Welcome to Graham Scientific Scientific Laboratory

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Comprehensive Summary of Proteomics Technologies 

Below are brief summaries of the major proteomics techniques Graham Scientific has experience with and protocols in place with our partner laboratories.  Each application is categorized as either routine (R - assays performed regularly), special (S - assays requiring some adaptation and customer collaboration) or custom (C - working closely with the customer in a collaborative manner).

Techniques:

1. High-throughput and Advanced Proteomics Approaches

DIA Proteomics (R): Data-Independent Acquisition (DIA) proteomics is a cutting-edge approach to comprehensively analyze proteomes with high reproducibility and depth. By systematically collecting all fragment ions in a sample, DIA enables accurate quantitation and broad proteome coverage, making it ideal for biomarker discovery and systems biology research.

SEER (R): SEER technologies revolutionize liquid biopsy proteomics by combining untargeted nanoparticle protein enrichment and advanced mass spectrometry. This approach enables ultra-sensitive detection of low-abundance proteins in plasma, urine or CSF, offering unparalleled insights into complex biological systems, such as early disease detection and personalized medicine. 

Advanced Separation Techniques (2D/3D) (Two-dimensional (2D) and three-dimensional (3D) (S): separation methods enhance the resolution of complex proteomic samples. These techniques provide a deeper understanding of protein diversity, ensuring higher accuracy numbers of detect proteins in mass spectrometry-based workflows. Key applications include cancer highly differentiated tissue proteomics and drug target validation.

2. Quantitative and Labeled Proteomics

Metabolic Labeling (S) Metabolic labeling techniques incorporate isotopic tags into proteins during cellular metabolism, enabling dynamic studies of protein turnover, synthesis, and degradation. These methods are essential for understanding cellular responses to external stimuli.

SureQuant (C) SureQuant technology provides highly targeted quantitation of proteins and peptides, leveraging internal standards for absolute quantification. It’s an invaluable tool for biomarker validation and precise pharmacokinetic studies.

Click Chemistry (C) Click chemistry enables selective labeling of proteins, particularly for studying post-translational modifications (PTMs). Its applications include monitoring acetylation, glycosylation, and other functional modifications critical to cell signaling and disease mechanisms. Click Chemistry approaches can also be used to identify unknown drug targets.

Labeled Proteomics (TMT, SILAC, etc.) (S)Techniques like Tandem Mass Tagging (TMT) and Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) allow multiplexed quantitation of protein samples, reducing variability and enhancing throughput. These approaches are widely used in comparative proteomics and large-scale biomarker studies.

3. Single-cell Proteomics

Single-cell proteomics technologies push the boundaries of sensitivity, enabling researchers to analyze the proteomes of individual cells. This transformative approach is critical for understanding cellular heterogeneity in complex tissues and uncovering insights into cancer progression, immune responses, and developmental biology. Currently we are limited to pre-sorted samples.

4. Post-translational Modifications (PTMs)

Key PTMs (S) (e.g., Ubiquitination, Oxidation, Nitrosylation) Post-translational modifications (PTMs) regulate protein activity, stability, and interactions. Studying PTMs such as ubiquitination, oxidation, and nitrosylation is crucial for elucidating disease mechanisms, including neurodegeneration and cancer.

Proximity Labeling Techniques (Bio-ID, APMS) (C) Techniques like BioID and Affinity Purification Mass Spectrometry (APMS) allow researchers to map protein-protein interactions and identify transient interactors. These methods are instrumental in understanding cellular pathways and discovering druggable targets.

5. Protein-Protein Interactions and Functional Characterization

Affinity Enrichment (R)Affinity enrichment methods isolate target proteins or complexes, enabling downstream analysis of protein-protein interactions. These tools facilitate studies in structural biology, pathway mapping, and drug development.

Protein Fingerprinting (GenNext) (C) Protein fingerprinting identifies unique protein signatures through advanced mass spectrometry workflows. This technology is critical for rapid diagnostics and precision medicine applications. This service is in collaboration with a partner company with the advanced software workflows required for protein fingerprinting.

