HUPO 2021 World Congress

industry seminars on-demand

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The following On-Demand Seminars (60 min) and Product Theatres (20 min) are organized by HUPO 2021 supporters and will be available for on-demand viewing at any time during the 2021 Live Days.

On-Demand Seminars (60 Minutes)

Determining calibration curves for robust, targeted, and high throughput proteomics with an Evosep One and Agilent 6495C LC/TQ

Chair: Gaëlle Bridon, Global Cellular Metabolism Segment Manager, Agilent
Speaker: Wendi Hale, LC/MS Applications Scientist, Agilent

When transitioning from discovery proteomics to targeted protein quantification, the multiple reaction monitoring (MRM)-based LC/MS method plays an essential role. Sample complexity and the low concentration of certain proteins are the major challenges encountered when performing protein analysis using targeted methods. Recent advancements in low-flow HPLC and acquisition rates in QQQ instrumentation is enabling MRM-based analytical methods using stable isotope-labeled standard (SIS) peptides for targeted quantitative proteomics to improve sensitivity, linear range, precision, accuracy, robustness, and most importantly throughput in the data acquisition as well as simplified data processing. Using a commercially available complex proteomics sample (PeptiQuant Plus 125 from MRM Proteomics) spiked in a plasma matrix, calibration curves were established highlighting the significant quantitative advantages of MRM-based targeted quantification. In addition, a select number of peptides from the complex proteomics sample were quantified with very high productivity methods combining the use of Evosep One and Agilent 6495C LC/TQ. Quantification with 3- and 5-min low-flow gradients (0.15 mm ID column) and 4-5 min re-equilibrations are demonstrated with short dwell times offering excellent quantitative performance with high throughput. Sensitivity, linearity, and precision is demonstrated with these fast low-flow methods demonstrating inject-to-inject cycle times under 10 minutes. This study demonstrated the suitability of this new high-performance LC/MS system configuration for high throughput protein quantification, even with very limited sample amount.

For Research Use Only.  Not for use in diagnostic procedures.  

We are happy to answer any questions you may have, please contact us at gaelle.bridon@agilent.com.

Characterization of glycan-protein interaction – the missing element in protein-protein interactions

Chair: Gaëlle Bridon, Global Cellular Metabolism Segment Manager, Agilent
Speaker: Carlito B. Lebrilla, University of California, Davis USA

Protein-protein interactions on the surface membrane are key to understanding the cellular function. The vast majority of studies focus on the interactions of polypeptides, however most surface proteins are glycosylated. In this presentation, newly developed tools for determining the role of glycans in protein-protein interactions are described. We developed a cross-linking mass spectrometry (XL-MS) workflow to directly identify the glycan-protein interactions on the cell membrane using liquid chromatography-mass spectrometry (LC-MS). This method involved incorporating azido groups to cell surface glycans through biosynthetic pathways, followed by treatment of cell cultures with a synthesized reagent, N-hydroxysuccinimide (NHS)-cyclooctyne, which allowed the cross-linking of the sialic acid azides on glycans with the primary amines on polypeptide backbones. The coupled peptide-glycan-peptide pairs after cross-linking were identified with the latest techniques in glycoproteomic and glycomic analyses and bioinformatics software. With this approach, information on the site of glycosylation, the glycoform, the source protein, and the target protein of the cross-linked pair were obtained. They also include lectin proximity oxidative labeling (Lectin PROXL) to identify cell surface glycoproteins that contain glycans that are recognized by lectins. Commonly-used lectins were modified with a probe to produce hydroxide radicals in the proximity of the labeled lectins. The underlying polypeptide of the glycoproteins recognized by the lectins are oxidized and identified by the standard proteomic workflow. As a result, approximately 70% of identified glycoproteins were oxidized in situ by all the lectin probes, while only 5% of the total proteins were oxidized. The correlation between the glycosites and oxidation sites demonstrated the effectiveness of the lectin probes. The specificity and sensitivity of each lectin were determined using site-specific glycan information obtained through glycomic and glycoproteomic analyses.

For Research Use Only. Not for use in diagnostic procedures.

We are happy to answer any questions you may have, please contact us at gaelle.bridon@agilent.com.

