About Bioproximity

Bioproximity has been a provider of contract research, specializing in biological mass spectrometry and informatics, since 2008. We offer a broad range of proteomic services designed for specific applications. We combine specialized sample handling and sample preparation tools and methods with state-of-the-art instrumentation, cloud-based computational resources and fit-for-purpose data analytic pipelines to yield the best quality data, consistently.

Our clients include over 400 institutions on four continents, including government researchers at institutions such as DOD, FDA (CBER, NCTA), NIH (NIH CC, NEI, NINDS, NIDDK, NCI CCR, NIEHS, NIDCR, NIAID, NHLBI, NIAAA) USDA, USGS and VA, academic researchers at institutions such as Baylor College of Medicine, Harvard Medical School, Johns Hopkins University, Stanford University and Yale Univeristy School of Medicine, research institutes such as J. David Gladstone Institutes, Mayo Clinic, Samuel Roberts Noble Foundation and Woods Hole Oceanographic Institution, as well as private companies in the agriculture, biotechnology, energy, food, healthcare and pharmaceutical industries.

We developed Proteome Cluster, an industry-first web application for storing and analyzing tandem mass spectrometry data in the cloud through the use of transient, on-demand, MPI Beowulf compute clusters using the high performance compute instances available via Amazon Web Services. This allows us to complete many large-scale, broad searches in parallel, and in minutes. By ‘wasting’ compute cycles we utilize multiple search algorithms to increase search sensitivity and identification confidence.

Additionally, Proteome Cluster addresses one of the major issues affecting lab-to-lab reproducibility of proteomic assays: variations in the bioinformatic processing pipeline. Proteome Cluster incorporates only open-sourced, freely-licensed software applications. Additionally, it stores search parameter settings and permits import of settings from other users or clients to ensure that any search is executed in exactly the same manner every time. And you can rest easy knowing your data is processed, stored and served from Amazon Web Services’ secure, reliable and responsive data infrastructure.

We are a small, dedicated group of scientists and software engineers, devoted to expanding the real-world applications of biological mass spectrometry. Please contact us to discuss your project aims.

About proteomics

Proteomics is the study of proteins. Shotgun proteomics is a method for identifying and quantifying proteins and has been optimized by the scientific research community to permit near-global profiling of almost any sample. Using modern methods and instrumentation, many thousands of proteins may be routinely identified at sub-nanogram quantities. Shotgun proteomics is currently used in a wide variety of applications, from discovery of biomarkers for disease diagnosis and prognosis to quality control of bioprocessing pipelines to validation of moclonal antibodies.

At its core, shotgun proteomics consists of using an enzyme to digest proteins into peptides which are then sequenced by fragmentation in a tandem mass spectrometer followed by matching of the fragmentation pattern against protein sequence libraries or libraries of validated experimental spectra. Shotgun proteomics applications typically require a sequenced genome for the organism of interest. As the genomes of more and more organisms are sequenced the range of applications for shotgun proteomics are similarly increasing.