Peptide Mapping

Peptide Mapping

Obtain unparalleled insight into protein identification, stability, and modifications with Waters peptide mapping solutions. Waters fit-for-purpose system solutions integrate sample preparation, columns, automation, instrumentation, and software with methodology, usability, documentation, and application support, for better resolution of complex protein and glycoprotein digests with higher throughput.

Obtain unparalleled insight into protein identification, stability, and modifications with Waters peptide mapping solutions. Waters fit-for-purpose system solutions integrate sample preparation, columns, automation, instrumentation, and software with methodology, usability, documentation, and application support, for better resolution of complex protein and glycoprotein digests with higher throughput.
Peptide molecular structure in blue
Peptide molecular structure in blue

Overview

Peptide mapping is crucial for the comprehensive characterization and monitoring of biopharmaceuticals. Obtaining adequate chromatographic resolution to reliably separate each digest fragment requires robust, reproducible methods with exceptional chromatographic performance.

Waters peptide mapping solutions combine automation, sample preparation, chromatographic separation, mass spectrometry, and overarching software workflows to deliver unparalleled analysis of complex protein and glycoprotein digests with high throughput. Waters qualitative and quantitative analysis solutions support effective characterization, simple method transfer, and compliance ready monitoring for routine laboratories. Meet your research and development goals with Waters rugged and robust peptide mapping workflows.

Applications

Peptide map characterization is essential for elucidating the primary amino acid structure and quality attributes of proteins, including monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs).

Following protein digestion, each subsequent peptide provides sequence information, retention time, and intensity to confirm the whole protein sequence. Waters provides powerful mass spectrometry hardware and software workflows to understand complex digest mixtures and develop methodologies fit for transfer to routine laboratories.

Peptide map characterization is essential for elucidating the primary amino acid structure and quality attributes of proteins, including monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs).

Following protein digestion, each subsequent peptide provides sequence information, retention time, and intensity to confirm the whole protein sequence. Waters provides powerful mass spectrometry hardware and software workflows to understand complex digest mixtures and develop methodologies fit for transfer to routine laboratories.

Application Notes

Application Notes

LC-MS peptide attribute monitoring plays a crucial role in ensuring the quality and safety of biotherapeutics, with regulatory agencies requiring confirmation of desired product structure to demonstrate process understanding during development, and for lot release purposes.

Its adoption is expanding into areas like Multi-Attribute Methods (MAM), which allows for monitoring multiple product quality attributes (PQAs) and critical quality attributes (CQAs) within a single analysis. It also has the capability to detect unknown impurities and modifications such as oxidation, deamidation, succinimide modification, glycosylation, C- and N-terminal modifications, and isomerization.

LC-MS peptide attribute monitoring plays a crucial role in ensuring the quality and safety of biotherapeutics, with regulatory agencies requiring confirmation of desired product structure to demonstrate process understanding during development, and for lot release purposes.

Its adoption is expanding into areas like Multi-Attribute Methods (MAM), which allows for monitoring multiple product quality attributes (PQAs) and critical quality attributes (CQAs) within a single analysis. It also has the capability to detect unknown impurities and modifications such as oxidation, deamidation, succinimide modification, glycosylation, C- and N-terminal modifications, and isomerization.

Application Notes

Application Notes

Optical detection (such as UV) is often used to monitor peptides. This approach is considered the gold standard for identity and quality testing in QA/QC environments. Peptides can be monitored based on profile, abundance, and retention time, which may denote CQAs.

Reproducible and robust analytical methods require thorough validation, resulting in methodology to provide critical insights into biotherapeutic proteins, aiding in their characterization and quality assessment.

Optical detection (such as UV) is often used to monitor peptides. This approach is considered the gold standard for identity and quality testing in QA/QC environments. Peptides can be monitored based on profile, abundance, and retention time, which may denote CQAs.

Reproducible and robust analytical methods require thorough validation, resulting in methodology to provide critical insights into biotherapeutic proteins, aiding in their characterization and quality assessment.

Application Notes

Application Notes

eBook: Peptide Mapping for Biotherapeutics

Peptide mapping remains one of the most important data-rich assays applied for biopharmaceutical characterization and monitoring. The solutions within this eBook— from sample preparation, automation, chromatographic separation, and mass identification— provide scientists with strategies to help improve and simplify the difficult task of peptide mapping. For example, innovations in tryptic digestions with RapiZyme Trypsin— a homogeneously methylated, recombinant trypsin, enables increased speed, digestion fidelity, and low levels of trypsin-derived peptides through its autolysis resistance, purity, and high activity for more confident and reproducible peptide maps.

