News Article | January 18, 2017
MORGANTOWN, W.Va., Jan. 18, 2017 (GLOBE NEWSWIRE) -- Protea Biosciences Group, Inc. (OTCQB:PRGB) (“Protea”) announced today that the Company has signed a renewal of its collaboration with California-based Protein Metrics Inc. for further applications development of their advanced analytical software for Protea’s molecular information services. “By combining our high-resolution mass spectrometry molecular data with the analytical power of Protein Metrics software, we are delivering more comprehensive molecular information to researchers who are developing complex biotherapeutics,” commented David Halverson, Protea’s President and Chief Business Officer. He added, “This collaboration will empower researchers with bioinformatics tools to facilitate the analysis of the structure of therapeutic proteins, including their disulfide linkages, glycoforms and other structural components.” Protea and Protein Metrics plan to create co-authored presentations this year to highlight the benefit of the combined analytical workflows with data processing and reporting capabilities. Eric Carlson, President and CEO of Protein Metrics, commented “We are delighted to renew our partnership with Protea Biosciences. It’s exciting to contribute to the quality analysis and reports that Protea provides to their many clients. Thanks to the input from Protea during the first stage of our collaboration, our latest releases include many new features that allow analysts to review all of their data on a common platform and share it with collaborators and customers in a clear, consistent fashion.” About Protea Biosciences Group, Inc.: Protea Biosciences Group, Inc. (OTCQB:PRGB) is a molecular information company providing proprietary, bioanalytical workflows to the pharmaceutical and life science industries. "Molecular information", the generation and bioinformatic processing of very large data sets, is obtained by applying the Company's technology to identify and characterize the proteins, metabolites, lipids and other biologically-active molecules which are the byproducts of all living cells and life forms. About Protein Metrics Inc. Protein Metrics has deep experience in protein identification software. With its current software products and multiple new products to be released shortly, Protein Metrics delivers tools to increase productivity and analytical quality, reduce costs and accelerate development timelines. Protein Metrics is a dynamic software company serving biopharmaceutical development professionals and proteomics researchers. The Company focuses on the analysis of mass spectrometric and other analytical data to provide detailed, efficient characterization of proteins and glycans. Over the past ten+ years, hardware for mass spectrometry has improved dramatically, and the company’s aim is to allow researchers to convert the new wealth of data from these instruments into to knowledge by providing innovative software that makes analytical results more accurate, more complete, and easier to achieve. The company is headquartered in San Carlos, California. For more information, visit www.proteinmetrics.com. Forward-Looking Statements; This press release may contain statements relating to future results or events, which are forward-looking statements. Words such as "expects", "intends", "plans", "may", "could", "should", "anticipates", "likely", "believes" and words of similar import may identify forward-looking statements. These statements are not historical facts, but instead represent only the Company's belief regarding future events, many of which, by their nature, are inherently uncertain and outside of the Company's control. It is possible that the Company's actual results and financial condition may differ, possibly materially, from the anticipated results and financial condition indicated in these forward-looking statements. Further, information concerning the Company and its business, including factors that potentially could materially affect the Company's business and financial and other results, are contained in the Company's filings with the Securities and Exchange Commission, available at www.sec.gov. All forward-looking statements included in this press release are made only as of the date of this press release, and we do not undertake any obligation to publicly update or correct any forward-looking statements to reflect events or circumstances that subsequently occur or of which we hereafter become aware. For more Information: Protea Biosciences Group, Inc., 1311 Pineview Dr., Morgantown, WV 26505 USA Phone: 304.292.2226 Fax: 304.292.7101 Details of Protein Metrics biopharma suite can be found at www.proteinmetrics.com Protea is a registered trademarks of Protea Biosciences Group, Inc.
Yin X.,King's College London |
Bern M.,Protein Metrics, Inc. |
Xing Q.,King's College London |
Ho J.,Thermo Fisher Scientific |
And 2 more authors.
