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Gel/LC-MS/MS Comprehensive analysis of a subproteome or proteome

eagle-i ID


Resource Type

  1. Material analysis service


  1. Fee for service
  2. Resource Description
    "Purpose: Identify as many proteins as possible in a subproteome or an entire proteome. Examples of subproteomes include analysis of a purified large macromolecular complex, a highly purified organelle, a phosphotyrosine sub-proteome, etc. Examples of proteomes include: a cell line, the secretome of a cell line grown in serum-free media, etc. Requirements: An intact 1D SDS mini-gel (see <i>In-gel protease digestion service</i> for details and detection limits/expected results). Depending upon the number of fractions that are to be analyzed and the complexity of the sample, the optimal electrophoresis distance will vary. For example, if the sample is relatively simple (<100 proteins), the SDS gel should only be run until the bromophenol tracking dye reaches either 1.0 or 2.0 cm. It is strongly recommended that you consult with the Facility Manager before preparing the sample to be submitted. Include a protein standard on the gel that is separated from the sample lane by one to two blank lanes. Submit an image of the gel with bands/spots of interest and standard Molecular Weights clearly marked and a completed MS/MS submission form (PDF). Complete all entries on the submission form, including the species of sample origin, Molecular Weight, gel thickness, type, etc. Results: A large number of high-confidence (>99%) identifications are expected where the proteins have been identified by two or more peptides, provided that the genome for the species analyzed is essentially complete. Integrating the protein identifications from multiple LC-MS/MS analyses requires extensive specialized computational analysis that will vary depending upon proteome complexity. Further extensive critical evaluation and data refinement by the investigator generally is recommended prior to publication of results."
  3. Service Fee URL
  4. Related Resource
    Thermo Fisher Hybrid LTQ-OrbitrapXL™ mass spectrometer with online Eksigent® Nano-capillary HPLC
  5. Related Resource
    Applied Biosystems® 5500 Q TRAP® Mass Spectrometer with online Waters NanoACQuity® Nano-capillary HPLC
  6. Service Provided by
    Proteomics and Metabolomics Facility (Wistar)
  7. Website(s)
  8. Related Technique
    Protein identification
  9. Related Technique
    Liquid chromatography-tandem mass spectrometry
  10. Related Technique
    Mass spectrometry data analysis
  11. Related Technique
    Protein expression profiling
Provenance Metadata About This Resource Record
Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016