Proteomics

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Unlock new, precise perspectives on the proteome

New technologies enable more research applications using proteomics by maximising the depth of data. MS-based proteomics offers the unique advantage to comprehensively analyze proteins and their changes, including post-translational modifications (PTMs), to give a global interpretation of biological systems.

This analytical capability has pushed the scientific community to develop new instrument features and novel workflows for increased versatility to enable applications that were previously sought impossible.

Proteomics research

Confidence from discovery to translational research and beyond

Maximize the depth of your data...

Unlock new, precise perspectives on the proteome

New technologies enable more research applications using proteomics by maximising the depth of data. MS-based proteomics offers the unique advantage to comprehensively analyze proteins and their changes, including post-translational modifications (PTMs), to give a global interpretation of biological systems.

This analytical capability has pushed the scientific community to develop new instrument features and novel workflows for increased versatility to enable applications that were previously sought impossible.

Overview

In pursuit of nanoscopic discoveries for big world impact

The inherent complexity of proteomes, with their variability and dynamic range, have dictated the need to maximize discovery and quantification capabilities without compromising one over the other.

In life science research, “shotgun” or bottom-up proteomics (tandem LC-MS/MS) is a key method used to comprehensively analyze proteins and their changes - including post-translational modifications (PTMs) - to give a global interpretation of biological systems. In general, there are two main approaches to generate tandem mass spectra, both which are supported by SCIEX solutions including: data dependent acquisition (DDA), also known as information dependent acquisition (IDA), and SWATH data independent acquisition (DIA).

Data/information dependent acquisition (DDA/IDA)

The speed and sensitivity of the ZenoTOF 7600 system, which uses using the Zeno trap at scan speeds in excess of >133 Hz, delivers the highest-quality MS/MS data during data-dependent acquisition (DDA), even on low-abundance proteins.

SWATH data independent acquisition (DIA)

SWATH DIA delivers precise, extensive, label-free quantification that drives biomarker discovery and identification of differentially expressed proteins. The ability to generate MS/MS data on all observable species at speed enables this approach to simultaneously identify and quantify thousands of proteins, even during short run times and with small sample loads.

discovery proteomics

Confident identification and quantification

Move research from discovery to translational, and beyond, with more confident and significant biomarker signatures to uncover insights in their biology and mechanism of action. Using the latest technologies from SCIEX, a whole new level of proteomic depth can be discovered by uncovering unique fragmentation patterns and low abundant species.

  • Large scale, high throughout analysis

    Analyze even more samples in less time

    Large scale experiments are often required to answer many of life’s biological questions. Not only does the higher throughput reduce the overall cost per sample analysis, but it is also very important in single cell proteomics, for example, which demands thousands of samples to be analyzed.

    To facilitate such workflows, the ZenoTOF 7600 system offers the fastest MS/MS speeds at up to 133 Hz and over 5 orders LDR without compromising speed or resolution.

    Extend coverage and enhance duty cycle

    Sensitivity gains are the result of the recovery of duty cycle losses that are a natural result of mating TOF analysis.

    The higher sensitivity and speed enabled by the Zeno trap improves MS/MS sensitivity across the entire mass range with Zeno trap on. As a result, ≥ 90% of all ions injected into TOF which increase the precursor ion signal by ~6-fold and the reporter ion signal by ~10-fold.

  • Biomarker discovery

    Discover candidate biomarkers

    The ability to confidently discover, quantify and translate new biomarkers that have been previously inaccessible as markers will enable researchers to develop tests that can identify and characterize disease at earlier stages, even discover markers that can guide treatment of these diseases. Catching diseases at earlier stages and giving people the right drugs at the right time will mean a more positive outlook and chance of recovery for many thousands of patients.​

    SCIEX solutions have the technology to give you the richest, most comprehensive data.

  • Single cell proteomics

    Proteomic depth and certainty like never before

    The significant potential hidden in single cell proteomics makes high throughput capabilities even more important than ever. Biological research that was previously believed to be not possible is now right within arms reach.

