Ycndmmsutih8vah5atmx avm

AVMBioMed, LLC

ic 10.0/10 Overall Rating No Reviews Yet
ic 2 Orders Completed
Limerick, Pennsylvania, US

About AVMBioMed, LLC

AVMBioMed is a contract research organization (CRO) specializing in novel proteomic discovery since 2013. Our Snapshot Proteomics™ technology uses protein microarrays containing over 20,000 purified and spatially addressable human proteins to capture the information that defines proteins and proteomes, namely... Show more »

AVMBioMed is a contract research organization (CRO) specializing in novel proteomic discovery since 2013. Our Snapshot Proteomics™ technology uses protein microarrays containing over 20,000 purified and spatially addressable human proteins to capture the information that defines proteins and proteomes, namely their splice variation, state of post-translational modification (PTM), and interactions with other proteins. This information is both more abundant (3-4 fold improvement) and reproducible (95% compared to 60%) than shotgun approaches. This makes proteomics finally useful in complex clinical samples that require experimental reproducibility like drug-treated cells or human serum. But most importantly, the information is actually proteomic: identifying tryptic fragments of proteins to identify the parents produces names of genes, not proteins.

AVMBioMed also provides solutions for questions that require targeted approaches to the proteome (e.g., identifying and quantifying specific proteins within complex samples). We maintain a state-of-the-art mass spec facility including the latest in orbitrap technology, Q-Exactive Plus and Q-Exactive-HF spectrometers. We also have a fully-automated BI-4500 5-Channel Surface Plasmon Resonance (SPR) system (Biosensing Instrument) with Bi-DirectFlowTM technology, ideal for ultra-fast kinetics. We are truly a one-stop shop for all things protein and proteomic. From protein production to systems analysis, we have you covered. Click on the application most closely describing your needs or send us a message to learn more.

Recent Publications

  • DeMarshall CA, Nagele EP, Sarkar A, Acharya NK, Godsey G, Goldwaser EL, Kosciuk M, Thayasivam U, Han M, Belinka B, Nagele RG. Detection of Alzheimer’s disease at mild cognitive impairment and disease progression using autoantibodies as blood-based biomarkers. Alzheimers Dement (Amst). 3:51-62. (2016) PubMed 27239548

  • Yang L, Wang J, Li J, Zhang H, Guo S, Yan M, Zhu Z, Lan B, Ding Y, Xu M, Li W, Gu X, Qi C, Zhu H, Shao Z, Liu B, Tao SC. Identification of serum biomarkers for gastric cancer diagnosis using a human proteome microarray. Mol Cell Proteomics 15(2)614-23 (2016) PubMed 26598640

  • Cox E, Uzoma I, Guzzo C, Jeong JS, Matunis M, Blackshaw S, Zhu H. Identification of SUMO E3 ligase-specific substrates using the HuProt human proteome microarray. Methods Mol Biol 1295:455-63 (2015) PubMed 25820740

  • Dwyer SF, Gao L, Gelman IH. Identification of novel focal adhesion kinase substrates: role for FAK in NFκB signaling. Int J Biol Sci 11(4):404-10 (2015) PubMed 25798060

  • Merbl Y, Refour P, Patel H, Springer M, Kirschner MW. Profiling of ubiquitin-like modifications reveals features of mitotic control. Cell 152(5):1160-72 (2013) PubMed 23452859

  • Woodard CL, Goodwin CR, Wan J, Xia S, Newman R, Hu J, Zhang J, Hayward SD, Qian J, Laterra J, et al. Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PLoS One 8(9):e72671 (2013) PubMed 24023761

  • Loch CM, Strickler JE. A microarray of ubiquitylated proteins for profiling deubiquitylase activity reveals the critical roles of both chain and substrate. Biochim Biophys Acta 1823(11):2069-78 (2012) PubMed 22626734

  • Merbl Y and Kirschner MW. Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays. PNAS 106:2543-2548 (2009) PubMed 19181856

