Peptide Mapping

Peptide maps that detail the entire protein (100% sequence coverage) are required to prove molecular structure as well as determine post-translational modifications (PTMs) and sequence variants. Complex protein digests (from monoclonal antibodies (mAbs), antibody-drug conjugates (ADCs) and bi-specifics) require high peak capacity, high-resolution separations, and reliable detection combined with confident data analysis.

Discover a peptide mapping workflow solution that includes fast, reproducible protein digestion and comprehensive peptide identification software, with Thermo Scientific™ Vanquish Flex™ UHPLC systems and the Thermo Scientific™ Q Exactive™ BioPharma platform at its heart.

Sample preparation › Separations › Detection › Data processing › Savings calculator ›

Peptide Mapping Workflow

"Peptide mapping is easy", said no scientist, ever. The typical challenges that face anyone undertaking a peptide mapping experiment would be the amount of time and effort that it takes, from the numerous in-solution tryptic digest steps, through to the variability in digestions leading to an overall lack of reproducibility, and the difficulty in interpreting complex results. Thankfully, we’ve looked at these challenges and are challenging the status quo that peptide mapping is complex!




Mass Detection

Data Interpretation

Peptide Mapping Workflows: Upgrade Your Maps

Find out what it takes to streamline your peptide mapping workflows, allowing you to deliver robust, reproducible results time after time.

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Peptide Mapping Know-how: Whitepaper

Ever wanted to understand what peptide mapping is, and why we perform peptide mapping? This whitepaper guides you through everything that you need to know and consider.

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New, Rapid and Reproducible Peptide Mapping Workflows

Find out in-detail how each part of the peptide mapping workflow can be addressed in this presentation.

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So how do I put my peptides on the map?

This handy eBook pulls together numerous examples of how to perform each step of a peptide map, from digestion to separation to detection to interpretation. See the impact that novel technologies can have upon your peptide maps and in your lab.

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Navigating Biologic Medicines Infographic

Are you interested in understanding more about biologics and where peptide mapping fits in? This infographic shows you how!

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What is Peptide Mapping Infographic

Peptide mapping reveals the detail behind biotherapeutics - see what peptide mapping can tell you and how!

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Upgrade Your Peptide Maps Infographic

An easy-to-digest infographic overview of the complete workflow solution for peptide mapping - find out how!

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Amino Acid Quick Reference Guide

This should always be within reach! Quick reference information about amino acids, handy to have available at all times.

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Webinar: Take the smart route to protein digestion

Learn how to increase reproducibility while reducing preparation time.

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Webinar: Peptide separations with pinpoint precision

Find out how to achieve ultimate retention time reproducibility & high resolution separation of peptides.

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Webinar: Don't miss a thing on your peptide mapping journey

Find out how to get full coverage peptide maps using high resolution accurate mass spectrometry.

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Webinar: Easily navigate biotherapeutic modifications

Learn how to confidently compare and interpret your peptide maps with powerful, yet intuitive software.

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Finding HOPE Using Peptide Mapping?

See how scientists use peptide mapping to help bring new drugs to market and provide hope to patients with rare diseases.

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SMART Sample Preparation

Being SMART doesn't have to be hard. A significant advance in sample preparation for biopharmaceutical and protein research, The Thermo Scientific™ SMART Digest™ kits provide fast and simple digestion with reproducibility unlike ever before.

Available with several proteases, from trypsin to proteinase K and chymotrypsin to a range of immunoaffinity kits: protein A, protein G and streptavidin kits, each with magnetic bead options for the most comprehensive coverage available.

Three-step sample preparation, providing you with higher sequence coverage. Every time.

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Get SMART with Protein Digestion

Watch a comparison of traditional digestion vs. SMART

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SMART Digest Kit Animation

Find out how SMART is faster, easier and more reproducible

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SMARTening up on Protein Digestion

Follow our Vlog to get behind the scenes understanding of SMART

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SMART digest kits allow you to obtain high quality analytical results from protein digests as they provide fast and simple protein digestion with high reproducibility, high sensitivity, and high levels of data quality in a format that's compatible with automation. The SMART Digest Kits are a significant improvement over current in-solution protein digestion technologies, which are not reproducible, have poor sensitivity, and employ protracted methodologies not amenable to automation.

SMART Time Savings

SMART vs. traditional digest: there’s no competition.

Use our Digestion Time Calculator to see how quickly the SMART Digest Kit can digest proteins for your application.

Time Savings Calculator

SMART Technology

Unlike traditional digestion which requires reduction and alkylation to enable complete digestion, SMART heat denatures the protein, ensuring it is in its unfolded state.

The imobilized trypsin can be present in excess, meaning significantly reduced digestion times and also a cleaner final sample with no trypsin autolysis peptides, reduction or alkylating agents present.

