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Analytical Solutions for Pharma and Biopharma

Progress in medical and pharmaceutical technology is a key driver to increasing people’s life expectancy. Nowadays, besides the classic small molecule driven pharmaceutical development, constantly are new biopharmaceuticals developed, for use in treatment and therapy. This brings up new challenges in diagnostics and analytics. 
Modern pharmaceuticals are applied more individually to patients and illnesses, help to overcome chronic or incurable diseases. Development and production of modern drugs require state of the art analytic. 
 

Challenges in Pharmaceutical & Biopharmaceutical Industry

 

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Bioprocessing and Cell Culture

 

Bioprocessing

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Bioprocessing is the use of living cells, biological materials, or their components to develop and manufacture products such as biopharmaceuticals, vaccines, enzymes, and biofuels. This multidisciplinary field combines biology, engineering, and technology to transform raw materials into high-value products through controlled biological processes. 

Key stages of bioprocessing include upstream processing (cell cultivation and fermentation), downstream processing (purification and recovery), and formulation of the final product. Advanced techniques such as bioreactor systems, chromatography, and filtration ensure efficiency, scalability, and compliance with regulatory standards. Bioprocessing is critical for producing safe, effective, and high-quality biologics that meet the growing demands of healthcare and industry. 

Cell Culture

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Cell culture is a method to study the behavior of cells in a controlled environment, free of systematic variations. Different types have been adapted and developed based on the purpose of the investigation, such as interactions of drugs and other chemicals with cells, production of vaccines and proteins, and advanced analysis using the C2MAP System and Cell Culture Profiling Ver. 3. To care for optimal conditions, the composition of the media is checked regularly; therefore different chemical compounds and parameters are controlled, and different techniques and applications are used, including solutions such as CELL POCKET.

Solution Highlights

 

 

 

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Candidate Selection, Development and Optimisation

 

Medicinal Chemistry

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Medicinal chemistry is a common practice in pharmaceutical research and development. It describes the steps in the process from target definition, lead discovery and evaluation up to first studies related to metabolism, pharmacokinetics and toxicology, often supported by purification and separation workflows using Nexera PrepNexera UC Prep, and Liquid Chromatograph-Mass Spectrometry.

The focus is set on the discovery of new drugs, mainly based on small organic molecules. Those can be the result of classic organic-chemical synthesis, out of natural products, or out of computational chemistry in combination with chemical biology, enzymology and structural biology, where advanced analytical platforms such as Liquid Chromatograph-Mass Spectrometry play an important role.

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Purification

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Purification is one of the most essential processes in pharmaceutical production, as it removes harmful impurities such as residual solvents, heavy metals, microbial contaminants, and by-products, which can pose serious health risks to patients. Regulatory agencies like the FDA and EMA mandate strict limits on impurities in pharmaceutical products, making advanced purification and analytical solutions such as Nexera PrepNexera UC PrepLiquid Chromatograph-Mass Spectrometry, and Gas Chromatograph-Mass Spectrometry highly relevant in ensuring product safety and compliance.

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Method Development and Scale Up

Method Development

 

Liquid chromatography (LC) is a powerful analytical technique widely used in pharmaceutical, chemical, and biotechnological industries for separating, identifying, and quantifying compounds. Method development for LC focuses on optimizing parameters such as column selection, mobile phase composition, flow rate, and detection methods to achieve efficient and reproducible separation. This process ensures robust analytical performance and compliance with regulatory standards, supported by solutions such as the Method Scouting System and Nexera ASAPrep.

Scaling up LC methods to preparative separation is essential for isolating larger quantities of target compounds, such as active pharmaceutical ingredients or biomolecules, while maintaining high purity and yield. The transition from analytical to preparative LC requires careful optimization of column dimensions, flow rates, and solvent usage to ensure scalability without compromising separation efficiency. With precise method development and scale-up strategies, preparative LC becomes a critical tool for supporting research, production, and quality control in various industries, where systems like the Method Scouting System and Nexera ASAPrep can be seamlessly integrated into the workflow.

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Proteins, Peptides, mAbs, ADCs, Glycans

Proteomics is an academic discipline involving the comprehensive study of protein structure and function, typically by mass spectrometry and electrophoresis. Unlike the genome, the cells of an organism do not all contain the same complement of proteins, but different cells contain different proteins at different times. Proteomics uses this phenomenon to enable more efficient drug development and to determine the mechanisms of disease.

 

Analysis of Proteins and Peptides

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Proteins are a versatile group of macromolecules; peptides are smaller in size with a limited number of building stones. Both consist out of a chain of amino acids, their structure is determined not only by the amino acids, but also by interactions between them, forming a secondary and tertiary structure which is important for the activity of the molecule and its chemical and physical characteristic.  
Proteins are present in all cells, functioning e.g. as enzymes, as transmitters or as biomarkers. Understanding about conditions and mechanism of their expression or absence is crucial for further development of biopharmaceuticals for a targeted therapy of diseases. 

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Analysis of Monoclonal Antibodies and Antibody Drug Conjugates (ADCs)

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Monoclonal antibodies (mAbs) have emerged as revolutionary therapeutic agents for an array of human diseases. In addition to their large mass and complex structure, mAbs are varied in their origin, makeup, effector function and delivery, and therefore require thorough formulation development, including characterization, quantitation and preservation. 
More and more special designed Antibody drug conjugates (ADCs) are under development as targeted therapy for treating cancer.  ADCs combine the targeting capabilities of monoclonal antibodies with the cancer-killing ability of cytotoxic drugs. 