Show less

Diversity Certificates

Woman owned small business

Our Services (25)


ic

Proteomics

Price on request

Proteomic instrumentation and approaches are as varied as the applications to which they are applied. AVMBioMed is a one-stop, complete proteomic service provider. The process begins with one of our scientists learning about your specific interests, questions, and needs. We then design a customized recommendation and present... Show more »

Proteomic instrumentation and approaches are as varied as the applications to which they are applied. AVMBioMed is a one-stop, complete proteomic service provider. The process begins with one of our scientists learning about your specific interests, questions, and needs. We then design a customized recommendation and present our optimized strategy to you in a transparent and understandable quote including detailed costs and timelines. Numbers and deliverables vary according to the nature and scope of work to be done, but a typical project costs a few thousand dollars and is delivered within a few (3-5) weeks. We are passionate about the power of information, particularly from the deepest and most relevant biological source- the proteome. We produce informed clients, not simply information, and we NEVER just hand clients a list of proteins and wish them well. Our final report will include:

-a list of statistically significant hits also corrected for false discovery
-bioinformatic analysis of your hits, including ontology clustering to identify pathways and molecular functions over or under-represented among them
-raw data
-controlled, normalized, and processed data
-detailed descriptions of all methods used and all results obtained, suitable for publication
-recommendations for “next-steps”.
-a conference call with our scientists who will present their findings
-24/7 lifetime support of all work performed should questions ever arise

For specific applications, please see the relevant product pages listed within Science Exchange. The following description may be considered a VERY brief overview of our capabilities:

For discovery proteomics (identifying novel proteins or events in samples), we utilize protein microarrays containing >20,000 human proteins individually produced, purified, and printed onto slides at spatially addressable locations. Advantages over traditional techniques (e.g., MS/MS) include more data (20,000 > 6,000), better reproducibility (>90% compared with ~50-70%), less sample manipulation yielding more physiological relevance, and no bias towards concentration (since there is no competition at a detector). Services require only 100l of either complex mixture (sera or cell lysate) or purified protein.

For targeted proteomics (identifying changes to levels of known proteins within complex mixtures) we utilize two Thermo Fisher Hybrid LTQ-OrbitrapXL Mass Spectrometers with nano-capillary HPLC, Applied Biosystems 5500 Q Trap with HPLC, Applied Biosystems Voyager-DE PRO MALDI TOF spectrometer, or the latest in orbitrap technology currently available- the Thermo Fisher Q Exactive Plus and Q Exactive HF spectrometers. We can utilize standard databases or create one customized to your needs. All we require from you is the sample to be analyzed (traditionally a gel-slice) and the names of your proteins of interest.

To characterize known proteins for interaction with drugs, antibodies, and/or other proteins, we utilize a fully-automated BI-4500 5-Channel SPR system (Biosensing Instrument) with Bi-DirectFlowTM technology, ideal for ultra-fast kinetics which produces superior data at an affordable price. Material needed is only 50 g of protein(s), concentration, and molecular weight(s).

Examples of questions answered for clients:

  • Which kinases regulate my protein of interest (POI)?
  • Which phosphatases regulate my POI?
  • Is my POI a good target of pharmacological intervention?
  • What are the protein-protein interactions involving my POI?
  • What are the substrates of my E3?
  • What are the substrates of my deubiquitylase (DUB)?
  • What is the cellular response to a mutation/deletion/knockdown/overexpression of a gene of interest?
  • What is the cellular response to a specific environmental/growth condition, extracellular stress, or pharmacological intervention?
Show less

ic

Antibody Screening

Price on request

Few antibodies recognize just their intended target, and most that we've profiled preferentially bind other proteins entirely. This raises questions about basic science from IHC to Western blotting, and serious concerns about the development of therapeutic biologics. At AVMBioMed, we utilize your antibody to challenge in... Show more »

Few antibodies recognize just their intended target, and most that we've profiled preferentially bind other proteins entirely. This raises questions about basic science from IHC to Western blotting, and serious concerns about the development of therapeutic biologics. At AVMBioMed, we utilize your antibody to challenge in parallel over 20,000 recombinant, purified human proteins present on our microarray under native or denatured conditions. This nearly-complete specificity profile allows you to do better science, and make better decisions.