Native IMS/MS Studies of Protein Folding and Stability: Structural Insights from Native and Non-native States using Electron-Based Fragmentation

Chair: Gaëlle Bridon, Global Cellular Metabolism Segment Manager, Agilent
Speakers: David H Russell, Texas A&M University and Joseph S Beckman, e-MSion

Our understanding of protein structure is largely based on the end products of a series of biological and/or chemical processes. The accepted models for protein native states are based on traditional structure analysis techniques, X-ray crystallography, NMR, and cryo-electron microscopy. While non-native states play key roles in many biological and disease processes, they are not typically detected by these techniques owing their transient nature or low abundance. We know little about the conformations of non-native states, how they are affected by their local environment and by temperature, pH, ionic strength, or concentration. A plethora of new native MS-based structural methods now make it possible to compare native and non-native protein states.  For example, variable-temperature (~ 278 – 373 K) electron spray ionization (ESI) provides new means for studies of both native and non-native states in solution under cold- and heat-conditions. The combination of variable-temperature-ESI and collision-induced unfolding CIU with ion mobility-MS allows for the structural stability of proteins in solution and in the gas phase to be rapidly probed. The ExD technology allows for electron-based fragmentation to be performed on protein and complexes even after ion mobility separations. This allows unfolded domains to be sequenced and thereby identified.  The subunit composition of protein complexes can be additionally probed by surface-induced dissection (SID) prior to IMS and electron-based fragmentation. The combinatorial application of these new technologies opens new possibilities to elucidate structural features and energetics of protein complexes, even when embedding in lipid bilayers.

For Research Use Only.  Not for use in diagnostic procedures.

We are happy to answer any questions you may have, please contact us at gaelle.bridon@agilent.com.

Micro Pillar Array Column (µPAC™) Technology driving LC-MS : From single cell proteomics to biotherapeutic peptide mapping 

Speakers: Mr. Robert van Ling (PharmaFluidics),  Dr. GrietDebyser (Research Institute for Chromatography, Kortrijk, Belgium),  Prof. Erwin Schoof (Technical University of Denmark, Lyngby, Denmark)

Over the last five years, micro Pillar Array Columns or µPAC™ columns, have proven to be ideally suited for the analysis of complex peptide mixtures in combination with Mass Spectrometry. With its innovative pillar backbone, created within a silicon wafer via lithographical micro-machining, highly robust nanoLC and capLC columns offer significant advantages for proteomics and related research fields. With precise control over dimension and positioning of the pillar backbone, perfectly ordered homogeneous flow channels are created, minimizing peak dispersion and allowing highest peak capacities. It also results in low back pressure separation channels, creating more robust columns and instrumental workflows, as well as the possibility to increase the separation path up to 200 cm, resulting in higher separation power without any loss in resolution and retention stability. 

In this webinar, we proudly introduce two guest speakers, Dr. Debyser from the RIC Biologics group at the Research Institute for Chromatography and Prof. Schoof from the Technical University of Denmark. Dr. Debyser will present her work on biotherapeutics, with the µPAC™ column applied to a high resolution LC-MS workflow for applications such as host cell protein (HCP) analysis and characterization of glycosylation of therapeutic enzymes. Prof. Schoof will present the integration of the µPAC™ columns into his single cell proteomics MS workflow, demonstrating the quantification of over 1000 proteins/cell from multiplexed single cell samples.  

If you would like to send in a question on the use of µPAC™ columns, please feel free to send to: robert.vanling@pharmafluidics.com.

Product Theatres (20 Minutes)

QPrEST – A tool for high accuracy targeted quantification using mass spectrometry

In this presentation you will learn about the QPrEST™ technology and discover the benefits of using it in your quantitative proteomics assay.  

Stable isotope-labeled standards (SIS) in combination with Mass Spectrometry based targeted proteomics provide researchers with a powerful analytical tool for protein quantification, with an assay performance now suitable for clinical studies. Assays designed for bottom-up proteomics workflows suffer from differences in digestion efficiency, which can vary significantly between peptides within a protein leading to overall compromised accuracy and precision. This can be solved by using QPrEST standards which are added to the sample prior to proteolytic digestion as both the standard and endogenous target protein are digested together.  

Please use the following email for any questions: marie.utterback@atlasantibodies.com, Marie Utterback.

Unbiased deep quantitative proteomics with TIMS technology

Since launched the capabilities of trapped ion mobility spectrometry (TIMS) have enabled researchers to go deeper into the proteome at scale. Stay abreast of the current technology and capabilities including the timsTOF Pro 2, timsTOF SCP and PaSER in this webinar.

Your data is only as good as your chromatography

Efficient separation of samples and maximum peak capacity are critical components of LC-MS proteomics, with greater sample definition enabling deeper insights. In this talk we will demonstrate how significant improvements are achievable through our range of UHPLC columns across a number of applications including analysis of complex proteomes, post-translational modifications and large cohorts of clinical samples.  

Using our 25cm column, we are able to identify more than 10,000 proteins using a 90-minute sample gradient and characterize drug treatment responses by achieving robust phosphoproteomic results. We also demonstrate that comprehensive proteome analysis no longer requires long sample gradients or extensive sample fractionation. For rapid sample analysis, our 15cm column can identify more than 6,500 proteins per sample in less than 30 minutes, and more than 320 proteins from neat plasma samples can now be achieved 125 times per day using our 5cm column.