Solution Highlights

 

nSMOL™ - unique method of sample preparation for LCMS bioanalysis of monoclonal antibody in blood

 

nSMOL (nano-surface and molecular orientation limited proteolysis) is Shimadzu’s proprietary, innovative technique that enables selective proteolysis of the Fab region of monoclonal antibodies. The nSMOL Antibody BA Kit is a ready-to-use reagent kit for collecting monoclonal antibodies from blood or other biological samples using immunoglobulin collection resin, and then performing selective proteolysis of the Fab region of these antibodies via trypsin-immobilized nanoparticles. Variable region-derived peptides produced by limited proteolysis can then be quantified via MRM measurements utilizing a high-performance LCMS-8050/8060 triple quadrupole liquid chromatograph mass spectrometer.

  • Faster, Less Expensive Method Development

 Dramatically improves response and quantitative repeatability. No capture antibodies or ligands are required.

  • nSMOL Proteolysis

 Selective collection of Fab peptides. Limits contamination from excessive peptides or trypsin.

  • Performance

 Highly sensitive and accurate essays are possible for a variety of antibodies

  • Highly Versatile

 Applicable to a wide variety of pharmaceutical antibodies.

  • Simple Workflow

 This kit enables highly reproducible data and avoids the troublesome steps of denaturing, reduction, and alkylation normally associated with protein digestion. There is also no need for solid phase extraction after reaction. After nSMOL preparation, samples can be injected directly into the LCMS.

Solution Highlights

Host Cell Protein Analysis

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Host cell proteins (HCPs) are process related impurities expressed by host cells during the production of biopharmaceuticals. The purification process eliminates the majority, but residual HCPs remain in the distributed products. 
Regulatory authorities require that these impurities must be analyzed and purified to reduce the HCPs to an acceptance level. This is evaluated case by case and depend on a lot of factors, such as dose, frequency of drug administration, type of drug and severity of the disease. 
The analytic is not simple as the HCP mixture contains a large number of protein species, unique to the host and not related to the biopharmaceutical. 

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Post translational Modification Analysis

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Post-translational modifications (PTMs) are chemical changes that occur in proteins after their synthesis, significantly influencing their structure, function, stability, and activity. Common PTMs include phosphorylation, glycosylation, acetylation, methylation, ubiquitination, and disulfide bond formation. These modifications play vital roles in cellular processes such as signal transduction, immune responses, and protein regulation.
Analyzing PTMs is essential for understanding protein function and developing therapeutic applications, particularly in biopharmaceuticals. Advanced techniques like mass spectrometry (MS), high-performance liquid chromatography (HPLC), and antibody-based assays are used to identify, quantify, and characterize PTMs. Precise analysis enables researchers to study disease mechanisms, optimize drug development, and ensure the quality of protein-based therapeutics.

Solution Highlights

 

Glycan Analysis

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Many protein-based biopharmaceutical products, typified by antibody drugs, are synthesized in cultured cells derived from eukaryotes such as CHO (Chinese hamster ovary) cells. For this reason, there are inevitably many post-translational modifications to the biosynthesized proteins. Among these, modifications of glycans have gained attention as items for evaluating the quality of biopharmaceuticals since they are associated with the adjustment of protein functions, as well as with the unwanted development of antigenicity depending on their structure. 

Glycan characterization is important in the process of protein drug development, from early stage candidate selection to late stage regulatory submission. Glycan variants of a glycoprotein product must be adequately analyzed and controlled to ensure product quality. The inherent complexity of protein glycosylation poses an analytical challenge.
 

Solution Highlights

 

 

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Nucleotide Analysis

nucleotide analysis

 

The main dogma of molecular biology states that DNA is transcribed into RNA, which then is translated into the amino acid sequence of an expressed protein. Knowledge about the DNA structure and sequence is important to gain a better understanding of genes, protein expression, and the complex regulatory mechanisms in cells. Analysing the nucleic base sequence and structure-determining elements of DNA and RNA is often the starting point, supported by advanced analytical technologies such as the MALDI-8030OAD-TOF SystemRF-6000UV-1900i Plus, and LabSolutions Insight Biologics.

Diagnosis of gene defects as a cause of rare diseases and their treatments are the driving force for the development of new-generation medications, such as gene therapy. After synthesis of the special DNA or RNA pieces, the verification of their structure and sequence are key tasks to cover, where instruments like the MALDI-8030, OAD-TOF System, and LabSolutions Insight Biologics can be integrated naturally into the workflow.

Modern vaccines based on mRNA and their production once more underline the importance of having state-of-the-art techniques and solutions for fast and precise analysis, including spectroscopic support from the RF-6000 and UV-1900i Plus, alongside data analysis capabilities provided by LabSolutions Insight Biologics.

 

Solution Highlights

 

 

 

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Preclinical & Clinical Testing 

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After finding and defining a new drug candidate, a series of tests related to harmlessness, effective dosage, distribution, pharmacological and toxicological parameters, and its use for a specific disease or its healing must be performed. Analytical methods therefore need to be validated, registered, and must follow international standards and guidelines as given by regulatory bodies concerning their documentation and data integrity. In these workflows, technologies such as Triple Quadrupole LC-MS/MSiMScope QT, and Nexera Series can be incorporated naturally to support compliant and reliable analysis.

Solution Highlights

 

 

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Veterinary drugs

Health of animals, both companion and farm ones, is important not only for their well-being but also for human life. As people and animals live together in limited spaces, the risk of illnesses and parasites can increase. Veterinary drugs, also known as medicinal products for veterinary use, veterinary medicine, or veterinary medicinal products (VMPs), are substances or combinations of substances used to treat, prevent, or diagnose disease in animals. To ensure these products meet the necessary quality and safety standards, laboratories rely on advanced analytical solutions, from routine testing with the i-Series HPLC/UHPLC systems and high-performance workflows enabled by the Nexera Series, to sensitive detection and quantification using Triple Quadrupole LC-MS/MS systems.