Molecular and Cellular Proteomics | Year: 2013
Previous proteomics studies have partially unraveled the complexity of endothelial protein secretion but have not investigated glycosylation, a key modification of secreted and membrane proteins for cell communication. In this study, human umbilical vein endothelial cells were kept in serum-free medium before activation by phorbol-12-my-ristate-13 acetate, a commonly used secretagogue that induces exocytosis of endothelial vesicles. In addition to 123 secreted proteins, the secretome was particularly rich in membrane proteins. Glycopeptides were enriched by zwitterionic hydrophilic interaction liquid chromatography resins and were either treated with PNGase F and H 2 18O or directly analyzed using a recently developed workflow combining higher-energy C-trap dissociation (HCD) with electron-transfer dissociation (ETD) for a hybrid linear ion trap-orbitrap mass spectrometer. After deglycosylation with PNGase F in the presence of H 2 18O, 123 unique peptides displayed 18O- deamidation of asparagine, corresponding to 86 proteins with a total of 121 glycosylation sites. Direct glycopeptide analysis via HCD-ETD identified 131 glycopeptides from 59 proteins and 118 glycosylation sites, of which 41 were known, 51 were predicted, and 26 were novel. Two methods were compared: alternating HCD-ETD and HCD-product-dependent ETD. The former detected predominantly high-intensity, multiply charged glycopeptides, whereas the latter preferentially selected precursors with complex/hybrid glycans for fragmentation. Validation was performed by means of glycoprotein enrichment and analysis of the input, the flow-through, and the bound fraction. This study represents the most comprehensive characterization of endothelial protein secretion to date and demonstrates the potential of new HCD-ETD workflows for determining the glycosylation status of complex biological samples. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.
Bern M.,Protein Metrics, Inc. |
Bern M.,Palo Alto Research Center PARC |
Kil Y.J.,Protein Metrics, Inc. |
Becker C.,Protein Metrics, Inc.
Current Protocols in Bioinformatics | Year: 2012
Byonic is the name of a software package for peptide and protein identification by tandem mass spectrometry. This software, which has only recently become commercially available, facilitates a much wider range of search possibilities than previous search software such as SEQUEST and Mascot. Byonic allows the user to define an essentially unlimited number of variable modification types. Byonic also allows the user to set a separate limit on the number of occurrences of each modification type, so that a search may consider only one or two chance modifications such as oxidations and deamidations per peptide, yet allow three or four biological modifications such as phosphorylations, which tend to cluster together. Hence, Byonic can search for tens or even hundreds of modification types simultaneously without a prohibitively large combinatorial explosion. Byonic's Wildcard Search allows the user to search for unanticipated or even unknown modifications alongside known modifications. Finally, Byonic's Glycopeptide Search allows the user to identify glycopeptides without prior knowledge of glycan masses or glycosylation sites. © 2012 by John Wiley & Sons, Inc.
Tang H.,Van Andel Research Institute |
Hsueh P.,Van Andel Research Institute |
Kletter D.,Protein Metrics, Inc. |
Bern M.,Protein Metrics, Inc. |
Haab B.,Van Andel Research Institute
Advances in Cancer Research | Year: 2015
Recent research has uncovered unexpected ways that glycans contribute to biology, as well as new strategies for combatting disease using approaches involving glycans. To make full use of glycans for clinical applications, we need more detailed information on the location, nature, and dynamics of glycan expression in vivo. Such studies require the use of specimens acquired directly from patients. Effective studies of clinical specimens require low-volume assays, high precision measurements, and the ability to process many samples. Assays using affinity reagents-lectins and glycan-binding antibodies-can meet these requirements, but further developments are needed to make the methods routine and effective. Recent advances in the use of glycan-binding proteins involve improved determination of specificity using glycan arrays; the availability of databases for mining and analyzing glycan array data; lectin engineering methods; and the ability to quantitatively interpret lectin measurements. Here, we describe many of the challenges and opportunities involved in the application of these new approaches to the study of biological samples. The new tools hold promise for developing methods to improve the outcomes of patients afflicted with diseases characterized by aberrant glycan expression. © 2015 Elsevier Inc.
