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Proteomics Core Lab

St. Louis, Missouri, US

The Proteomics Core provides established and innovative services for the proteomics analysis of human biological fluids (e.g. plasma/serum, CSF, urine, and saliva), tissue-culture cells and tissues using both 2D dimensional difference gel electrophoresis and comparative, label-free quantitative proteomics on nano-LC-linear quadrupole ion trap-Fourier transform ion cyclotron mass spectrometers (LTQ-Orbitrap and LTQ-FTICR). Customized sample preparation methods have been developed for proteomic analysis of frozen tissues, formalin-fixed in tissue blocks, RNAlater, and tissue culture cells. Robotic sample preparation methods have been deployed to meet the stringent reproducibility demands of label-free LC-MS proteomics.

The Proteomics Core is organized and managed to provide users with the expertise that is needed to design and execute proteomics experiments. The Core has the capabilities to perform complex as well as... Show more »

The Proteomics Core provides established and innovative services for the proteomics analysis of human biological fluids (e.g. plasma/serum, CSF, urine, and saliva), tissue-culture cells and tissues using both 2D dimensional difference gel electrophoresis and comparative, label-free quantitative proteomics on nano-LC-linear quadrupole ion trap-Fourier transform ion cyclotron mass spectrometers (LTQ-Orbitrap and LTQ-FTICR). Customized sample preparation methods have been developed for proteomic analysis of frozen tissues, formalin-fixed in tissue blocks, RNAlater, and tissue culture cells. Robotic sample preparation methods have been deployed to meet the stringent reproducibility demands of label-free LC-MS proteomics.

The Proteomics Core is organized and managed to provide users with the expertise that is needed to design and execute proteomics experiments. The Core has the capabilities to perform complex as well as simple proteomics experiments. Services that have been performed range from quantitative proteomics comparisons of two samples to studies that routinely involve 30-50 clinical samples as part of biomarker development programs. The Director, Manager and other staff members as needed meet to plan and determine the feasibility of proposed experiments. The Core maintains a suite of software tools that are available to users. For gel-based proteomics, image analysis is performed using software DeCyder (DIA, BVA and EDA modules). Protein identification and quantification are accomplished using mass spectrometry, database search engines (MASCOT and SEQUEST), Q/C and visualization tools (SCAFFOLD), statistical packages (Rosetta Elucidator and Dante-R), and knowledge-based network software (Ingenuity Pathways and MetaCore). Other software packages are available for specialized proteomics analyses. The Core has fifty terabytes of RAID array storage capacity that hosts ongoing acquisition of gel images, mass spectrometric, and meta data and legacy data that have been acquired since the establishment of the Core in August, 2003.