Reproducibly SMART

You can have analytical technologies that provide all the reproducibility and accuracy that you require, but if your sample preparation cannot deliver reproducibility then you could be setting up to fail from the start.

User-to-user, lab-to-lab, SMART takes the worry out of sample preparation and allows you to focus your efforts elsewhere.

A Significant Advance in Sample Preparation

SMART Digest Kits

The Thermo Scientific™ SMART Digest™ Kits provide fast and simple protein digestion with high reproducibility, high sensitivity, and high levels of data quality in a format that's compatible with automation. The SMART Digest Kits are a significant improvement over current in-solution protein digestion technologies, which are not reproducible, have poor sensitivity, and employ protracted methodologies not amenable to automation.

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Learn more about SMART Digest Kits:

Trypsin kits › Chymotrypsin kits › Proteinase K kits › ImmunoAffinity (IA) Protein A kits › ImmunoAffinity (IA) Protein G kits › ImmunoAffinity (IA) Streptavidin kits ›


SMART Digest and SMART Digest ImmunoAffinity (IA) Kit Technical Guide

The SMART digest technical guide shows data detailing how SMART is better.

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SMART Digest Kit Q&A

Got a question? The answer is here.

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SMART Digest Kit User Guide

The SMART digest user guide provides an overview of the procedure.

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Fast Digestion Method Optimization Using Innovative Trypsin Technology

Find out how quick your digestion optimization can become.

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Improvement in Speed and Reproducibility of Protein Digestion and Peptide Quantitation, Utilizing Novel Sample Preparation Technology in a Full Solution Workflow

In this application note, learn about the advantages of the SMART Digest kit with regards to workflow efficiency and reproducibility.

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Automated biopharmaceutical protein digestion optimization for peptide mapping method development

In this application note, see how combining the SMART Digest magnetic kits with the Thermo Scientific™ KingFisher™ Duo Prime purification system provides an automated approach to protein digest method optimization.

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SMART Digest compared to classic in-solution digestion of rituximab for in-depth peptide mapping characterization

Interested in how SMART digest compares to traditional in-solution digestion? Find out all of the benefits in this comparative analysis.

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SMART eBook: A Compendium of Everything SMART

This eBook contains everything you need to know about being SMARTer. From data showing how SMART is more reproducible, faster, simpler and more sensitive, to application focuses on optimization and buffers.

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Take the Smart Route to Protein Digestion: How to Increase Reproducibility Whilst Reducing Prep Time

Find out how SMART works and can deliver significant reductions in digestion time, increases in reproducibility and streamlining of your mapping workflows, with customer insights from Merck.

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Bringing GC and Orbitrap
Technology Together

Click on the dots to learn more about the technology behind the worlds most anticipated GC-MS system

Switch to explore the Exactive GC System

HCD Collision Cell

Higher-energy collisional dissociation for MS/MS characterization of ions-used in combination with chemical ionization to help elucidate chemical structures


Curved linear trap for precise ion injection-delivers excellent in-spectrum dynamic range and ensures outstanding HRAM performance across a wide range of concentrations through automatic gain control (AGC)

Advanced Quadrupole Technolgoy (AQT)

High transmission of selected masses for low-level detection and quantitation of lowabundance compounds in highly complex matrices

Orbitrap Mass Analyzer

Incredible resolving power up to 120,000 FWHM for the Q Exactive GC at m/z 200 and up to 50,000 FWHM for the Exactive GC at m/z 272, sub-ppm mass accuracy with a high acquisition rate, driving unrivaled spectral quality.

Mass calibration of the Orbitrap Analyzer is extremely fast and complete within 30s. The resulting calibration is stable for many days under normal condisions.

* videos recorded on Q Exactive GC

Every single scan taken using an Orbitrap mass analyzer is accurate and acquisitons rates are fast enough even for narrow GC peaks that are 1-2s wide.

* videos recorded on Q Exactive GC

Switching between resolving powers on the Orbitrap mass analyzer does not significantly compromise sensitivity.

* videos recorded on Q Exactive GC

Bent Flatapole

For lowest possible noise and maximum robustness

Thermo Scientific™ ExtractaBrite™ Ion Source

Robust, rugged electron impact (EI) and chemical ionization (CI) performance - proven in routine applications in the Thermo Scientific™ ISQ™ and TSQ 8000 series GC-MS systems. Fully removable without breaking vacuum for maintenance or switching to chemical ionization (CI). Also exchangeable for a unique source plug, making GC columns easily exchanged, without venting the MS system.

The Q Exactive GC system source tuning is incredibly fast. The process is complete in ~ 30s.