Mechanism of Action (MoA) Studies (R) MoA studies employ proteomics to elucidate the mechanisms by which drugs or biomolecules exert their effects. These insights are vital for therapeutic development and optimization.

6. Advanced Mass Spectrometry Techniques

Protein Mapping and Ion-mobility MS (R) Protein mapping integrates ion-mobility mass spectrometry to enhance spatial and structural resolution. This technique is pivotal for identifying protein isoforms and post-translationally modified species.

EAD and Cell-signaling Kits (C) Electron Activated Dissociation (EAD) methods and cell-signaling pathway kits accelerate the identification of signaling cascades and pathway dynamics. These tools support drug discovery and functional genomics. 

Whole-Protein Sequencing (R)Whole-protein sequencing techniques provide intact protein analysis, allowing researchers to map proteoforms and understand functional diversity. This capability is essential for characterizing complex protein therapeutics.

7. Niche Applications in Protein Characterization

Global Phosphorylation and Tandem Mass-tags (S)Global phosphorylation analysis, coupled with tandem mass-tagging, advances our understanding of cellular signaling networks and kinome activity. This approach is crucial for studying diseases like cancer and diabetes.

N-link Glycosylation Mapping (R)N-link glycosylation mapping identifies glycoproteins and their modification sites, providing insights into protein folding, stability, and function. These studies are essential in vaccine development and biomarker discovery.

1. Host Protein Composition in HIV Virions: Our team characterized the incorporation of host proteins into HIV-1 virions, identifying a conserved set of 79 host proteins through advanced purification techniques and proteomics. These findings revealed critical interactions between viral and host proteins essential for viral replication and phenotypic diversity​.
2. HIV Neurological Disease: We explored proteomic and metabolomic alterations in HIV-associated neurological conditions. Our studies revealed that ATP and other immuno-/neuromodulatory nucleotides released from HIV-infected macrophages dysregulate glutamatergic tone, impacting neuronal structure. Additionally, elevated brain monoamine oxidase (MAO) activity was observed, suggesting a link between oxidative stress and cognitive decline in HIV patients. These findings highlight therapeutic targets, such as MAO inhibitors, for HIV-associated neurological complications​​.
3. Glycosylation Patterns in HIV/SIV: Our research detailed distinct glycosylation patterns of HIV and SIV envelope glycoproteins, affecting viral infectivity and immune evasion. Techniques such as two-dimensional gel electrophoresis and mass spectrometry enabled detailed mapping of these modifications, advancing understanding of viral pathogenesis​​.
4. Malaria (Anopheles) Proteomics: We extended proteomic studies to malaria vectors, revealing the midgut brush border proteome of Anopheles mosquitoes and its role in host-parasite interactions. Comparative analysis of the Plasmodium vivax and An. albimanus transcriptome and proteome led to the identification of novel biomarkers and potential transmission-blocking vaccine candidates. Additionally, lipid raft microdomains were found to facilitate parasite invasion, expanding the scope for targeted malaria interventions​​​.
5. Protein Acylation and Post-Translational Modifications: Our studies demonstrated the impact of acylation on viral protein localization and function, critical for HIV assembly. Mass spectrometry-based methods identified novel host protein modifications, elucidating their roles in viral infectivity​​.
6. Refinement of Analytical Techniques: We developed novel proteomic methodologies for purifying virions and enhancing gel-based separation systems. These innovations facilitated precise mapping of protein modifications and host-pathogen interactions, advancing the field of proteomics​​.
7. Insights into Host-Virus Interactions: Our work on microvesicle contamination correction in HIV virion purification ensured the accurate identification of host proteins critical for viral infectivity. These studies contribute to a deeper understanding of host-pathogen dynamics​​.

Our state-of-the-art facilities include advanced laboratories, specialized equipment including instrumentation from all major vendors, and a team of experienced technicians. We provide a range of services, including sample analysis, testing, and consultation.

We collaborate with partners in academia, industry, and government to advance research and development. We welcome new partnerships and opportunities to work together towards common goals.

We are always looking for talented and motivated individuals to join our team. If you are passionate about science and technology, and want to make a difference, we encourage you to apply.