Solution Highlights

 

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Crude drugs

Classical drugs are often based on natural products, for example leaves, blossoms, roots, or fruits from plants, as well as secretions from small animals or insects. Their proven effects and the experience gained over many years continue to make them relevant today. The ingredients, pharmacologically active compounds, and their interactions are the subject of extensive analytical work, supported by technologies such as the Nexera Series for high-performance chromatography, the Nexera-e for efficient routine HPLC analysis, and the LCMS-2050 for reliable mass spectrometric detection.

Solution Highlights

 

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Pharmaceutical Water

Pharmaceutical water is a vital component in drug manufacturing, used in processes ranging from formulation to cleaning and sterilization. Its quality directly impacts product safety and efficacy, making rigorous analysis essential. Different grades of pharmaceutical water, such as Purified Water, Water for Injection (WFI), and Sterile Water, must meet strict regulatory standards to ensure purity, microbial control, and compliance with pharmacopeial requirements.

Analysis of pharmaceutical water involves testing for chemical contaminants, microbial content, endotoxins, conductivity, and pH levels using advanced techniques. These tests are critical to maintaining the integrity of manufacturing processes and ensuring the final product meets the highest quality standards. Discover how precise water analysis, supported by solutions such as the eTOC series and TOC-L Series, supports reliable pharmaceutical production and patient safety.

When used in the pharmaceutical and semiconductor industries, it is important to continuously control the quality of pure water to keep the impurities at low level. For optimum quality control of ultra-pure water, and for pharmaceutical water where the US Pharmacopoeia (USP) specifies total organic carbon (TOC) management of organic impurities according to USP 643, TOC analyzers used for analysis of bulk purified water and water for injection must satisfy the TOC system suitability test using test water with a carbon content of 0.500 mg/L.

 

Solution Highlights

 

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Manufacturing and QA

Production of pharmaceuticals follows high quality standards for safety, cleaning and traceability. Robust and reliable analytical instruments and methods used in production and quality control care that patients and doctors can rely on these products. Quality control starts with check of incoming raw materials, the water used in the process and includes on the other side also packing materials, physical properties as well as a strong control of waste water. 
In the pharmaceutical industry, the importance of Quality Assurance (QA) and Quality Control (QC) is very high. It relates to factors such as safeguarding patient safety, complying with regulatory requirements, ensuring product quality consistency, and improving production efficiency. However, due to the diversity of product forms and the complex and fluid regulatory environment, advanced expertise in analysis is required to apply QA/QC. Shimadzu Corporation contributes to the improvement of quality assurance and quality control processes through innovative solutions in precise measurement, automation, and data management.

 


Raw Material testing

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Ensuring the quality and safety of pharmaceutical products begins with rigorous raw material testing. In pharmaceutical manufacturing, raw materials such as active pharmaceutical ingredients (APIs), excipients, and packaging components play a critical role in determining the efficacy and stability of the final product. Comprehensive testing of these materials is essential to meet regulatory standards, prevent contamination, and guarantee consistency across production batches.
Raw material testing involves evaluating physical, chemical, and microbiological properties using advanced analytical techniques. This process helps identify impurities, confirm compliance with pharmacopeial specifications, and verify supplier certifications. By implementing stringent testing protocols, pharmaceutical companies safeguard patient health and maintain the integrity of their production processes.
Explore how our expertise in raw material testing supports the foundation of high-quality pharmaceutical manufacturing.

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 Residual Solvent Analysis

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Residual solvent analysis is a crucial step in ensuring the safety and quality of Active Pharmaceutical Ingredients (APIs). Residual solvents are organic chemicals used during API synthesis that may remain in trace amounts after production. If not properly controlled, these solvents can pose risks to patient health or impact the stability of pharmaceutical products.
Using techniques such as gas chromatography (GC), residual solvent analysis identifies and quantifies these solvents to ensure compliance with regulatory limits, such as those outlined in ICH Guideline Q3C. This process helps manufacturers eliminate harmful levels of solvents, ensuring that APIs meet strict safety standards and are suitable for therapeutic use.

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Impurity Analysis

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Impurity analysis is a critical aspect of pharmaceutical development and manufacturing, aimed at identifying, quantifying, and controlling unwanted substances that may arise during synthesis, storage, or packaging. These impurities, including degradation products, residual solvents, and trace contaminants, can impact drug efficacy, stability, and patient safety.
Genotoxic impurities are critical components of pharmaceutical development and manufacturing, focusing on the detection, identification, and control of impurities with the potential to damage genetic material. These impurities, which may arise during synthesis, degradation, or from raw materials, pose serious safety risks even at trace levels, making their control essential to protect patient health. 

Sophisticated analytical techniques, such as high-performance liquid chromatography (HPLC), gas chromatography (GC), and mass spectrometry (MS), are employed to detect and quantify genotoxic impurities with high sensitivity and precision. Compliance with regulatory guidelines, such as ICH M7, ensures the effective management of these impurities throughout the drug lifecycle. By prioritizing genotoxic impurity analysis, pharmaceutical manufacturers can uphold product safety, meet stringent regulatory requirements, and minimize risks to public health.

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Nitrosamine Impurities

Nitrosamine Impurities

 

Nitrosamines are chemical compounds that have raised significant concerns due to their potential carcinogenic properties. Found in various industries, including pharmaceuticals, food, cosmetics, and water treatment, their presence can result from chemical reactions or contamination during manufacturing processes. Accurate nitrosamine analysis is essential to safeguard public health, ensure regulatory compliance, and maintain product integrity.
Modern analytical techniques, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), enable precise detection and quantification of nitrosamines even at trace levels. These methods support diverse applications, from pharmaceutical quality control to environmental monitoring and food safety testing.
Explore our application examples to learn how advanced nitrosamine analysis solutions can address challenges across industries, ensuring safety and reliability in your products and processes.