Peptide mapping remains one of the most important data-rich assays applied for biopharmaceutical characterization and monitoring. The solutions within this eBook— from sample preparation, automation, chromatographic separation, and mass identification— provide scientists with strategies to help improve and simplify the difficult task of peptide mapping. For example, innovations in tryptic digestions with RapiZyme Trypsin— a homogeneously methylated, recombinant trypsin, enables increased speed, digestion fidelity, and low levels of trypsin-derived peptides through its autolysis resistance, purity, and high activity for more confident and reproducible peptide maps.
Download eBook

Solutions

Waters LC and LC-MS systems offer leading separations performance and sensitivity for peptide mapping analysis.

Waters LC and LC-MS systems offer leading separations performance and sensitivity for peptide mapping analysis.

Efficient peptide characterization and monitoring throughout the product lifecycle

Efficient peptide characterization and monitoring throughout the product lifecycle
BioAccord LC-MS System

Enable LC-MS biopharmaceutical analyses in every GxP lab with Waters BioAccord LC-MS System, including high-resolution MS and waters_connect software for compliance-ready data analysis and reporting.

  • Peptide Map Characterization
  • Peptide Multi Attribute Monitoring

Complete high-resolution capability for confident characterization and method transfer

Complete high-resolution capability for confident characterization and method transfer
Xevo G3 QTof

Accelerate multi attribute characterization and monitoring with the Xevo G3 QTof high-performance HRMS benchtop system, delivering accurate qualitative and quantitative results.

  • Peptide Map Characterization
  • Peptide Multi Attribute Monitoring

Ultra-low adsorption for maximum sensitivity and reproducibility

Ultra-low adsorption for maximum sensitivity and reproducibility
MaxPeak Premier Solutions

Eliminate the unpredictability of analyte losses due to metal interactions, which can be especially pronounced with biological molecules, using MaxPeak Premier columns and systems.

  • Peptide Map Characterization
  • Peptide Multi Attribute Monitoring
  • Peptide Mapping with Optical Detection

Compliance-ready, networkable applications-based software to streamline LC-MS data acquisition, processing, and reporting.

Compliance-ready, networkable applications-based software to streamline LC-MS data acquisition, processing, and reporting.

 Streamline data analysis and processing

 Streamline data analysis and processing
waters_connect for biopharmaceuticals

Accelerate the journey from sample analysis to decision-making with waters_connect for biopharmaceuticals that offers dedicated apps and workflows for MAM, intact mass analysis, sequence confirmation, and more.

  • Peptide MAM
  • Intact and Subunit MAM
  • Peptide Multi Attribute Monitoring

Simplify data acquisition, processing, and reporting

Simplify data acquisition, processing, and reporting
Empower Chromatography Data System (CDS)

Equip your lab with Empower Chromatography Data System (CDS) and gain advanced laboratory data management for your impurity analyses, including acquisition, processing, and reporting for liquid chromatography instruments.

  • Peptide Mapping with Optical Detection

Columns and consumables that deliver leading-edge LC and LC-MS performance for peptide mapping.

Columns and consumables that deliver leading-edge LC and LC-MS performance for peptide mapping.

Maximize sensitivity while minimizing metal adsorption of acidic deamidated peptides 

Maximize sensitivity while minimizing metal adsorption of acidic deamidated peptides 
MaxPeak Premier Peptide Columns

Gain enhanced recovery and sensitivity for acidic peptides with Waters ACQUITY, XSelect, and XBridge Premier Peptide Columns that are QC batch-tested with Waters Cytochrome c Digest Standard for increased column-to-column performance consistency. 

  • Reversed-Phase Peptide Columns
  • Peptide Mapping
  • Protein Digestion
  • Tryptic Digestion

Achieve quick, clean and complete protein digestion.

Achieve quick, clean and complete protein digestion.
RapiZyme Trypsin, Mass Spectrometry (MS) Grade

Achieve quick, clean, and complete mAb digestions in just 30 minutes with RapiZyme Trypsin, Mass Spectrometry (MS) Grade, a highly activie autolysis-resistant enzyme that reduces the likelihood of artificial modifications occurring during sample preparation prior to LC-MS analysis.

  • Tryptic Digestion
  • Protein Digestion
  • Peptide Mapping

Streamline peptide mapping sample preparation

Streamline peptide mapping sample preparation
PeptideWorks Tryptic Protein Digestion Kits

Achieve high efficiency, reproducible peptide maps in under 2.5 hours with PeptideWorks Tryptic Protein Digestion Kits for manual or automated workflows that are 4x faster than average home-brew methods and provide a 78% reduction in missed cleavages.

  • Tryptic Digestion
  • Protein Digestion
  • Peptide Mapping

Benchmark and validate your peptide columns with ease

Benchmark and validate your peptide columns with ease
Peptide Standards and Kits

Verify column performance and monitor column condition over its column lifetime with Waters Peptide Standards and run your peptide separations on any UPLC, HPLC, or LC-MS system using specifically formulated, prepackaged standards to minimize sample loss and discrepancies.

  • Peptide Standards
  • Peptide Mapping
  • Protein Digestion
  • Tryptic Digestion

Gain efficiency and walk away time with verified lab automation solutions.