Agency: Department of Health and Human Services | Branch: | Program: STTR | Phase: Phase I | Award Amount: 576.98K | Year: 2012
DESCRIPTION (provided by applicant): Mass spectrometry has become a method of choice for identifying and characterizing small quantities of proteins in complex mixtures. However, the ability to perform the identification in a high- throughput fashion hasdepended on the availabilit of protein sequence databases. This means that proteins from organisms with unsequenced genomes (e.g. peptide toxins) and proteins that modify their primary sequence rapidly in response to the environment (e.g. antibodies) havebeen excluded from high-throughput analysis. We propose to develop algorithms and software along with improving laboratory methods that make sequencing of antibodies and peptide toxins a fast and low-cost effort. This will allow us to access the circulating antibody repertoire of individuals for clinical application including vaccine development, and to access the vast number of bioactive venom components for basic research and ion-channel drug development. For the laboratory improvements, antibody peptides and toxins will be chemically labeled to improve spectral quality and we will use different types of mass spectrometric fragmentation. Data acquisition will be optimized to facilitate identification of diagnostically relevant peptides and a gas- phase digestion strategy will be used to increase the sequence coverage for larger peptides. We propose to develop improved algorithms for sequencing of antibodies and peptide toxins. These will integrate de novo and database sequencing and will include candidate generation algorithms incorporating multiple channels of information: spectra from different charge states and fragmentation methods, homology constraints, composition constraints, and in silico mutation of databases. Improved scoring algorithms will also be developed using subtle spectrum clues, currently used only in manual de novo sequencing. We will produce prototype software, and benchmark it against manually annotated mass spectra. The software will then be applied to automatically sequence a largeset of antibody data from long- term non-progressors of HIV, and spider and cone snail toxin data. PUBLIC HEALTH RELEVANCE: We propose to develop algorithms and software that make sequencing of antibodies and peptide toxins a fast and low-cost effort. This will enable the effortless generation of large amounts of antibody and peptide toxin sequences; a critical step for vaccine and ion-channel drug development, respectively.
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 188.80K | Year: 2012
DESCRIPTION (provided by applicant): Due to the complexity of proteins and their biological production, characterization of protein pharmaceuticals ( biologics ) poses much more demanding analytical challenges than do small-molecule drugs. Consequently,many disparate biochemical analytical techniques are needed to characterize biologics. Because of the rapidly increasing power of mass spectrometry (MS), many of the measurements to characterize therapeutic proteins are now handled by MS, and that trend can be expected to continue owing to the accuracy and precision provided by state-of-the-art instrumentation. However, biotech companies currently make do with a patchwork of inefficient or ineffective software and manual data analysis for peptide identification, amino-acid-substitution evaluation, glycosylation characterization, disulfide-bond evaluation, and so forth. Current data analysis significantly lags behind the information content inherent in the complex data sets produced. We propose commercialdevelopment of software, named Byologic, which will make major improvements in the characterization of biologics via a range of mass spectrometric assays. Protein Metrics Inc. is a spin-off of Palo Alto Research Center where a variety of algorithms have been developed in recent years to address these analytical challenges. The proposed Phase I feasibility study will allow us to perform controlled studies to determine if MS- based assays and our algorithms are robust enough to satisfy the exacting standardsof the biotech industry. If so, we will then build robust and GMP-compliant Byologic in Phase II. Both generic ( biosimilar ) and innovator drug companies stand to gain from Byologic. Public health, and regulatory agencies like the FDA charged with protecting the public, stand to gain too because better characterization will improve quality control, safety, and increase the efficiency of drug development, leading to consumer and Government savings. PUBLIC HEALTH RELEVANCE: The proposed projectwill lead to commercial software for improved characterization of the detailed composition of therapeutic proteins. Better characterized protein drugs will lead to better quality assurance, enhanced public safety, more informed regulatory decisions, and lower overall costs.
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 525.67K | Year: 2012
DESCRIPTION (provided by applicant): Molecular signatures collected from intact tissue sections by MALDI imaging mass spectrometry (MALDI IMS) have shown high potential for use as a prognostic or diagnostic pathology tool in the clinical setting. A majorobstacle to the widespread deployment of MALDI IMS, however, is the difficulty of identifying the proteins contributing to the signatures. Researchers have tried a number of approaches, including in situ digestion, MALDI TOF/TOF tandem mass spectrometry, and top-down proteomics on specific image regions. In preliminary work, we have obtained promising experimental results using top-down proteomics on intact proteins in the 2 - 20 kDa range. However, the lack of successful algorithms and software to identifythe proteins in IMS mass signatures poses a major bottleneck. In particular, available top-down proteomics software relies heavily on high-accuracy mass spectrometry. The requirement for high accuracy precludes the use of some of the most sensitive mass analyzers such as linear ion traps, especially useful for these very small and complex samples. Protein Metrics Inc. is a new software company building on six years of algorithms and software research at Palo Alto Research Center. We plan to extend Byonic,our next- generation proteomics search engine, to intact proteins up to about 20 kDa. For proteins larger than 20 kDa, we will also build software for middle-down proteomics, specifically for assembling large peptides (2 - 20 kDa) produced by limited digestion to recover the identity of the intact proteins observed in IMS. The proposed Phase I feasibility study will allow us to perform controlled studies to determine the best experimental and bioinformatics approaches. Phase II will then build commercial-grade software. The proposed project will advance the state of the art in imaging mass spectrometry. Translation of imaging mass spectrometry to routine clinical pathology use will advance the state-of-the-art in disease diagnosis and treatment, and advance medical imaging and public health. PUBLIC HEALTH RELEVANCE: The project will develop commercial software that will improve our ability to identify the proteins and modifications represented in imaging mass spectrometry molecular signatures. Project success will make imaging mass spectrometry much more useful as a clinical pathology tool.