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Quality Control 

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Quality control (QC) is a cornerstone of pharmaceutical production, ensuring that every product meets stringent standards for safety, efficacy, and consistency. Through systematic testing and monitoring at every stage of manufacturing, QC verifies that raw materials, intermediates, and final products comply with regulatory requirements and industry specifications.
Advanced analytical techniques, such as chromatography, spectroscopy, and microbiological testing, play a vital role in detecting impurities, confirming active ingredient concentrations, and assessing product stability. Additionally, QC processes validate packaging integrity and ensure batch-to-batch uniformity. By prioritizing quality control, pharmaceutical manufacturers safeguard patient health, enhance product reliability, and maintain compliance with global regulatory frameworks such as GMP (Good Manufacturing Practices).

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Formulation & Final Product Analysis

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Pharmaceutical formulation is the process of designing and producing drug products with the desired therapeutic efficacy, stability, and patient acceptability. This involves combining active pharmaceutical ingredients (APIs) with excipients to create a final product in the form of tablets, capsules, injections, or other dosage forms. Ensuring the accuracy of the formulation is critical to achieving consistent content uniformity and maintaining product quality.
Analytical techniques such as high-performance liquid chromatography (HPLC), UV-Vis spectroscopy, and dissolution testing are essential for confirming the API content, verifying excipient compatibility, and ensuring batch-to-batch consistency. Final product testing focuses on key parameters like potency, purity, stability, and bioavailability to meet regulatory requirements and ensure patient safety. By integrating robust formulation practices with precise analytical methods, pharmaceutical manufacturers can deliver high-quality, reliable medicines to the market.
 

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Cleaning Validation 

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Cleaning validation is a critical process in pharmaceutical manufacturing that ensures equipment and facilities are thoroughly cleaned to prevent cross-contamination, maintain product integrity, and comply with regulatory standards. As pharmaceutical production involves handling various active ingredients, excipients, and chemicals, residues left behind can compromise product quality and pose risks to patient safety.
The cleaning validation process involves establishing scientifically proven cleaning procedures, testing for residual contaminants, and setting acceptable limits for residues such as active pharmaceutical ingredients (APIs), cleaning agents, and microbial contaminants. Analytical methods like high-performance liquid chromatography (HPLC), total organic carbon (TOC) analysis, and swab testing are commonly used to verify cleaning effectiveness.
By implementing robust cleaning validation protocols, pharmaceutical manufacturers can ensure consistent product quality, meet Good Manufacturing Practices (GMP) requirements, and uphold patient safety. Explore our solutions to learn more about advanced tools and techniques for cleaning validation in pharmaceutical production.
 

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Data Integrity and Compliance

Data Integrity in the pharmaceutical industry is an essential concept for ensuring the quality, safety, and efficacy of products, and it is of utmost importance for patient safety. If data tampering or unauthorized changes occur, product quality can be compromised, potentially posing serious health risks to patients. Moreover, data integrity is a crucial factor in audits and reviews by regulatory authorities such as the FDA, serving as a key indicator of regulatory compliance. Solutions such as LabSolutions CS and Total Solution for PIC/S and FDA Compliance support pharmaceutical laboratories in establishing secure, compliant, and traceable data management practices.

Pharmacopoeia provides an overview of testing methods, such as chromatography, as a general chapter that must be satisfied when conducting tests according to pharmacopoeia regulations. The Pharmacopoeial Discussion Group (PDG) decided in November 2021 to standardize general chapter chromatography in the United States Pharmacopoeia (USP), the European Pharmacopoeia (EP), and the Japanese Pharmacopoeia (JP).

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Spectroscopy / Elemental Analysis

Measuring Instruments

FAQ's

 

What are the main challenges of biopharmaceuticals compared with small-molecule pharmaceuticals?
Biopharmaceuticals are generally more complex to develop, manufacture, and store than small-molecule drugs. They often require living systems for production, which can make them more expensive and harder to scale consistently. They may also be less stable, more sensitive to temperature changes, and require stricter handling and distribution conditions. In contrast, small-molecule pharmaceuticals are usually simpler to synthesize, characterize, and store.
What are the main differences between SFC and UHPLC for pharmaceutical applications?
Supercritical fluid chromatography (SFC) often offers faster separations, lower solvent use, and good performance for nonpolar to moderately polar compounds, making it useful for chiral separations and purification. UHPLC is generally more versatile for a wider range of polar and nonpolar analytes and is often preferred for routine quantitative analysis due to its strong robustness and compatibility with many detection methods. The choice depends on the compound properties, separation goal, and method requirements.
What are the main cell culture media components, and why and how are they optimized?
Cell culture media typically contain amino acids, vitamins, salts, glucose or other energy sources, trace elements, buffering agents, and growth supplements such as serum or defined proteins. These components are optimized to support cell growth, productivity, viability, and product quality while minimizing unwanted byproducts. Optimization is usually done by systematically varying component concentrations, testing different media formulations, and using design-of-experiments approaches to identify the best balance for a specific cell line and process.
What are analytical methods for cell culture media analysis?

Analysis of compounds in cell culture media is usually done by sample preparation + chromatographic or spectroscopic analysis, depending on what you want to measure.