    Take single cell proteomics to the next level using Zeno SWATH DIA which leverages Zeno trap activation for 5-6x increases in peptide MS/MS sensitivity in high throughput, SWATH DIA workflows to maximize results from delicate sample sets.

  • Immunopeptidomics

    Enhance unique peptide detection in efforts to advance personalized medicine

    Peptides bound to major histocompatibility complexes (MHC) play a critical role in immune cell recognition and can trigger an antitumor immune response in cancer. However, these peptides exist in low-level abundances.

    SCIEX Zeno trap technology helps overcome this limitation by enhancing MS/MS sensitivity across the entire mass range and increase precursor ion signal by ~6-fold and reporter ion signal by ~10-fold.

    Generate diagnostic ions detrimental for disease studies

    Electron activated dissociation (EAD) offers alternative fragmentation capabilities to generate signature ions to differentiate isobaric amino acids important in cellular interactions, immunotherapy and drug development.

    Although isobaric amino acids share the exact same molecular weight, the different structures may dramatically influence protein functions especially when found in the complementarity-determining region (CDR) in antibodies and T-cell receptors.

Next-generation proteomics

Protein profiling and characterization

From post-translational modifications (PTMs) to full proteome profiling and characterization, the dynamic nature of proteins make them very challenging to analyze. Researchers require advanced technology to study protein dynamics reliably and reproducibly to determine profile protein structure changes, including PTMs profiling. SCIEX solutions allow researchers to reliably and reproducibly profile protein structure changes using the latest innovations in fragmentation technology to yield rich and informative MS/MS. Benefit from 100% sequence coverage in a single injection with and identify low-level PTMs faster than ever before.

  • PTM profiling

    Improve confidence in PTM localization

    The preservation of post-translational modifications (PTMs) to the modified amino acid residue is required for accurate PTM localization and quantification analyses. Electron activated dissociation (EAD) cell prevents neutral loss from labile PTMs (ex. malonylation, phosphorylation, etc.) by producing alternate fragmentation patterns resulting in c- and z- ions. Tunability in the cell from 0-25 eV further provides access to different fragmentation regimes.

    Furthermore, significant improvements in signal intensity and thus spectral quality was observed while using the Zeno trap in combination with EAD, enabling more confident PTM localization.

    Overcome challenges in disulphide bond analyses

    EAD fragmentation shows a preference to cleave the disulfide bond, leading to superior sequence coverage that enables the identification of the linked peptides and locations of cysteine residues.

    Fast and comprehensive LC-MS/MS glycan characterization

    Activation of Zeno trap for significant sensitivity improvements provides high peptide cleavage coverage even at fast spectrum accumulation times; fast fragmentation and MS/MS acquisition allows EAD reaction times on the order of 10-30 msec.

  • Peptide mapping

    New depths of confidence for QA/QC analysis

    As next generation biologics become more complex and sophisticated in terms of structure, the requirements of analytical tools for characterization and quality assessment are consequently increasing. SCIEX solutions offer the latest technology to address the rigorous analytical challenges of biopharmaceuticals.

    Electron activated dissociation (EAD) with fast data/information dependent acquisition (DDA or IDA, respectively) enables alternative fragmentation for routine, in-depth analysis of next-generation protein therapeutics and standard monoclonal antibodies (mAbs).

  • Quantification

    Relative quantification is a valuable approach in MS-based proteomics. Since peptides with different sequences may have different ionization efficiencies, the resulting intensities on a mass spectrum do not correspond to their true abundances. To overcome this problem however, various label and label-free methods have been developed to enable comparative proteomics analyses.

    By comparing the same peptides from one sample state (such as healthy or diseased cells) to the next, researchers are able to determine which peptides (and proteins) are being upregulated or downregulated under certain conditions.

    Label-free quantification

    Label free quantification (LFQ) analyses require high quality data to obtain meaningful results, since it does not utilize labels to calculate the relative abundance of proteins and peptides between samples.