Another tool useful to characterize antibody-protein interactions is to immobilize one and flow a panel of the other in our fully-automated BI-4500 5-Channel SPR system (Biosensing Instrument) with Bi-DirectFlowTM technology, ideal for ultra-fast kinetics which produces superior data at an affordable price.

Show less

ic

Enzyme Assays

Price on request

The rapid nature of enzyme-substrate interaction makes it difficult to identify the pairings. However, the effect of the interaction is a stable chemical change that betrays the occurrence of the interaction. We exploit this principle within the context of a protein microarray containing over 20,000 purified human proteins to... Show more »

The rapid nature of enzyme-substrate interaction makes it difficult to identify the pairings. However, the effect of the interaction is a stable chemical change that betrays the occurrence of the interaction. We exploit this principle within the context of a protein microarray containing over 20,000 purified human proteins to examine your sample or purified enzymes for specific activities. Your choice of sample determines the nature of the experiment. Cell lysates with and without your kinase of interest can be used to identify substrates within the context of cellular machinery including competing substrates, antagonistic activities, and relevant cofactors. Using purified recombinant kinase loses some physiological context, but ensures that all phosphorylation events observed were the direct result of your kinase of interest specifically.

Proteins immobilized to the array are randomly deposited to the nitrocellulose surface, ensuring that virtually all epitopes are exposed to aqueous phase. Differential proteomics (comparing treated and mock-treated arrays) removes potential noise arising from immobilization-induced mis-folding. Signals are obtained with antibodies specific to the modification of interest, and results are semi-quantitative exactly like a Western blot. Correction: exactly like 20,000 Western blots.

Advantages over traditional techniques include breadth of coverage (20,000 > 6000), and depth of coverage since there is no competition at a detector and signals to arrayed proteins are enzymatically amplified. Unlike MS/MS, data is >90% reproducible (compared to 50-70%). Since the arrayed proteins cannot be degraded through proteasomes, there is no bias either towards or against degradative signals (as is the case when degradation inhibitors are or are not used, respectively). Last but not least, because trypsin is not used, information within complex ubiquitin structures are retained and can be revealed through the use of chain-specific reagents. As with all of our services, in addition to raw data you will receive:
-bioinformatic analysis to reveal the underlying biology
-a full report with detailed methods and explanation of results
-a conference call with our scientists who will present their findings
-24/7 lifetime support of the work should additional questions ever arise

Show less

ic

Protein-Protein Interaction Analysis

Price on request

Proteins are like teenagers: you can learn a lot about them by the company they keep. Various approaches have been developed to identify interacting proteins for a given protein of interest (POI), but none superior to biochemically profiling them simultaneously across 20,000 putative interacting partners on microarray. Your... Show more »

Proteins are like teenagers: you can learn a lot about them by the company they keep. Various approaches have been developed to identify interacting proteins for a given protein of interest (POI), but none superior to biochemically profiling them simultaneously across 20,000 putative interacting partners on microarray. Your choice of starting material- purified recombinant POI or cell lysate containing POI- determines whether the observed interactions are direct but absent physiological context, or within context but potentially indirect (respectively). The process is physically identical to performing 20,000 GST-pulldown or Co-IP experiments simultaneously, an economically and temporally prohibitive number to attempt in sequential fashion. Unlike yeast (or mammalian) 2-hybrid, the readout is proteomic not genomic, neither bait (POI) nor prey is fused to other proteins, and the process is complete in days or weeks rather than months or years. Cross-linking approaches are useful for targeted use (verifying suspected PPI), but horribly flawed for discovery. That is because proteins are constantly “feeling” their surroundings by bumping into their neighbors in search of productive interaction; furthermore, the most productive interactions are enzyme/substrate and by nature extremely rapid. The former point explains the high rate of false discovery associated with cross-linking, while the latter explains the low rate of true positive. As with all of our services, in addition to raw data you will receive:
-bioinformatic analysis to reveal the underlying biology
-a full report with detailed methods and explanation of results
-a conference call with our scientists who will present their findings
-24/7 lifetime support of the work should additional questions ever arise