Common analytical methods
Method What it is used for Notes
HPLC/UHPLC with UV or PDA detector Small molecules, nutrients, metabolites, drugs Good for targeted analysis if the compound absorbs UV
LCMS/MS Low-level metabolites, drugs, amino acids, biomarkers Very sensitive and selective; often preferred for complex media
GCMS Volatile compounds, some metabolites Usually needs derivatization
Spectrophotometric assays Glucose, lactate, ammonia, etc. Fast and routine
There are application packages for analysis of cell culture media compounds Beside the listed ones, there are other methods e.g. Immunoassay or benchtop NMR systems which are used for biological targets or for additional information about the molecule structure.
Protein structure analysis, what are the differences between Edman degradation and de novo sequencing for protein structure analysis?
Edman degradation, is a classical method that sequentially removes and identifies one amino acid at a time from the N-terminus of a peptide or protein. It is highly specific but works best for short, pure peptides and requires a free N-terminus. It becomes less effective for longer proteins, blocked N-termini, or mixtures. (please find details about the PPSQ systems) De novo sequencing usually refers to mass spectrometry-based methods that infer the amino acid sequence without needing a reference database. It can analyze peptides from complex samples and is more flexible than Edman degradation, but the sequence interpretation can be more challenging and may be less certain in ambiguous regions. (Please find information about suited MALDI instruments)
What are the benefits of method development software for fulfilling Quality by Design (QbD) requirements?
Method development software helps support QbD by enabling systematic, data-driven optimization of analytical methods. It can reduce trial-and-error work, identify critical method parameters, and map the design space more efficiently. This improves method robustness, reproducibility, and understanding of how changes affect performance. It also helps generate documentation and traceable data, which supports regulatory compliance and faster method transfer. Please click for more information for LabSolutions MD software.
What are the advantages and key features of multidimensional liquid chromatography?
Multidimensional liquid chromatography combines two or more separation mechanisms in one workflow, which greatly improves resolution for complex samples. Its main advantages are higher peak capacity, better separation of co-eluting compounds, and improved analysis of difficult mixtures such as biopharmaceuticals, impurities, and metabolites. Key features include orthogonal separation modes, fraction transfer between dimensions, and the ability to couple with advanced detectors like MS. The main drawback is greater method and instrument complexity compared with single-dimensional LC.
Is the longer runtime of multidimensional liquid chromatography worth it for comprehensive LC?
Often, yes. The longer runtime can be justified when the sample is highly complex and requires much higher separation power than one-dimensional LC can provide. Multidimensional LC can reveal co-eluting compounds, improve impurity profiling, and give a more complete analytical picture. However, if the sample is simple or the routine goal is fast quantitation, the added time, method complexity, and instrument burden may not be worth it. Pleased click for more information about the Nexera-e system.
What are the differences and advantages of oligonucleotide analysis by reversed-phase chromatography versus supercritical fluid chromatography?
Reversed-phase chromatography (RPC) ) is the more established approach for oligonucleotide analysis. It offers strong robustness, good compatibility with ion-pairing reagents, and reliable separation of closely related impurities, truncated sequences, and product variants. Its main drawbacks are relatively high solvent use and sometimes longer run times. Click for more information about our Nexera UHPLC series.
Supercritical fluid chromatography (SFC) can provide faster separations, lower organic solvent consumption, and good efficiency for certain oligonucleotide-related impurities, especially when method conditions are well optimized. However, oligonucleotides are highly polar and charged, so SFC can be more challenging to develop and may have narrower method applicability than RPC. Click for  more information about the Nexera UC system.
What advantages does a bioinert or biocompatible LC system have compared to a standard LC system when analyzing biomolecules?
A bio-inert or bio-compatible LC system reduces unwanted interactions between biomolecules and metal surfaces in the flow path. This can improve recovery, peak shape, sensitivity, and reproducibility, especially for proteins, peptides, oligonucleotides, and other metal-sensitive analytes. It also helps minimize adsorption, sample loss, and carryover, which is important for low-level or highly reactive biomolecule analysis. In contrast, standard LC systems may cause more analyte binding, peak tailing, and variability. Please find information about the Nexera lite inert and Nexera XS inert.
What methods are available for elemental impurity analysis?
Common elemental analysis methods include ICP-MS, ICP-OES, AAS, EDX, and combustion-based elemental analysis
What are the arguments for a compact all-in-one LC system versus an individually configured LC system?
A compact all-in-one LC system (i-Series) offers a smaller footprint, simpler setup, faster installation, and easier operation. It is often more convenient for routine work, training, and labs with limited space. An individually configured system (Nexera UHPLC systems) offers greater flexibility, easier customization, and simpler upgrading or replacement of individual modules. It is usually better when specific applications require specialized components or future expansion.
What detectors are there for (U)HPLC systems in pharmaceutical applications, and what are the main features and limitations?
the following table shows an overview about detectors provided by Shimadzu.
 
Detector Suitability for pharmaceutical analysis Main advantages Main limitations Best use case
UV/Vis 
(SPD-40A/AV)
Very common for assay and impurity testing Robust, inexpensive, easy to validate, widely accepted in QC Requires UV-active compounds; limited for non-chromophoric APIs/excipients Routine assay, related substances, stability-indicating methods
Fluorescence
(RF-20A/AXS)
Useful for trace-level impurities and selected APIs Very high sensitivity and selectivity Limited to fluorescent compounds or derivatized analytes Trace impurities, bioanalysis, highly sensitive targeted methods
Refractive Index (RI)
(RID-20A)
Mainly for simple formulations and excipients Broad applicability for non-UV compounds Low sensitivity; poor for gradient methods; less suitable for routine pharma QC Sugars, polymers, excipients, simple non-UV analytes
ELSD
(ELSD-LTIII)
Useful for sugars, lipids, lipophilic excipients, and some APIs Detects non-volatile analytes; more universal than UV Response can be non-linear; method conditions must be tightly controlled Non-volatile excipients, lipids, carbohydrates, some API impurities
MS
(LCMS-2050)
Excellent for identification, impurity profiling, and bioanalysis High sensitivity and structural information Higher cost; more complex validation; ionization differences can affect quantitation Structure confirmation, unknown impurity ID, bioanalysis, metabolite studies
Which UV detector is the best choice for which application?