    Using the latest SCIEX technology, MS/MS sensitivity increases ~5-6 fold for peptides with activation of the Zeno trap, which restores instrument duty cycle to >90%.
    As a result, precursor ion signals are increased ~6-fold and reporter ion signals are increased ~10-fold.

    iTRAQ

    iTRAQ reagents are an isobaric, peptide-tagging technology that enable you to label all primary amines, regardless of peptide class. Because important information, such as post-translational modifications (PTMs), is retained, this tagging system allows you to extract more detailed information from your samples. When combined with the high-resolution and increased duty cycle of Zeno trad trap technology, iTRAQ reagent labeling is a robust approach for quantitative proteomics.

targeted proteomics

Monitor and quantify proteins of interest with absolute precision

Verification and validation of protein biomarkers require precise, targeted quantification across large numbers of samples to enable translation into clinical research. SCIEX solutions for targeted proteomics are driven by renown MS/MS sensitivity and precision further enhanced by Zeno trap and Zeno SWATH DIA technology.

  • Multiple reaction monitoring (MRM)

    Highly multiplexed and sensitive targeted protein assays require reproducible, robust quantification methods that meet the throughput demands of large sample sets. In proteomics, MRM approaches are the most sensitive and accurate approaches to relative and absolute protein quantification.

    Whether derived from biological hypotheses or from discovery data, the ZenoTOF 7600 and SCIEX 7500 systems deliver precise targeted quantification via MRM approaches.

    stMRM

    Data rich workflow, scout triggered MRM (stMRM), brings efficiecy, greater levels of depths and opens new and exciting potential to your research.

    MRM and Zeno MRMHR

    MRMHR and MRM approaches are the most sensitive and accurate approaches to relative and absolute protein quantification. Combined with quantitative robustness and high-throughput analysis, both large and small biological changes can be accurately measured for extensive protein panels across large sample cohorts.

Resources

ZenoTOF 7600 resources

Pharma
Biopharma
Life Science
New

Going library-free for protein identification using Zeno SWATH DIA and in silico-generated spectral libraries

This Zeno SWATH DIA workflow, using an in silico-generated library processing with DIA-NN software, was superior to the traditional shotgun proteomics approach using Zeno DDA for the identification of large numbers of proteins from complex samples, and agreed with two commonly used experimentally generated libraries.

Pharma
Biopharma
Life Science
New

Zeno MS/MS with microflow chromatography powers the Zeno SWATH DIA workflow to quantify more proteins

As quantitative proteomics evolves, larger biological cohorts are being studied, often with precious samples. This creates the need to acquire data faster and with smaller amounts. Zeno SWATH DIA, with Zeno MS/MS and microflow LC, has the potential to significantly enhance core quantitative proteomics workflows.

Pharma
Biopharma
Life Science
New

High-throughput quantitative proteomics using Zeno SWATH DIA and the Evosep One system

Proteins and peptides are important in translational research to understand biological function. This method achieves 5-6x more MS/MS sensitivity, resulting in this DIA approach surpassing DDA for protein identifications and quantification in complex matrices.

Pharma
Biopharma
Life Science
New

Nanoflow Zeno SWATH DIA for high-sensitivity protein identification and quantification

Nanoflow chromatography is used in workflows to obtain the highest sensitivity. High-quality chromatographic separations are important, as good peak shape and peak resolution can reduce ion suppression and allow the MS system to sample as many unique peptides as possible.

Pharma
Biopharma
Life Science
New

Protein quantification at subnanogram loads using Zeno SWATH DIA and nanoflow chromatography

DIA has emerged as a comprehensive workflow for label-free quantitative proteomics, allowing for the acquisition of MS/MS spectra on all detectable peptides. Zeno SWATH DIA in the ZenoTOF 7600 system leverages Zeno trap activation for 5-6x increases in peptide MS/MS sensitivity in SWATH DIA workflows.

