CellCarta® proteomics platform
Caprion’s proteomics platform - CellCarta® - is the leading means for profiling proteins in solid tissues and plasma. This proprietary, state-of-the-art proteomics technology platform serves as an engine for both unparalleled disease target identification and predictive medicine. It is scalable and provides unparalleled sensitivity and utility. The platform has been successfully leveraged to secure multiple, platform-validating, revenue generating partnerships surrounding oncology target identification and clinical biomarker discovery.
CellCarta®’s core competitive advantages:
- its ability to comprehensively, reproducibly and quantitatively profile expression of proteins in tissues and plasma across large sample sets;
- it allows for more comprehensive detection of disease-relevant protein targets and of biomarkers across a wider dynamic range of concentrations;
- it produces a complete audit trail and data analysis/validation toolset.
CellCarta® Discovery Process
 |
 |
 |
 |
 |
|||
PROTEIN/TARGET IDENTIFICATION |
|||
Sample Preparation and Purification
Caprion has developed a deep expertise in cell and molecular biology, in particular in the analysis of cellular phenotypes, intracellular protein trafficking, and in the isolation of highly purified sub-cellular organelle preparations. The Company has developed novel methods for isolating organelles such as the plasma membrane, phagosomes, and golgi, to an unprecedented degree of purity, and has years of experience with standard approaches to isolating other organelles such as mitochondria, endoplasmic reticulum, and nuclear membranes. By enriching for these compartments, Caprion enables more comprehensive proteomic comparisons of normal and diseased cells and provides the biological and functional context for the identification of high value, disease-relevant protein targets.
Caprion has fully equipped tissue culture suites and a research staff with extensive experience in ex vivo tissue processing, cell line propagation, and transfection of exogenous genes into cultured cells. Caprion has also implemented standardized automated methods for depleting highest abundant proteins from plasma and other accessible fluids in a reproducible and high throughput manner. Samples are handled under rigorous and standardized QA/QC “chain of custody” including a bar-coding LIMS and processed using SOPs. Samples are digested to tryptic fragments and fractionated by strong cation exchange (SCX) to achieve a more comprehensive analysis.
Mass Spectrometry Analysis
Caprion has a state-of the art, automated and industrialized mass spectrometry facility equipped with 11 LC-MS and LC-MS-MS instruments, operating in a high throughput production environment that is capable of processing 150-250 biological samples (up to 2000 LC-MS injections) per week. The facility was custom built to maximize the performance and efficiency of the protein expression profiling analyses. Its special structural features include double reinforced and isolated concrete slabs on which the mass spectrometers sit and micro temperature controlled heating, ventilation and air conditioning (HVAC) units that separate the offices from the laboratories, as well as the labs from each other.
Other key enabling features of Caprion’s MS operation include the high mass accuracy (11 ppm after mass correction) and high LC retention time reproducibility (+/- 10 seconds after normalization) of the LC-MS instruments in operation, The Mass Spec analysis of samples in a given project consists of two phases, an initial phase of analysis in LC-MS mode for the detection of differentially expressed peptide ions contained in the samples, and a subsequent re-injection of the same samples in LC-MS-MS mode in order to obtain sequence information for those differentially expressed peptides.
Quantitative Expression Profiling of Peptides
Caprion has developed an industry-leading suite of proprietary analytics tools that transform raw LC-MS and LC-MS-MS data into reliable and actionable protein expression information. Caprion’s integrated proteomics data analysis software is capable of routinely detecting over 25,000 peptides per sample, reproducibly tracking these peptides across large sample sets and measuring their relative expression levels with high accuracy.
Bioinformatics Analysis
The CellCarta® integrated suite of Proteomics Data Analysis Software combines data analysis, management, storage, and interface into one central unit for easy access and data analysis. The development of the CellCarta® integrated software suite, which comprises over 30 internally developed and proprietary bioinformatics software tools and services for proteomics, began in 2000 supported by the combined efforts of Caprion, SUN, Oracle, and CGI consortium. The software and IT platform have been operational since 2002 and our internal development teams ensure constant evolution. Its development and implementation has to date involved resource commitment of over 120 person-years by Caprion. The platform currently supports the continuous operation and data generation of over 11 MS instruments, a database containing more than 100 million entries, and more than 10 terabytes of data files. The platform design and evolution make it fully scalable and transportable to new architectures.