Pre-register here to find out more about the world’s best chromatography. (Please note you still need to register for HUPO ReCONNECT 2021: click here to register.)  

Enzomnia: the incapacity to sleep due to extreme interest in enzymes 

You love proteins, we love proteins, we all love proteins. At Blikka we can’t sleep thinking about proteins, but not any proteins, catalytic proteins, enzymes!  

After years of experience developing drug testing enzymes, we transformed the enzymatic process into a magic show: disappearing the steps. How? By mastering the art of enzymes discovery, improvement, and formulation.  

We believe that proteins are our next border to help you discover more and use that to improve the world. 

There is no reason to keep adapting your process to the enzymes available, our job is to do just the opposite for you. 

Don’t miss our presentation to see the first Blikka portfolio for Proteomics, the first one of many more to come! 

Contact us to know more: help@blikka.com.

The Target Engagement Atlas – Mapping cellular responses through proteome thermal stability changes 

Speaker: Daniel Martinez Molina 

More details coming soon.

New School tissue Homogenization: PreOmics present a simple high-throughput tissue lysis workflow for 1 to 96 samples in a novel bench top platform for in-depth proteomic coverage

Efficient Tissue and cell sample preparation is the foundation for effective outcomes from LC/MS protein analysis and yet until now, this process has been complex and time-consuming. Physical disruption is typically used to homogenize rigid tissue structures and make proteins accessible for further processing steps, these conventional methods have significant challenges such as cross-contamination, heat induction, and low throughput. Simply the size and space needed within the laboratory for these instruments are inefficient.

Here we present a tissue lysis workflow on the newly developed small benchtop platform enabling efficient protein extraction of 1- 96 samples in parallel in just 10 minutes. New School Tissue Prep. d together.  Please use the following email for any questions: demianova@preomics.com, Zuzana Demianova.

New perspectives in proteomic applications

Proteomics is one of the most demanding mass spectrometry-based disciplines. Wide dynamic range, identification, and quantification with low sample volumes and accurate reproducibility are just some of the challenges proteomics researchers face. In this talk, we will highlight the technology behind the new ZenoTOF 7600 system and how it can change the way you do proteomics.

We will demonstrate how you can achieve sensitivity for simultaneous identification and quantification of low abundance species, use tunable fragmentation mechanisms to characterize large molecules including post-translational modifications, and use fast MS/MS scan rates to keep up with any sized experiment.

Join the Zeno revolution and hear about our latest developments in DIA workflows, providing you a glimpse into what’s coming next!

Please use the following email for any questions: naomi.diaz@sciex.com.

A New Gateway to the Proteome with the Proteograph Product Suite – A Multi-nanoparticle Platform to Explore the Depth and Breadth of the Plasma Proteome

Speaker: Khatereh Motamedchaboki, Ph.D., Associate Director, Product Marketing, Seer Inc.  

  • An overview of Proteograph™ Product Suite: A New Gateway to the Proteome 

Seer’s Proteograph™ Product Suite, allows deep and  untargeted access to the proteome and the next frontier of biology. In this two-minute video, learn more about how each part of the suite works together.  

  • Introducing the Proteograph™ Product Suite 

This 10-minute overview of the Proteograph™ Product Suite provides a detailed explanation of how the platform works, what is included, how it differs from other approaches and its application in biomarker discovery research. 

  • Early Access Customer Experience

In this video, Dr. Mark Flory describes his work with the Proteograph™ Product Suite, his collaboration with Seer, and the application of this untargeted, deep proteomics biomarker research platform for early cancer detection in a prostate cancer study.  

Please use the following email for any questions: kmotamed@seer.bio, Khatereh Motamedchaboki.

Taking a closer look at glycans on the table ~Glycan isomer analysis by benchtop MALDI-MS~ 

Glycans are involved in a wide variety of biological phenomena. Of particular importance is the role of sialic acid in modulating protein-protein interaction occurring at cell surfaces, for example upon viral entry. Numerous studies have suggested that not only the abundance of sialic acid but also their linkage types can be critical. For example, human influenza viruses show higher affinity to receptor proteins with α2,6-linked sialic acids than α2,3-linked sialic acids, and vice versa for avian influenza. Hence, close examination of glycan structure including the sialic acid linkage types gives valuable insight into the viral tropism and to combat against viral infection. Mass spectrometry (MS) is widely used for glycan characterization in combination with a variety of separation techniques and ionization techniques. However, sialoglycan analysis has been challenging for two reasons. First, sialic acids are susceptible to gas-phase autodissociation. Second, and more importantly, linkage isomers are identical in both the intact and fragment masses.  