Pharma
Biopharma
Life Science
New

Large scale protein identification using microflow chromatography on the ZenoTOF 7600 system

Generation of spectral libraries is often thought of as a time consuming procedure, but in reality, they can be generated quickly. Using microflow chromatography with fast MS/MS acquisition on a QTOF, then searching the data in the cloud can enable library generation in <48 hrs.

Pharma
Biopharma
Life Science
New

Zeno MS/MS significantly improves quantification for iTRAQ reagent labeled proteomic samples

Differential protein expression analysis using isobaric labelling reagents and mass spectrometry requires instrumentation that can acquire high resolution MS/MS at high acquisition rates with excellent sensitivity for good quantification. The ZenoTOF 7600 system provides large improvements in MS/MS sensitivity.

Pharma
Biopharma
Life Science
New

Over 40% more proteins identified using Zeno MS/MS

Proteomics samples are some of the most complex samples analyzed by mass spectrometry. The ZenoTOF 7600 system delivers a ~5-fold gain in MS/MS sensitivity when analyzing peptides, so this study investigates the impact of this large sensitivity gain on identification rates.

Pharma
Biopharma
Life Science
New

Large-scale, targeted, peptide quantification of 804 peptides with high reproducibility, using Zeno MS/MS

A highly multiplex targeted peptide quantification assay has been developed to explore the quantitative capability of Zeno MS/MS. Using a mixture of 804 heavy labeled synthetic peptides dosed into plasma, the increase in peptide sensitivity due to Zeno MS/MS was found to be 5.6 fold.

Pharma
Biopharma
Life Science
New

PTM site localization and isomer differentiation of phosphorylated peptides

Specific location of phosphorylation sites on proteins is important in fully understanding their role in cellular processes. Here, the use and benefits of tunable electron activated dissociation (EAD) for phosphopeptide analysis and confident site-localization was evaluated on the ZenoTOF 7600 system.

Pharma
Biopharma
Life Science
New

Tunable electron activated dissociation (EAD) MS/MS to preserve particularly labile PTMs

Determining the identity and the precise location of a post-translational modification (PTM) on a protein is important to fully characterize function. Here, the utility of electron activated dissociation on the SCIEX ZenoTOF 7600 system was investigated for the characterization of labile PTMs.

Pharma
Biopharma
Life Science
New

Highly sensitive quantification of proteins from the SARS-CoV-2 antigen in nasopharyngeal swab samples

Investigation of the nasopharyngeal swabs use in a saline matrix for the quantification of SARS-CoV-2 proteins using LC-MS/MS. The gains in sensitivity attained by moving the assay onto the 7500 system and reducing matrix effects by changing swab storage medium were characterized.

Pharma
Biopharma
Life Science
New

Reproducible targeted peptide profiling using highly multiplexed MRM assays

Using the scheduled MRM algorithm to build highly multiplexed peptide MRM methods enables a higher number of MRMs to be monitored concurrently while maintaining optimal dwell and cycle times. The 7500 system for large scale targeted peptide quantification was evaluated using microflow chromatography.

Pharma
Biopharma
Life Science
New

Improved LC-MRM quantification sensitivity for cyclic peptides from the natriuretic peptide family

Cyclic peptides have been identified as important therapeutic modalities. This is related to their stability in blood and their potential for oral dosing. LC-MS method development to quantify trace levels of cyclic peptides in biological matrices has remained challenging.

Pharma
Biopharma
Life Science
New

Significant gains in quantitative sensitivity using microflow chromatography

Increasingly, microflow chromatography is being adopted in applications because of the “sweet spot” it occupies between increased sensitivity and solid robustness.

Pharma
Biopharma
Life Science
New

Enhancing the sensitivity of peptide quantification for the targeted HCPs analysis

Host cell proteins (HCPs) are a major class of process-related impurities that accompany a recombinant biotherapeutic product during production. As their levels impact the potential toxicity and efficiency of the therapeutics, there are significant requirements for the quantitative measurement of HCPs across the entire development paradigm.

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