UV detector measures absorbance at one fixed wavelength (or a small number of wavelengths, depending on the instrument); PDA detector measures the full UV-Vis spectrum across many wavelengths at once.

  • Use UV when you need a simple, cost-effective, routine assay
  • Use PDA when you need identity support, peak purity, impurity detection, or stability-indicating methods
Which cell culture compounds are analysed with by HPLC?
Table: compounds vs best analytical method
 
Compound / analyte type Best analytical method Notes
Glucose HPLC-RID/ELSD Enzymatic methods are most common for routine monitoring
Lactate HPLC-RID/ELSID Fast and routine
Ammonia IC Useful for cell culture monitoring
Amino acids HPLC-RF, LCMS/MS Often need derivatization for HPLC-FLD
Small-molecule drugs HPLC-UV/PDA or LCMS/MS LC-MS/MS if sensitivity/selectivity is critical
Vitamins HPLC-UV/PDA or LCMS/MS Depends on the vitamin and concentration
Nucleotides / nucleosides HPLC-UV/PDA or LCMS/MS HILIC or ion-pair methods may help
Organic acids HPLC-UV, IC, LCMS/MS LCMS/MS for low levels
Peptides LCMS/MS or HPLC-UV/PDA LCMS/MS preferred for specificity
Proteins / cytokines ELISA / Immunoassay* HPLC is usually not the first choice
Lipids LCMS/MS Best for complex lipid profiling
Volatile compounds GCMS Requires volatility or derivatization
Global metabolite profiling HR-MS / NMR LC-MS is more sensitive; NMR is more robust for profiling
*not provided by Shimadzu 
HPLC in pharmaceutical development, which parameters should be optimized and what criteria need to be met?
Parameters typically optimized:
  • Column: Chemistry (e.g., C18, C8, phenyl; Dimensions (length, ID, particle size)
  • Mobile phase (Composition/ratio; Organic solvent type; Buffer type, pH and concentration)
  • Mode (Isocratic vs gradient; Gradient slope and hold times)
  • Flow rate
  • Column temperature
  • Detection (Wavelength; Detector settings)
  • Injection (Volume; Sample solvent strength)
  • Sample preparation (Diluent, filtration, extraction conditions)


Criteria typically fulfilled

  • Adequate resolution between analytes, impurities, and degradants
  • Suitable peak shape (Minimal tailing/fronting)
  • Acceptable retention (Not too early, not excessively long)
  • System suitability (Resolution, tailing factor, theoretical plates, %RSD)
  • Specificity / selectivity (Method must separate analyte from impurities, excipients, and degradants)
  • Precision (Repeatability and intermediate precision)
  • Accuracy
  • Linearity and range
  • Sensitivity (LOD/LOQ where relevant)
  • Robustness (Small deliberate changes should not affect performance)
  • Stability-indicating capability (Especially for assay and impurity methods)
  • Regulatory compliance (Method should be suitable for validation per ICH expectations)


Practical targets

Depending on the method and company standards, some typical value are given here:

  • Resolution: ≥ 2.0 for critical pairs
  • Tailing factor: often ≤ 2.0
  • Peak Area %RSD: usually low, e.g. ≤ 2.0% for repeatability
  • Recovery: commonly around 98–102% depending on method purpose
Genotoxic Impurities in Active Pharmaceutical Ingredients (APIs), which compounds are relevant?
Genotoxic impurities (GTIs) are trace-level chemicals that can damage DNA and may increase cancer risk. In APIs, they are usually not the API itself, but residual process-related compounds or degradation products.
Concrete we are talking about:
  • Alkylating agents - e.g. alkyl halides, sulfonates, epoxides, aziridines
  • Aromatic amines / nitroso compounds - especially nitrosamines and nitrosamine precursors
  • Reactive intermediates - e.g. acylating agents, isocyanates, aldehydes in some contexts
  • Residual starting materials or reagents - if they have known mutagenic alerts
  • Process by-products - formed during synthesis, workup, or purification
  • Degradation products - if they are structurally alerting and genotoxic
Genotoxic impurities in active pharmaceutical ingredients (APIs), which compounds are relevant? Which references and guidelines are valid?
Because GTIs are often at very low levels (ppm to ppb), methods must be highly sensitive. The following techniques are widely used:
GCMS / GCMS/MS
  • good for volatile/semi-volatile impurities
  • widely used for nitrosamines and small alkylating agents


LCMS / LCMS/MS

  • good for non-volatile, polar, or thermally unstable impurities

 
HPLC with UV or RF detector

  • good for non-volatile, polar, or thermally unstable impurities


Derivatization methods 

  • used when the impurity is too reactive or hard to detect directly


References / Guidelines 

  • ICH M7 for mutagenic impurities
  • ICH Q3A/Q3B for organic impurities
  • FDA / EMA / MHRA guidance for nitrosamines and other GTIs

 

Having a closer look on Nitrosamines, what are the analytical challenges? 
Nitrosamines in pharmaceutical APIs are a significant safety concern because many are potent genotoxic impurities with carcinogenic potential, requiring control at very low levels. Their analysis is challenging due to the need for highly sensitive and selective methods, complex API matrices, possible contamination during sampling or analysis, and the presence of multiple nitrosamine species with different physicochemical properties. In addition to detection, interpretation is difficult because results near the reporting limit must be judged against toxicological thresholds, while also distinguishing true contamination from analytical artifacts and identifying whether the source is process-related, raw-material-related, or storage-related. Effective control therefore relies on risk assessment, validated trace-level analytical methods, and strong process understanding.
Which method for the determination of Nitrosamines are used and what are the differences ?
Table: nitrosamine detection methods and pitfalls
 