Show less

ic

Post-Translational Modification Analysis

Price on request

UMAP™ is a broadly applicable tool for basic science that uses Snapshot Proteomics™ to reveal changes to the proteome of your manipulated cells or clinical samples. For example, if you provide experimentally manipulated cells, we can determine the changes in post-translational modification across ~20,000 human proteins.

The... Show more »

UMAP™ is a broadly applicable tool for basic science that uses Snapshot Proteomics™ to reveal changes to the proteome of your manipulated cells or clinical samples. For example, if you provide experimentally manipulated cells, we can determine the changes in post-translational modification across ~20,000 human proteins.

The result is the novel discovery of wide range of physiologically relevant information, including modified proteins, substrates, and biochemical pathways. A single UMAP™ screen could potentially provide an entire career’s worth of leads and ideas.

With UMAP™ (and all of our services) you get far more than just the raw data. You will also receive:
bioinformatic analysis to reveal the underlying biology, a full report with detailed methods and explanations of results, a conference call with our scientists who will present their findings, and unlimited technical support should additional questions arise

UMAP™ is an acronym for the commonly evaluated types of post-translational modifications: Ubiquitination, Methylation, Acetylation, and Phosphorylation. To get started with UMAP™, contact us so we can discuss your specific project or idea!

To characterize the state of specific proteins, we utilize two Thermo Fisher Hybrid LTQ-OrbitrapXL Mass Spectrometers with nano-capillary HPLC, Applied Biosystems 5500 Q Trap with HPLC, Applied Biosystems Voyager-DE PRO MALDI TOF spectrometer, or the latest in orbitrap technology currently available- the Thermo Fisher Q Exactive Plus and Q Exactive HF spectrometers. We can utilize standard databases or create one customized to your needs. All we require from you is the sample to be analyzed (traditionally a gel-slice) and the names of your protein(s) of interest.

Show less

ic

Compound Profiling

Price on request

SMART™ (Small Molecule Accelerated Research Tool) is a revolutionary product for the preclinical development of lead compounds. SMART™ uses Snapshot Proteomics™ to reveal changes to the proteome of pharmacologically treated cells. This information is then analyzed with our proprietary database to gain a deeper understanding of the... Show more »

SMART™ (Small Molecule Accelerated Research Tool) is a revolutionary product for the preclinical development of lead compounds. SMART™ uses Snapshot Proteomics™ to reveal changes to the proteome of pharmacologically treated cells. This information is then analyzed with our proprietary database to gain a deeper understanding of the proteomic molecular mechanisms that are a result of the pharmacological treatment.

The result is a better understanding of the cellular response to treatment, allowing you to fail compounds early and reliably, or to repurpose previously failed compounds to responsive subpopulations. We can also suggest combination therapy to improve efficacy and avoid resistance.

SMART™ is capable of measuring compound effects on a wide array of targets from multiple therapeutic areas. The ideal candidates for SMART™ are large or small molecule leads that emerge successfully through cell-based assay development.

Show less

ic

Biomarker Discovery

Price on request

ProActiN™ (Proteomic Activity Networks) is a specialized tool for clinical biomarker discovery that uses Snapshot Proteomics™ to provide information about changes to the proteome of individuals in response to drug or disease. Specifically, ProActiN™ compares the proteomic differences in post-translational modification between... Show more »

ProActiN™ (Proteomic Activity Networks) is a specialized tool for clinical biomarker discovery that uses Snapshot Proteomics™ to provide information about changes to the proteome of individuals in response to drug or disease. Specifically, ProActiN™ compares the proteomic differences in post-translational modification between related samples, such as a treated group vs. a control group, or responders vs. non-responders, to discover molecular signatures that can be prospectively used to identify one of the sample cohorts.