Gain efficiency and walk away time with verified lab automation solutions.

Enhance sample prep efficiency and throughput

Enhance sample prep efficiency and throughput
Laboratory Automation and Equipment

Streamline sample preparation for LC-MS analyses with Waters Laboratory Automation and Equipment that deliver verified workflows to help minimize variability, improve traceability, and simplify method transfer.

  • Peptide Map Characterization
  • Peptide Multi Attribute Monitoring
  • Peptide Mapping with Optical Detection

Your success is just a click away

Your success is just a click away
Waters Global Services

Optimize your laboratory's productivity and success with Waters Global Services to maintain peak system performance, minimize downtime, address application challenges, and support stringent compliance requirements.

  • Peptide Map Characterization
  • Peptide Multi Attribute Monitoring
  • Peptide Mapping with Optical Detection

Make science more accessible with Waters Capital

Make science more accessible with Waters Capital
Payment Solutions

Maximize resources and minimize risk with payment options from Waters Capital, including upgrading aging equipment, getting customized support, and bundling services into one monthly payment.

  • Peptide Map Characterization
  • Peptide Multi Attribute Monitoring
  • Peptide Mapping with Optical Detection

The data speaks for itself

The data speaks for itself
Area (%) comparison of the ACQUITY UPLC I-Class PLUS System and ACQUITY UPLC H-Class PLUS Bio Binary System (with 340 µL mixer and gradient delay) over four injections. Data indicates that peak area is preserved between the systems.
The peptide mapping workflow of the BioAccord System provides PTM identifications. The figure shows the review panel following automated data processing. The component table contains: sequence information, m/z and neutral mass, mass tolerance, %rel. abundance as well as fragmentation information for each peptide. The summary table provides a concise view of selected peptide modifications across all samples. The consistency in retention times is shown in the bottom left panel using TIC’s for injections 1 and 25.
IC overlay of mAb Tryptic Digest Standard injections with IDC off and IDC enabled with thresholds of 5, 10, and 20. The associated table shows total file size, percent reduction, and data processing time with UNIFI Scientific Information System.
XIC profiles demonstrating the effect of particle surface chemistry (BEH and silica) on selectivities for selected NIST mAb tryptic peptides using 0.1% TFA in water/acetonitrile mobile phases. Chromatograms have been aligned based on the retention time of the H38. The MW and pI values for the peptides (Da) are provided in the table inset. Peak identities are provided in Table 3.
Relative abundance of missed and non-specific cleavages for NISTmAb digests prepared using the manual and automated PeptideWorks workflows and a leading immobilized trypsin kit. Error bars represent one standard deviation. PeptideWorks delivers a more complete and specific digestion.
1:5 enzyme:protein ratio digestions of Remicade, highlighting cleanliness of the baseline with RapiZyme trypsin (blue) vs. an industry leading competitor (black). Y-axis is % TIC intensity.

Webinars and Resources

Peptide Multi-Attribute Method (MAM) on the SmartMS-Enabled BioAccord LC-MS System
Peptide Multi-Attribute Method (MAM) on the SmartMS-Enabled BioAccord LC-MS System
  • eBook

Peptide Mapping for Biotherapeutics

Peptide Mapping for Biotherapeutics
Download
  • Infographic

Protein Digestion, Gets Intelligent

Protein Digestion, Gets Intelligent
Download
  • Infographic

RapiZyme Quick, Clean, Complete

RapiZyme Quick, Clean, Complete
Download
  • Infographic

RapiZyme Flexible Use 

RapiZyme Flexible Use 
Download
  • Poster

Improved Biopharmaceutical Peptide Mapping Workflows Using a Novel Autolysis-Resistant Trypsin Enzyme

Improved Biopharmaceutical Peptide Mapping Workflows Using a Novel Autolysis-Resistant Trypsin Enzyme
Download
  • Support Articles

Novel Automated Method for Sample Preparation for Peptide Mapping

Novel Automated Method for Sample Preparation for Peptide Mapping
Download

Related

Multi-Attribute Analyses
Increase your understanding of bioanalyses of biotherapeutics and vaccine products with Waters comprehensive LC-MS and MS workflows for multi-attribute method (MAM) characterization and routine monitoring.

Synthetic Peptide Analysis
Ensure drug development and quality standards are met with Waters leading solutions for lab-scale synthetic peptides like glucagon-like peptide 1(GLP-1) purification, characterization, and monitoring.

Intact and Subunit Protein Analysis Solutions
Evaluate protein identity, glycoforms, and modifications with intact mass and subunit mass spectrometry techniques in Waters solutions for understanding protein structures and advancing biopharmaceutical research.

Learn more about Peptide Mapping Solutions.

Learn more about Peptide Mapping Solutions.
Peptide molecular structure in blue
Back To Top Back To Top