Method Strengths Main pitfalls
LCMS/MS High sensitivity and selectivity; widely used for trace nitrosamines Matrix effects, ion suppression, method transfer issues, contamination risk
GCMS / GCMS/MS Very good for volatile nitrosamines; strong separation Sample prep may be more demanding; thermal instability for some compounds
HPLC-UV/PDA Simple and robust Usually not sensitive enough for regulatory trace levels
HRMS (QToF) Useful for screening and unknowns Quantitation at very low levels can be less robust than LC-MS/MS
Head Space GCMS Good for volatile nitrosamines and cleaner extracts Limited to more volatile analytes; sensitivity depends on setup
Derivatization-based methods Can improve detectability for some analytes Adds complexity, possible artifacts, lower reproducibility
Testing of microbiological impurities in pharmaceutical industry, which methods are used and what are the regulatory references?
Testing of microbiological impurities includes several methods, please find in the following table an overview:
 
Method Typical use in pharma Common compendial / regulatory references
Bioburden testing (membrane filtration, plate count, MPN) Raw materials, intermediates, bulk drug substance, water USP <61>, USP <62>, USP <1227>; Ph. Eur. 2.6.12 / 2.6.13; ICH Q7
Sterility testing (membrane filtration, direct inoculation) Sterile products, injectables, ophthalmics USP <71>; Ph. Eur. 2.6.1; JP sterility test; FDA aseptic processing guidance
Bacterial endotoxin testing (LAL, rFC) Parenterals, WFI, process intermediates USP <85>; Ph. Eur. 2.6.14; JP endotoxin test
Environmental monitoring (air, surfaces, personnel) Cleanrooms, aseptic areas, utilities EU GMP Annex 1; FDA aseptic processing guidance; USP <1116>
Microbial identification (biochemical, MALDI-TOF, sequencing, PCR) Isolate ID, contamination investigations, trending USP <1113>; USP <1117>; Ph. Eur. general microbiology guidance; ICH Q9
Rapid microbiological methods (RMMs) Faster release testing, in-process control USP <1223>; USP <1223.1> (where applicable); Ph. Eur. 5.1.6; FDA PAT / alternative method expectations
Cleaning validation / sanitization (swab/rinse, efficacy studies) Equipment and facility hygiene verification ICH Q7; EU GMP Annex 15; FDA cleaning validation guidance
Water system monitoring (TVC, endotoxin, objectionable organisms) Purified water, WFI, clean steam USP <1231>; USP <61> / <85>; Ph. Eur. 2.6.12 / 2.6.14

Exact requirements depend on product type, market, and sterile vs non-sterile status.
Some references are general guidance rather than strict test methods.
Companies often add internal SOPs and risk-based acceptance criteria on top of compendial tests.
What types of formulations are there for pharmaceutical and biopharmaceutical products, and what requirements need to be met in their production and packaging?
Main formulation types and resulting requirements
 
Formulation type Production requirements Packaging requirements
Tablets / capsules Blend uniformity, compression/filling control, moisture control, content uniformity Blister or bottle, moisture protection, child resistance if needed
Oral liquids / suspensions Dissolution, pH control, microbial control, homogeneity, viscosity control Tight closure, light protection if needed, dosing device, tamper evidence
Sterile injectables Aseptic processing or terminal sterilization, endotoxin/bioburden control, particulate control Sterile vials/ampoules/syringes, container-closure integrity, low extractables/leachables
Topicals / creams / ointments Emulsion stability, viscosity, preservative effectiveness, microbiological quality Tubes/jars/pumps, barrier to water/oxygen/light as needed
Inhalation products Particle size control, dose uniformity, aerodynamic performance Moisture protection, unit-dose or device-based packaging, robust device compatibility
Eye drops / ophthalmics Sterility, particulate control, isotonicity, pH control Sterile dropper systems, container-closure integrity, low leachables
Modified-release solids Polymer/coating control, release profile control, content uniformity Packaging that protects from moisture and damage, often blister or bottle with desiccant
Biologics Cold chain, protein stability, aggregation control, low shear handling Refrigerated/frozen packaging, light protection, validated transport systems
What are typical requirements resulting from the formulation:
Formulation properties usually determine:
 
Formulation property Requirement
Stability Maintain chemical, physical, and biological stability; prevent degradation, aggregation, precipitation, or phase separation
Solubility Keep the product fully dissolved; avoid crystallization or turbidity
pH control Maintain the product in its optimal pH range; minimize hydrolysis and denaturation
Isotonicity / tonicity Ensure compatibility with the intended route of administration; avoid irritation or cell damage
Viscosity Allow easy mixing, pumping, filtration, and injection; avoid overly thick formulations
Sterility / microbial control Prevent contamination and preserve safety
Compatibility with excipients and container Avoid adsorption, leaching, or chemical interaction with packaging
Shelf-life Support storage over the required time and temperature conditions
Bioavailability / release profile Achieve the desired onset and duration of action, if applicable
Processability Remain suitable for manufacturing, filling, and downstream handling
The formulation of a pharmaceutical products requires certain packing strategies, what are the challenges for this?  
Pharmaceutical packaging analysis must ensure that the package is safe, compatible, protective, and functional throughout shelf life. 
Material compatibility
  • Drug–container interactions
  • Adsorption/absorption of API or excipients
  • Leachables from plastics, elastomers, inks, adhesives