Equipment

  • ETTAN IPGphor(GE Healthcare) and Protean IEF cell (Bio-Rad) isoelectric focusing units
  • Ettan DALT12 system (12 gel capacity with integral power supply), an Ettan DALTSix (GE Healthcare) gel tank, two Criterion (Bio-Rad) mini gel tanks (Bio-Rad)
  • Typhoon 9400 (GE Healthcare) laser scanner (GE Healthcare)
  • Vision LC Workstation (Applied Biosystems)
  • Bravo™ (Velocity 11) Liquid Handling System
  • ERENNA™ (Singulex) immunoassay system
  • Multi-dimensional nanoLC-LTQ-Orbitrap-MS (Thermo Fisher)
  • TripleTOF 5600+ (AB Sciex) Quadrupole TOF Mass spec system
  • Image Quant (GE Healthcare) software - Image acquisition and adjustment software for multi-color images
  • DeCyder 6.5 2D (GE Healthcare) - Automated image analysis software suite enabling detection, quantitation, matching and analysis of DIGE gel images
  • DeCyder Extended Data Analysis (GE Healthcare) – Proteomics informatics software for analysis of large and combined data sets from 2D DIGE gel images
  • Software for MS data generation, processing and analysis
  • Sorcerer Enterprise (Sage-N) - a high-performance blade server, expandable disk storage subsystem and the SORCERER™ Proteomics Edition workflow software for rapid searching of protein and conceptually-translated whole genome databases with peptide fragmentation spectra
  • Protein Pilot (Applied Biosystems) – Software for protein identification and quantification, enabling identification of hundreds of peptide modifications and non-tryptic cleavages simultaneously, distinguishing protein isoforms, protein subsets, and suppress false positives, and visualizing peptide-protein associations and relationships
  • PEAKS Studio 7 (Bioinformatic Solutions Inc.) - Mass spectrometry data analysis software utilizing multiple search algorithms for accurate identification of proteins, their post-translational modifications, and mutations
  • Mascot Distiller (Matrix Science) - Interface to a wide range of native (binary) mass spectrometry data files preparing them for database searching
  • MASCOT search engine (Matrix Science) – A search engine that uses mass spectrometry data to identify proteins and protein modifications from primary sequence databases
  • XCaliber (Thermo Fisher Scientific) – Windows-based data system providing instrument control and detailed data analysis for individual mass spectra
  • Analyst Software (Applied Biosystems) – Windows-based data system providing instrument control and data analysis for small molecules from triple quadrupole analyses
  • Peakview (ABSciex) - Stand-alone software for the qualitative review of LC/MS and MS/MS data from the TripleTOF 5600 system. The software allows exploration and interpretation of mass spectral data with special tools for processing accurate mass data, structural interpretation, and batch analysis
  • Eternus 4000 disk storage system(Fujitsu Global) – RAID array disk data storage with 50Tb capacity
  • Mass QC (Proteome Software, Inc.) –Software to monitor and troubleshoot the performance of LC-MS/MS instrumentation on a daily basis
  • Rosetta Elucidator (Rosetta Biosoftware) - Data management and analysis software for mass spectrometry data, supporting multiple workflows (label-free, SILAC, and shotgun proteomics and metabolomics), data from different instruments, and integration with different search engines for accurate peptide and protein identifications
  • Progenesis LC-MS (Non-linear Dynamics) - Data analysis software that helps find and quantify proteins showing interesting behavior in label-free samples. It is useful for both differential protein expression and protein characterization
  • Sieve software for Differential Expression Analysis (Thermo Fisher Scientific) – Supports automated, label-free, semi-quantitative analysis of proteins, peptides, and metabolites based on comparisons of LC/MS and GC/MS data
  • DanteR (Pacific Northwest National Laboratory) - an entirely R-based program that provides a graphical front-end for common data analysis tasks in "omics", with an emphasis on proteomics
  • Partek Genomics Suite (Partek, Inc.) - a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data
  • Scaffold 4 (Proteome Software,Inc.) – Portable software framework with the ability to display a visual comparison of the proteins found by multiple search engines across all the samples of an experiment
  • Scaffold PTM (Proteome Software, Inc.) - An extension of Scaffold 4 which allows confident positional assignment of post-translational modifications
  • Scaffold Q+ (Proteome Software, Inc,) - A stand-alone version of Scaffold 4 designed to provide accurate quantitation of mass-labeled and Label-free mass spectrometry data, with extensive statistical support
  • Ingenuity Systems Pathway Analysis (Ingenuity Systems) – Software to model, analyze, and understand the complex biological and chemical systems at the core of life science research using a knowledge-based approach
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Proteomics Core Lab has not listed any services.

Biomarker Analysis
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LC-MS/MS
Assay Development
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Immunometric protein assay development and execution

Immunometric protein assay development and execution

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Proteomics Data Analysis
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Analysis, statistics, and bioinformatics for Proteomics data streams

Analysis, statistics, and bioinformatics for Proteomics data streams

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LC-MS
Liquid Chromatography-Coupled Mass Spectrometry
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Label Free Quantitative Proteomics
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PAGE
Polyacrylamide Gel Electrophoresis
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Electrophoresis
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Biomarkers
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Data Services
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Biochemistry & Molecular Biology
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Spectroscopy
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Biology
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Protein Purification
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Mass Spectrometry
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Computational Modeling
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Omics
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Drug Discovery & Development
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Drug Discovery & Development Services

Drug Discovery & Development Services

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Pharmacology & Toxicology
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Protein Sequencing
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Purification Services
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Imaging & Spectroscopy
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Experimental Design
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Gel Electrophoresis
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Chemistry and Materials
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Project and Process Management
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Protein Services
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Customized sample preparation for a wide range of sample types and protein compartments

Customized sample preparation for a wide range of sample types and protein compartments

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Bioanalysis
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Liquid Chromatography Coupled Mass Spectrometry Methods
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Proteomics
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Analytical Chemistry Services
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Protein Depletion
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