RCMI Translational Proteomics Center

Director: Meléndez, Loyda

Summary:

The Translational Proteomics Center provides training, resources, and tools for new and established investigators seeking to use innovative approaches of proteomics to their research, as well as to undergraduate and graduate students in the biomedical field. The Center fosters collaborations and partnerships among researchers aiming to reduce health disparities, including infectious diseases, cancer, and neurological/neurodegenerative diseases.

Currently located at the second floor of the Comprehensive Cancer Center, Laboratory # 5.

People:

• Director: Meléndez, Loyda
  

Resources:

Instruments

• 2D-DIGE ( Gel electrophoresis system )
  

  Includes:
  Ettan IPG Phor 3 & manifold
  Ettan Dalt TwelveSeparation Unit
  Ettan DIGE Imager
  Ettan Spot Picker & Base

• Agilent OFFGEL Fractionator ( Field flow fractionator )
  

• Bio-Rad Gel Doc XR System ( Gel imaging system )
  

  "The Gel Doc™ XR+ system is based on CCD high-resolution, high-sensitivity detection technology and modular options to accommodate a wide range of samples and support multiple detection methods including fluorescence and densitometry. The system is controlled by Image Lab™ software to optimize imager performance for fast, integrated, and automated image capture and analysis of various samples.
  The system accommodates a wide array of samples, from large handcast polyacrylamide gels to small ReadyAgarose™ gels and various blots. The system is an ideal accompaniment to PCR, purification, and electrophoresis systems, enabling image analysis and documentation of restriction digests, amplified nucleic acids, genetic fingerprinting, RFLPs, and protein purification and characterization."

• Branson Sonicator ( Sonicator )
  

• Electrophoresis Station ( Instrument )
  

• Exactive Plus System with Easy-nLC1200 system ( Instrument )
  

  (purchase in process)

• Nano Easy instrumentation of the LTQ ( Instrument )
  

• NuAire CO2 water jacketed incubator ( CO2 incubator )
  

  Bio Med #1 Lab 302

• Omni Overhead Stirrer ( Homogenizer )
  

• Savant speed vac plus ( Vacuum centrifuge concentrator )
  

• SmartSpec Plus Spectrophotometer ( Spectrophotometer )
  

  "The SmartSpec Plus spectrophotometer has a wider range of features and functions than many other benchtop spectrophotometers, offering performance, stability, and functionality at an affordable price.
  The UV/visible SmartSpec Plus spectrophotomer has a working wavelength range of 200–800 nm. It is the perfect tool for routine applications such as:
  Quantitation of DNA, RNA, and oligonucleotides
  Quantitation of proteins via the Bradford, Lowry, and BCA assay methods
  Monitoring bacterial culture growth
  Simple kinetic assays
  Wavelength scans with peak detection"

• Sorvall Legend Microcentrifuge Series ( Microcentrifuge )
  

  Includes:
  Micro 17 and Micro 21R

• Sorvall WX Ultra Series Ultracentrifuge and Rotor ( Instrument )
  

• Thermo Easy Nano LC 1000 ( Instrument )
  

• Thermo LTQ XL Mass Spectrometer ( Ion trap mass spectrometer )
  

  Includes:
  Thermo Finnigan Surveyor MS Pumps
  Thermo Finnigan Micro AutoSampler
  Eksigent Nano LC
  
  "The LTQ XL extends the legendary MSn performance of the LTQ, incorporating more techniques to generate structural information through innovations in Thermo Scientific ion trap technology.
  Unparalleled sensitivity and unmatched MSn spectral quality
  Pulsed Q Dissociation (PQD) for generating more fragments and extending the low mass range
  Electron Transfer Dissociation (ETD) option provides sequence information not available from conventional methods
  High Resolution Isolation (HRI) enables isolation of isobaric mass peaks for cleaner MSn spectra
  Ultra-fast polarity switching for high sensitivity analysis of unknowns
  Automated Data Dependent neutral loss for PTM and biotransformation analyses
  Excellent charge state determinations with Ultra ZoomScan™
  Upgradeable to LTQ Orbitrap XL accurate mass technology"

• Turbo Trans Blot Transfer System ( Instrument )
  

• Vacufuge plus sytem ( Instrument )
  

• Varioskan Flash Spectral Reader ( Multimode microplate reader )
  

Protocols

• Ingenuity Pathway Analysis (IPA) ( Protocol )
  

• Mass spectrometry analysis ( Protocol )
  

• Protein expression profiling ( Protocol )
  

  2D/DIGE

• Protein identification ( Protocol )
  

• Protein validation ( Protocol )
  

  Includes:
  1D SDS-Page
  Western blot
  Elisa's

• Quantitative proteomics analysis ( Protocol )
  

  Use techniques such as: Itraq, SILAC and others.

• Sample preparation, quantitation and fractionation ( Protocol )
  

Services

• 1D and 2D SDS PAGE gel analysis ( Analysis service )
  

  Itraq, ICAT, SILAC, enzymatic digestion of samples (in gel, in solution or in beads), C18 zip-tip sample clean up and MS/MS analysis.

• Consulting ( Support service )
  

  Consulting about proteomics, platforms, experimental design, support letters, methods preparation for proposals, budgets, results analysis and reports preparation.

• Data analysis ( Data analysis service )
  

  Includes: statistics, database search and pathways elucidation using Proteom Discoverer, Mascot, Scaf fold and Ingenuity Pathway Analysis (IPA).

• Immunoprecipitation and in bead digestion for studies of protein interactions ( Service )
  

• Post-translational modification analysis ( Service )
  

• Protein extraction and purification ( Service )
  

• Protein separation and fractionation ( Service )
  

• Proteomics Workflow ( Service )
  

• Protocol optimization and sample preparation ( Service )
  

• Quantitative Proteomics ( Service )
  

• Training and Instrument usage coordination ( Service )
  

• Validation Analyses ( Service )
  

Software

• DeCyder 2D ( Software )
  

  "2D gels differential analysis software specifically designed for 2-D fluorescence (DIGE) analysis using the Ettan DIGE system, multivariate statistics module for biomarker discovery"

• Eksigent Control software ( Software )
  

  Nano LC control software

• Graph Pad Prism ( Software )
  

  Data analysis, statistics and graphics

• Image Quant TL ( Software )
  

  "Imaging software and toolbox for area and profile analysis of acquired images, software contains several independent modules, which may be run simultaneously."

• ImageLab 5.1 ( Software )
  

  Imaging and data analysis software.

• Ingenuity Pathways Analysis ( Software )
  

• Mascott Premium ( Software )
  

  "Database search engine tool for the analysis of protein sequencing data"

• Proteome Discoverer ( Software )
  

  "Database search engine tool for the analysis of protein sequencing data from Thermo Scientific"

• Scaffold ( Software )
  

  "Database search engine tool for the analysis of protein sequencing data, including quantitative proteomics methods"

• SkanIt ( Software )
  

• Tune Plus ( Software )
  

  MS/MS Spectrometer control software

• X-Calibur ( Software )
  

  LTQ MS/MS data acquisition and control software.

Web Links:

• http://rcmi.rcm.upr.edu/resreso/corefacnetwork/tpc