Being able to achieve robust and reproducible separations is an absolute requirement for peptide mapping. Both column and UHPLC must be capable of performing even under challenging BioPharma conditions.

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Delivering for BioPharma

Find out how Vanquish makes all the difference for Aijnomoto Althea, a CMO.

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Reproducibility from run to run delivers retention time stability, with RSDs lower than 0.1% across the gradient

A Biocompatible Masterpiece

The story behind Vanquish told with passion by those who made it happen.

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Robust, Reproducible Separations

Vanquish UHPLC Platform

Designed with innovative technology and engineering excellence, the Thermo Scientific™ Vanquish™ UHPLC System delivers a new standard in high-end UHPLC—more results with better separations and easier interaction simultaneously, without compromise. This fully integrated and biocompatible system features high sample capacity for high-throughput workflows, industry-leading pumping performance, amazingly high S/N and linearity, two-mode thermostatting, active preheating, and more...

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Acclaim VANQUISH 120 C18 Columns

Improve the separation efficiency of your peptide maps with Thermo Scientific™ Acclaim™ VANQUISH™ 120 C18 columns. Featuring an ultrapure silica substrate with extremely low metal content to minimize tailing effects and deliver symmetrical peak shapes, with unique bonding chemistry yielding excellent surface coverage to provide highly predictable separations that are unaffected by secondary interactions.

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Vanquish UHPLC Platform - Built for BioPharma Brochure

From aggregates, charge variants, glycans and peptides, through to intact, find out how the Vanquish UHPLC Platform is the ultimate for biotherapeutic characterization.

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Vanquish UHPLC System Brochure

Discover next generation UHPLC that was developed by our customers, for our customers.

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Piecing Together Protein Analysis

See how the Christian Doppler Laboratory for Biosimilar Characterization, located at the University of Salzburg in Austria, has set out to address the challenges presented by protein analysis for biosimilars.

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Ultra-Engineering UHPLC from Scratch

Read this short article discussing how more than just incremental gains were required to truly deliver UHPLC.

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How to Stand Out from the Biopharmaceutical CMO Crowd

Discover how Ajinomoto Althea, Inc. partnered with Thermo Scientific and use the Vanquish UHPLC Platform to shorten the amount of time taken for that next discovery.

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High Throughput, High Resolution Peptide Maps

See what it takes to obtain high quality peptide maps.

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UHPLC, Ultra-Biotherapeutic Characterization

Unravel what what your UHPLC needs to be able to deliver confident biotherapeutic characterization.

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Peptide Separations with Pinpoint Precision - Why Compromise?

When it comes to separations, the Vanquish UHPLC Platform can handle complex peptide maps with ease, delivering high levels of reproducibility combined with simple set-up. See NIBRT's perspective on how Vanquish has helped their workflows.

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The state-of-the-art peptide mapping data possible with the Thermo Scientific™ Q Exactive™ BioPharma platform is a culmination of decades of leadership in the development of data dependent acquisition (DDA) combined with the unmatched accuracy and resolution achieved by the Thermo Scientific™ Orbitrap™ mass analyzer.

With the addition of superior denatured and native MS intact analysis and subunit top/middle-down analysis capabilities this platform provides a complete BioPharma characterization solution.

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The unmatched mass accuracy and resolution achieved by the Orbitrap mass analyzer allows full sequence coverage to be achieved confidently, each and every time. With its wide dynamic range the Q Exactive BioPharma platform on the Q Exactive Plus and HF instruments provide superior peptide mapping performance within the most complex samples.

Mass accuracy without compromise

Class leading accurate mass and resolving power together with high dynamic range provide the most effective way to accurately and confidently identify peptide within complex sample digests.

Catch all peptides and modifications with high dynamic range

Class leading accurate mass and resolving power, together with high dynamic range provide the most effective way to accurately and confidently identify peptides within complex sample digests. With peak widths of < 1s FWHM afforded by the Acclaim Vanquish C18 120 and Vanquish UHPLC, the Q Exactive BioPharma operating in DDA mode can aquire multiple MS and MSMS data points providing high quality full scan and product ion information for multiple precursor ions.

Complete BioPharma Characterization

The Q Exactive BioPharma platform

Realize complete BioPharma characterization with the Q Exactive BioPharma platform, which offers distinct operational modes optimized for the top three protein characterization workflows:

  • High Mass Range mode offers optimized intact protein analysis under both native and denaturing conditions providing the highest quality spectra.
  • Protein mode ensures isotopic resolution of subunits and and facilitates top/middle-down sequencing.
  • Standard mode performs peptide mapping with unparalleled acquisition speed, mass accuracy, and spectral quality.
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Q Exactive BioPharma Brochure

See how the Q Exactive BioPharma delivers class leading accuracy, sensitivity and experimental flexibility for BioPharma.