The result is the novel discovery of companion diagnostics (CDx), molecular diagnostics (MDx), and surrogate biomarkers for a wide range of therapeutic areas and drug treatments. Because ProActiN™ is measuring the pharmacodynamic changes to actual proteins, the results are both more accurate and reproducible than other leading biomarker techniques.

The ideal sample candidates for ProActin™ are from human clinical trials involving pharmaceutical compounds. To get started with ProActin™, please contact us to discuss your planned or ongoing clinical trial or biomarker discovery needs.

ProActiN™ reveals protein biomarkers for translational and clinical purposes including:

  • Companion biomarker discovery (CDx)
  • Diagnostic biomarker discovery (Dx)
  • Surrogate biomarker discovery

To identify levels of pre-identified biomarkers, samples are analyzed by mass spectrometry on either of our two Thermo Fisher Hybrid LTQ-OrbitrapXL Mass Spectrometers with nano-capillary HPLC, Applied Biosystems 5500 Q Trap with HPLC, Applied Biosystems Voyager-DE PRO MALDI TOF spectrometer, or the latest in orbitrap technology currently available- the Thermo Fisher Q Exactive Plus and Q Exactive HF spectrometers. We can utilize standard databases or create one customized to your needs. All we require from you is the sample to be analyzed and the names of your biomarker(s).

Show less

ic

Custom Protein Production

Price on request

We produce high-quality, well-folded, and functional proteins for use in assay, antibody development, or structural study. We utilize bacteria, yeast, and mammalian host systems, and are capable of producing large quantity using our bio-reactor (fermentor). Please request a quote and tell us about your needs for more information and pricing.

We produce high-quality, well-folded, and functional proteins for use in assay, antibody development, or structural study. We utilize bacteria, yeast, and mammalian host systems, and are capable of producing large quantity using our bio-reactor (fermentor). Please request a quote and tell us about your needs for more information and pricing.

Show less

ic

Recombinant Protein Expression

Price on request
Request a quote for more information about this service.

ic

Bioanalysis

Price on request
Request a quote for more information about this service.

ic

Drug Discovery

Price on request
Request a quote for more information about this service.

ic

Pharmacology & Toxicology

Price on request
Request a quote for more information about this service.

ic

Protein Production

Price on request
Request a quote for more information about this service.

ic

Biomolecular Interaction Analysis

Price on request
Request a quote for more information about this service.

ic

Biochemistry & Molecular Biology

Price on request
Request a quote for more information about this service.

ic

Biology

Price on request
Request a quote for more information about this service.

ic

Omics

Price on request
Request a quote for more information about this service.

ic

Biomarkers

Price on request
Request a quote for more information about this service.

ic

Drug Discovery & Development

Price on request
Request a quote for more information about this service.

ic

Protein Services

Price on request
Request a quote for more information about this service.

ic

Antibody Services

Price on request
Request a quote for more information about this service.

ic

Protein Characterization

Price on request
Request a quote for more information about this service.

ic

Lead Identification and Validation

Price on request
Request a quote for more information about this service.

ic

Therapeutic Monoclonal Antibody (mAb) Development

Price on request
Request a quote for more information about this service.

ic

Biochemical Assays

Price on request
Request a quote for more information about this service.

Not finding what you're looking for?

Get info on this provider's capabilities without requesting a quote.
FileType/PDF Created with Sketch.

Antibody Profiling_WhitePaper.pdf

FileType/PDF Created with Sketch.

Biomarkers.pdf

FileType/PDF Created with Sketch.

ExampleReport_UMAP_SubstrateID.pdf

FileType/Other Created with Sketch.

FAQ_AVM.docx

FileType/Other Created with Sketch.

PreclinicalRx.MP4

FileType/PDF Created with Sketch.

Repurposing_epi.pdf

FileType/PDF Created with Sketch.

Sorafenib.pdf

AVMBioMed, LLC has not received any reviews.

AVMBioMed, LLC has not received any endorsements.