Barrier performance

  • Moisture, oxygen, CO₂, and light protection

  Container-closure integrity (CCI)

  • Preventing microbial ingress and loss of sterility
Extractables and leachables (E&L)
  • Identifying and assessing potential contaminants
Mechanical robustness
  • Transport damage, breakage, seal failure, deformation
Sterility assurance
  •  Especially for injectables, Ophthalmics, and devices
Functionality of the pack
  • Dose delivery, opening/closing performance, child resistance, tamper evidence
Stability over shelf life
  • Packaging performance under real-time and accelerated conditions
Regulatory compliance
  • Meeting pharmacopeial and ICH expectations
In pharmaceutical production, there are different concepts: batch production and flow synthesis. What are the pros and cons of these concepts?
Batch synthesis is often preferred for early development, multipurpose plants, and complex multistep syntheses;
Flow synthesis is often preferred for hazardous chemistry, fast reactions, precise control, and continuous manufacturing. 
A more detailed comparison is given in the next table

 
Aspect Batch Flow
Operation Discrete lots Continuous or semi-continuous
Scale-up Increase vessel size Increase run time or number of channels
Heat transfer Often less efficient Usually excellent
Safety More inventory at risk Lower hold-up, often safer
Flexibility Very high Moderate
Automation Possible, but often less integrated Often highly automated
Development effort Usually lower Usually higher
Suitability Broad, especially established processes Strong for hazardous, fast, or highly controlled reactions
What is cleaning validation?
Cleaning validation, which is essential for quality assurance in pharmaceutical manufacturing, refers to the quantification of residues after cleaning of manufacturing facilities and equipment to verify that the amount is below a predetermined acceptable limit.
Regular equipment cleaning and post-cleaning validation are required to prevent cross-contamination and contamination of products.
Even in the case of exclusive facilities for the same product on the same line, regular cleaning is necessary due to risks of contamination.
 
Generally, total organic carbon (TOC) analysis and high performance liquid chromatography (HPLC) are the verification methods. As shown in the table below, each technique has its own characteristics, and it is necessary to select the one suitable for the circumstances and the target for verification. This page introduces the application of TOC analysis, which enables simple, rapid measurements and can detect all organic substances.
 
Technique Features
Total Organic Carbon (TOC) Analysis Rapid measurement
Simple operation
Detects all residual organic matters
High Performance Liquid Chromatography (HPLC) Separation analysis can be performed
High quantitative accuracy
High expandability
Online concentration of the sample can be performed
What are the main points to care for a cGMP/GMP compliant production?
Main points for cGMP/GMP-compliant production are:

Defined quality system -  documented procedures, responsibilities, and oversight

Validated processes - manufacturing steps must be shown to work consistently

Qualified equipment and facilities - installation, operation, and performance qualification

Controlled raw materials - approved suppliers, testing, traceability, and release

Trained personnel - staff must be competent and regularly trained

Written procedures - SOPs for all critical operations

Environmental control - cleanrooms, hygiene, contamination control, and monitoring

In-process controls - monitoring critical parameters and product quality during production

Documentation and traceability - complete batch records, deviations, and change control

Deviation and CAPA management - investigate problems and implement corrective/preventive actions

Quality control testing - identity, purity, potency, safety, and microbiological testing

Cleaning and sanitation - validated cleaning to prevent cross-contamination

Product release system - formal QA review before batch release

Stability program - confirm product remains within specification over time

Continuous improvement - periodic review and ongoing process monitoring
Residual solvents in medications, how are they analyzed? What standards need to be met?
Residual solvents are usually analysed by headspace gas chromatography, either with FID or with MS Detection. Last one for cases, which require more specific information about type and lower limits of detection. well suited for volatile compounds in APIs and excipients.
Residual solvents are differentiated according to ICH Q3C in several classes:
Class 1: solvents to be avoided
Class 2: solvents to be limited
Class 3: low toxic potential, higher permitted limits
Class 4: insufficient toxicological data; case-by-case evaluation
The measured levels must be below the permitted daily exposure (PDE) or concentration limits derived from ICH Q3C; beside this one also the ‘USP <467>: Residual Solvents’ and ‘European Pharmacopeia 2.4.24: Identification and control of residual solvents’ describe test methods and criteria.
Dissolution baths are often connected to analysis devices, what analysis methods are used, differences and advantages?
In pharmaceutical development, dissolution baths are connected e.g. to:
UV-Vis spectrophotometers
HPLC / UPLC systems
Online sampling systems with autosamplers
LC-MS systems in special development or research cases

Please find an overview of the different methods:
 
Instrument Best for Advantages Limitations
UV-Vis Simple, soluble APIs with clear absorbance Fast, low cost, easy automation Low specificity, interference from excipients or media
HPLC/UPLC Complex formulations, low-dose products, stability-indicating needs High specificity, separates API from impurities/degradants Slower, more expensive, requires sample prep
Autosampler + HPLC/UV Routine QC and development Flexible, reproducible, good throughput Not truly real-time, more handling
LC-MS Trace-level work, method development, mechanistic studies Very high sensitivity and specificity Expensive, complex, usually not routine dissolution
Which methods are used to purify a) small molecule pharmaceuticals and b) biopharmaceuticals?
a) For small molecules, beside known methods such as crystallization / recrystallization, filtration or distillation e.g. which are in practice for small scales of samples, for bigger scale the favor is on chromatographic methods. Besides preparative LC during the years also preparative SFC has been established, driven as alternative for chiral separation, it has now got its place also for non-chiral separations.
b) For biopharmaceuticals, chromatographic methods are favorized, depend on task and molecule Size exclusion, Ion exchange, Hydrophobic interaction, or Affinity chromatography is used.