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LC-MS for Comprehensive BioPharma Characterization

Complete Characterization of a Cysteine-linked Antibody-Drug Conjugate Performed on a Hybrid Quadrupole-Orbitrap Mass Spectrometer with High Mass Range

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MS Detection for Rapid UHPLC Separations

High Throughput Peptide Mapping with the Vanquish UHPLC System and the Q Exactive HF Mass Spectrometer

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High throughput Peptide Mapping by UHPLC-MS

Watch this short video for a top level overview of the poster note for high throughput peptide mapping.

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Don't Miss a Thing on Your Peptide Mapping Journey

Detecting peptides within complex matrix over a broad range of concentrations is a challenge. Watch how Orbitrap technology can be used to provide absolute confidence in your peptide maps, with some tips and tricks thrown in too!

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Data Processing

Typically one of the more time consuming processes for peptide mapping, data analysis was complex with significant amounts of manual interpretation and rejection of false positives. Thermo Scientific™ BioPharma Finder™ software significantly reduces the amount of manual interpretation through the use of novel chromatographic shading.

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A Journey in Biotherapeutic Peptide Mapping

See how Dr. Cheng, from Alexion Pharmaceutical Inc., focused on delivering innovative and life-transforming therapies, using Thermo Scientific™ Orbitrap™-based mass spectrometry combined with new BioPharma Finder software to make meaningful decisions in their development processes and reduced batch analyses from weeks to just a day.

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Typically, many software packages can be powerful, but take significant user investment to learn and become proficient with. BioPharma Finder is purpose built for biotherapeutic analyses, with efficient workflows that ensure it is quick and easy to get the right answers first time. Novel data visualization tools, from chromatographic shading and in-depth coverage maps means that you wont miss a thing.

Reducing bottlenecks

The use of novel chromatographic shading helps to easily identify peaks without any identification, shows peaks with multiple IDs and the relative amounts of each peptide (here, red = light chain, green = heavy chain and blue is unidentified)

Complete Coverage, Complete Confidence

When it comes to the great quality data obtained using SMART, the Acclaim Vanquish columns and Vanquish Flex UHPLC with the Q Exactive Orbitrap, you want to ensure that you can confidently see you have 100% coverage.

The coverage map shows all identified peptides across the whole sequence, and is color coded according to intensity – all helping you to quickly and confidently review your data, especially when comparing batches of samples.

Modifications, Modifications, Modifications

Missing modifications could have an impact. The sensitivity and dynamic range of Orbitrap-based mass spectrometers make sure that modified peptides are captured, and BioPharma Finder ensures that all modifications are determined.

Comprehensive tools from disulfide bond analysis, sequence variant analysis and de novo sequencing means you can characterize your protein sequence reliably, detecting all critical quality attributes required by regulators.

Complete BioPharma Characterization

BioPharma Finder Software

Save time and identify more with Thermo Scientific™ BioPharma Finder™ integrated software. Screen, identify and characterize intact proteins with higher productivity and confidence using Intact Protein workflow. Two deconvolution algorithms take full advantage of the high-quality, HRAM data produced by Thermo Scientific™ Orbitrap™ mass spectrometers. Confirm amino acid sequence, identify site and type of known/unknown PTMS while providing relative amounts using Peptide Mapping workflow. Additional features include disulfide linkage, sequence variant analysis and sequence alterations.

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BioPharma Finder Software Brochure

Workflow Driven Informatics for Complete Biotherapeutic Characterization

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Improved Characterization of Biotherapeutics with Better Peptide Mapping

Watch this webinar and find out how software delivers comprehensive maps, ensuring that you don’t miss a thing.

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Education Is Important, Getting The Right Answers Is Importanter...

This blog explores how software makes life easier, rather than harder.

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BioPharma Finder Software Download

Dig into the enabling features of BioPharma Finder and also download a demo version!

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Easily Navigate Biotherapeutic Modifications

Analyzing your mapping data can seem daunting, but this webinar shows how BioPharma Finder can easily, and rapidly, process your peptide mapping data - whilst still identifying any modifications in a quantitative manner. See how Coherus Biosciences rely on BioPharma Finder for their mapping analyses.

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Savings Calculator

Use the Digestion Time Calculator to see how quickly the SMART Digest Kit can digest proteins for your application!

Talk to an expert about the power of our solutions that apply to any stage of peptide mapping.

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Provide your contact information and we will have one of our experts contact you to answer any questions you may have about these solutions.

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Request a demo for one of our solutions that apply to any stage of peptide mapping.

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Thank you for your interest

Thermo Fisher Scientific is excited that you are interested in our peptide mapping solutions! One of our experts will contact you shortly.