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: STTR | Phase: Phase II | Award Amount: 988.84K | Year: 2015
DESCRIPTION provided by applicant Mass spectrometry has become a method of choice for identifying and characterizing small quantities of proteins in complex mixtures However the ability to perform the identification in a high throughput fashion has depended on the availability of high quality protein sequence databases This means that proteins from organisms with unsequenced or poorly sequenced genomes e g peptide toxins and proteins that modify their primary sequences rapidly in response to the environment e g antibodies have been excluded from high throughput analysis Widespread availability of Next Generation Sequencing NGS has not alleviated this problem but rather NGS has led to a proliferation of lower quality uncurated protein sequence databases including personalized databases cancer databases and databases with uncertain assembly The traditional division between database search proteomics and de novo peptide sequencing no longer holds many of the most interesting biological questions are now best addressed by data analysis that combines the best of both techniques In this Phase II STTR project we propose to develop two commercial software products for sequencing biologically interesting peptides and proteins regardless of the quality of sequence databases One product will be aimed at the peptide level with applications to variable regions of circulating antibodies peptide toxins and human leukocyte antigens The other product will be aimed at the protein level with applications to end to end sequencing of purified proteins especially therapeutic monoclonal antibodies This system will include the peptide level sequencer as a component as well as tools for assembly of the peptides into the full sequence and for visualization and manual validation The proposed project has the potential for great impact on human health in areas such as vaccine development therapeutic antibody development and cancer immunotherapies PUBLIC HEALTH RELEVANCE We propose to develop commercial software products for sequencing biologically important peptides and proteins regardless of the existence or quality of available protein sequence databases The proposed project has the potential for great impact on human health in areas such as vaccine development therapeutic antibody development and cancer immunotherapies
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase II | Award Amount: 965.52K | Year: 2015
DESCRIPTION provided by applicant Due to the complexity of proteins and their biological production characterization of protein pharmaceuticals andquot biologicsandquot poses much more demanding analytical challenges than do small molecule drugs Biologics are prone to production problems such as sequence variation misfolding variant glycosylation and post production degradation including aggregation and modifications such as oxidation and deamidation These problems can lead to loss of safety and efficacy so the biopharmaceutical industry would like to identify and quantify variant and degraded forms of the product down to low concentrations plus have tertiary structure information Because of the rapidly increasing power of mass spectrometry MS we can now conceive of an MS based platform for comprehensive measurement of almost all the relevant drugandapos s physical characteristics A crucial piece of such a platform is data analysis software focused to address the needs of the biopharmaceutical industry We propose commercial development of software named Byologic which will make major improvements in the characterization of biologics via a range of mass spectrometric assays Both generic andquot biosimilarandquot and innovator drug companies stand to gain from Byologic Public health and regulatory agencies like the FDA charged with protecting the public stand to gain too because better characterization will improve quality safety and increase the efficiency of drug development leading to consumer and Government savings PUBLIC HEALTH RELEVANCE The proposed project will lead to commercial software for improved characterization of the detailed composition of therapeutic proteins including degradative modifications glycosylation and tertiary structural changes More fully characterized protein drugs will lead to better assurance of efficacy enhanced public safety more informed regulatory decisions and lower overall costs to the consumer
Protein Metrics, Inc. | Date: 2015-08-30
Computer software and hardware for protein and carbohydrate analysis.