Recently, we released a reagent kit, “SialoCapper-ID Kit”, which was developed as a novel sialic acid derivatization method for facilitating sialoglycan analysis using MS. This unique derivatization leads two distinctive reaction products depending on the linkage types of sialic acid. Thus, a2,3-/a2,6-linked sialic acids can be discriminated using any type of MS. We will present a basic scheme of the derivatization and some applications of the SialoCapper-ID Kit. In this presentation, an analysis of a virus-related glycoprotein will be shown using our benchtop products, MALDI-8020 and MALDImini-1.  

Contact/Questions: shimadzu@shimadzu.eu.

Proteome Discoverer  – Go Beyond Searching

Proteomics data processing relies on search engines to identify and quantify peptides through the matching of tandem mass spectra to peptide sequences. Empowering the search engine algorithm with artificial intelligence allows for a deeper mining of proteomics data to uncover new insights.

Thermo Scientific™ Proteome Discoverer™ software with CHIMERYS® redefines proteomics search capabilities by considering all spectral peaks for peptide identification in tandem mass spectra. This powerful new approach drastically increases the number of unique peptide identifications, improving protein coverage and quantitation capabilities, enabling scientists to discover more in their data.

If you want to learn more please contact: CMDevents@thermofisher.com.

Going Beyond One Cell at a Time  

Single-cell proteomics approaches put significant strain on throughput requirements. Gaining comprehensive biological insights requires the ability to analyze a statistically significant number of cells.  

Multiplexing single cells using isobaric tags allows for up to 18 single cells per run when combined with the high-resolution and intelligent data acquisition delivered by the Thermo Scientific™ Orbitrap Eclipse™ Tribrid™ mass spectrometer delivering throughput gains that go beyond one cell at a time.  This unique approach enables the consistent quantification of thousands of proteins per cell across >200 single cells per day using limited instrument time thereby unleashing the potential to democratize global single-cell proteomics studies.

If you want to learn more please contact: CMDevents@thermofisher.com.

Vanquish Neo UHPLC system: the new standard in nano-, capillary- and micro-flow LC-MS 

For researchers pursuing the next scientific breakthrough, the Thermo Scientific™ Vanquish™ Neo UHPLC system offers the highest performance, productivity, and usability of any nano-, capillary-, and micro-flow UHPLC system enabling beyond brilliant proteomics research 

  • Beyond discovery: All-in-one nano-, capillary-, and micro-flow LC for high sensitivity LC-MS workflows. 
  • Beyond innovation: Accelerating productivity with long-term, trouble-free operation at maximum performance 
  • Beyond possibilities: Enabling LC-MS experts and novice users to get high-quality results, every time 

Looking for more details? Please send a message to CDMevents@thermofisher.com and a specialist will contact you.

Expanding Proteomics Multiplexing to 18 Samples using TMTpro Reagents

Over the last decade, tandem mass tag (TMT) technology has grown to become one of the predominant methods for global protein quantitation.  Advancements in isobaric tag reagent chemistry, instrument hardware and data analysis software over the years have helped expand the level of proteomic sample multiplexing from 6 to 18 samples.  This seminar will highlight advances in sample preparation necessary to prepare high quality peptide samples for isobaric tag labeling.  Additionally, this seminar will provide an overview of methods for improving proteomics sample preparation reproducibility and depth of coverage depth for different sample types and limited sample amounts. 

If you want to learn more please contact: CMDevents@thermofisher.com.

Post-Translational Modifications – Next Generation Tools for Improved Detection and Characterization

The primary focus of the talk is to highlight advancements in the LC-MS workflow for enhanced detection and greater structural characterization of post-translationally modified (PTM) proteins/peptides. From an LC perspective, incomplete recovery from the wetted components of an LC system compromises phosphopeptide detection efficiency. Metal ions interact with the phosphate group via Lewis acid/base interactions leading to partial or even complete retention and poor peak shape. A new generation of hybrid inorganic/organic barrier technology has been applied to the surface of the chromatographic system and column components showing mitigation of these unwanted interactions and thus improving the detection of phosphorylated peptides.

From a mass spectrometry perspective we introduce enhanced capabilities which allow for deeper elucidation and characterization of PTM’s. Ion mobility has been shown to be a powerful tool in characterizing PTM’s such as glycosylation and phosphorylation, however, the introduction of the cyclic ion mobility (cIMS) MS is demonstrated as a powerful approach to characterizing isomeric phosphopeptides for example. Coupling this with electron capture dissociation (ECD) provides high structural characterization of ion mobility separated isomers which are related to phosphorylated and glycosylated peptides.

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