• Type: Industry Seminar
• Presentations: 1
• Chair(s): Aaron Gajadhar

Chair:  Speakers:
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• Type: Industry Seminar
• Presentations: 1
• Chair(s): Stina Lundgren

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CETSA® MS allows for proteome-wide measurement of cellular target engagement using mass spectrometry by generating thermal profiles for 6000−7000 proteins in a single experiment. In contrast to conventional proteomics applications, CETSA MS measures the direct consequences of a drug on both its intended and off targets, as well as the immediate signaling cascade perturbed by the addition of a compound. This assay is free of labels and can be carried out in the live unmodified cells, thereby enabling the discovery of protein targets and pathways that would otherwise not be identified using traditional methods.

Further, machine learning algorithms allows for exploration of global patterns and differences as well as extraction of differential proteins or groups of proteins to explore and compare the molecular mode of action of the profiled compounds. Welcome to learn about the CETSA methodology and how the mass spectrometric readout can be used for drug profiling, target deconvolution, biomarker discovery and toxicology safety assessment studies.

• Type: Industry Seminar
• Presentations: 1
• Chair(s): Gary Kruppa

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• Type: Industry Seminar
• Presentations: 1
• Chair(s): Lukas Reiter

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A Biognosys seminar, featuring talks by speakers Mikhail Savitski and Erwin Schoof, who are both early access users of SpectroMine 2 software for DDA data analysis.

• Type: Industry Seminar
• Presentations: 1
• Chair(s): Arianna Jones

Chair: Speakers: 

The p53 protein is mutated in about 50% of human cancers. The mutant p53 proteins not only lose their normal function but often acquire novel oncogenic functions, a phenomenon termed mutant p53 gain-of-function (GOF).

Mutant p53 has been shown to affect the transcription of various genes, as well as by protein–protein interactions with transcription factors and other effectors, however no one has investigated which of these proteins has the potential for being targeted by immunotherapeutic interventions. We therefore investigated the changes occurring after the p53 Null SaOS-2 cells were transfected by conformational p53-mutants R-273 and R-175, examined phenotypic and functional differences using macroscopic observations, proliferation, overall mRNA and proteomic changes alongside immunopeptidome profiling of peptide antigens bound to molecules encoded by the major histocompatibility complex (MHC) and presented on the cell surface. 

Expression profiling using gene expression microarray, qRT-PCR, and quantitative proteomic mass spectrometry, were employed to identify proteins whose peptide repertoire may be targeted by future immunotherapy/vaccine. The phenotype of SaOS-2-273 and SaOS-175 cells were assessed using colony formation, and proliferation assays.

Using OneOmics™ Suite in SCIEX cloud, we identified several candidate markers in both p53 mutant cell lines with differential gene and protein expression from the p53 null control. Cross-comparison with the MHC bound peptides further identified potential targets.

• Type: Industry Seminar
• Presentations: 1
• Chair(s): Maximilian J. Helf

Chair: Speakers: SpectroMine is our powerful and user-friendly solution for shotgun proteomics. In its newest version, we have focused on further improving speed, performance, and support for powerful new acquisition methods to accommodate the needs of our growing user base. SpectoMine 2 integrates our state-of-the-art Pulsar search engine, now offering full support for ion mobility technologies (e.g., FAIMS and PASEF) and achieving more identifications thanks to deep learning augmentation.

In this seminar, we will give you insights into how the software works internally, and how you can easily analyze ILQ data (e.g. TMTpro) with SpectroMine 2.

• Type: Industry Seminar
• Presentations: 1
• Chair(s): Katherine Tran

Chair:
Speakers:

The use of cancer immunotherapy has become increasingly popular due to their precision and efficacy compared to other cancer treatments. To develop effective cancer immunotherapy treatments, of which the goal is the generation of adaptive immune responses and long-term immune memory, patient-specific tumor antigens need to be identified. Mass spectrometry (MS)-based workflows have been demonstrated to have great potential to identify HLA-peptide targets, an ideal target for tumor-specific antigens.

In the first portion of our talk, Dr. Robert Salzler will present his HLA immunopeptidome mapping workflow at Regeneron Pharmaceuticals. Here, a proteogenomics pipeline has been developed and applied to tumour samples to generate a comprehensive patient specific immunopeptidome catalogue. This multi-omics approach consequently results in a large number of datasets which require high-throughput clinical bioinformatics to feasibly assess the data. With this in mind, a new software platform, PEAKS Online Xpro was integrated into the workflow to meet this challenge of data analysis throughput, and complexity to support large-scale clinical proteomics studies and offer a versatile solution for any study. Further, by utilizing high-throughput PEAKS Online processing capabilities, this workflow has proven to generate more useful data to identify patient specific HLA-peptide targets and PTM libraries.

To get a more in-depth look at PEAKS Online Xpro, Dr. Jonathan Krieger of Bioinformatics Solutions Inc., will be presenting a quick walkthrough of the PEAKS Online platform. Users familiar with PEAKS software will quickly recognize the similarity of the new PEAKS Online graphical user interface (GUI) to other versions of PEAKS. The new architecture of the PEAKS Online platform offers users the ability to deploy a high-throughput, scalable PEAKS Xpro data processing pipeline within their own network. As a multi-user solution, PEAKS Online was developed to facilitate teamwork and foster collaboration by providing concurrent access from multiple users and parallel processing. Furthermore, with custom workflows and automation capabilities, PEAKS Online is the ideal solution to analyze large-cohort clinical proteomics studies.

• Type: Industry Seminar
• Presentations: 1
• Chair(s): Nicolas Autret

Chair:
Speakers:
This presentation intends to introduce how Covaris Adaptive Focused Acoustics has been used for sample preparation, introducing the technology and presenting the main results achieved with Covaris AFA®, including published data as well as unpublished results from collaborations with Mass Spectrometry leading laboratories.

• Type: Industry Seminar
• Presentations: 1
• Chair(s): Ali Pervez

Chair:

Speakers: 

This seminar will include the following three presentations:

• Type: Industry Seminar
• Presentations: 1
• Chair(s): Jason A. Anspach

Chair & Speaker: Jason A. Anspach, PhD, Phenomenex

As modern mass spectrometers (MS) have become ever increasingly more sensitive the limiting factor of the relative ionization efficacy has remained a constraint. The limit to any mass spectrometer’s sensitivity is the amount of sample that gets ionized and subsequently introduced into the MS. The sensitivity challenge can be great, especially in situations where your analytes of interest are hard to ionize, or you are limited in the amount of physical sample you have to work with.

To overcome these challenges scientists are turning to miniaturized separation scale columns either micro scale or nano scale. Miniaturization of HPLC columns, just as with any miniaturization comes with its unique challenges. In this talk, we will discuss some of the tools that are now available in terms of new column technologies, injection modes (trap and elute), and separation condition strategies, and even connection systems that can help with the miniaturization of analytical scale separations to micro and nano scale.