectrometer </a>operating in negative electrospray ionization mode. MS imaging was performed with a 50 µm pixel size, using a 95:5 methanol/water spray solvent, while sucrose (m/z 341.1089) served as the lock mass for accurate mass calibration. High mass resolution enabled tentative assignment of metabolites such as citric acid, asparagine, malic acid, glutamic acid, palmitic acid, stearic acid, and sucrose.The comparison of transfer substrates revealed significant differences in metabolite localization and image quality. Glass slides produced the strongest metabolite signals but also exhibited considerable metabolite delocalization during sample transfer, reducing spatial accuracy. Nitrocellulose membranes transferred a broader range of metabolites and provided complementary chemical information, although they also showed greater analyte spreading and suffered physical damage after a single DESI acquisition. In contrast, Poropare plates minimized metabolite delocalization and preserved fine structural details within the fruit cross-sections, despite producing somewhat lower signal intensities than glass slides.The study concludes that direct transfer combined with DESI MSI is an effective approach for imaging soft fruit tissues that are otherwise difficult to analyze because of their high water content. Among the evaluated substrates, Hamamatsu Poropare plates provided the best balance between spatial resolution and preservation of metabolite localization, making them particularly suitable for high-resolution metabolomic imaging, while high mass accuracy facilitated confident tentative metabolite identification.</div></div></div></div></div></div></section></div></div>

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News from LabRulezLCMS Library - Week 30, 2026

Pipetting Made Easy – Part 1: Best Practice Guide

Cracking the Code of PEGylated Proteins: How Advanced Mass Spectrometry Reveals What’s Really Attached