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About the Research Resource

The Proteomics Process

The Proteomics Facility processes biological materials to identify, and determine the quantities of, the proteins they contain. It uses mass spectrometry in combination with liquid chromatographic separation to identify characteristic peptide fragments that function as biomarkers for their parent proteins. A major challenge posed by proteomics research is managing the vast amounts of data produced. The facility has developed an automated data processing system to achieve high throughput and an integrated data management system that provides researchers with access to information at all levels of the process.

The following steps outline the process, which is also detailed in the interactive flowchart at left (click to view).

Step 1: The Process Flow

Biomaterial Preparation

  • Performed by the researcher before sample submission, or by researchers at the Proteomics Facility.
  • Organisms grown under different conditions (growth, environmental stresses, etc.).
  • Growth media might be labeled with stable isotopes.

Sample Preparation

  • Several biomaterials may be used in a given sample.
  • Proteins are purified, denatured, reduced and often alkylated, before addition of trypsin for digestion into peptides.
  • The digested peptides are purified before injection into the mass specrometer.

Mass Spectrometry

Aliquot drawn from sample and injected onto a capillary LC column coupled to either an ion trap mass spectrometer [tandem mass specrometry (MS/MS)] or a high mass accuracy FTICR-MS instrument to detect the species present.

Step 2: Tracking & Data Collection


The Proteomics Research Information Storage and Management (PRISM) is an information management system that assembles the data produced by multiple disparate mass spectrometers into information about the peptides and proteins that were present in biological samples. It is tightly integrated into the laboratory processes and instrumentation and highly automated in order to support high-throughput proteomics investigation while minimizing the time demand on the scientific and technical staff.

PRISM is divided into two major subsystems, the Data Management System (DMS) and the Mass Tag System (MTS). The two subsystems are composed of databases, web-based user interfaces, and autonomous programs (called "managers") that perform various automated processing tasks. The DMS is a Web-based subsystem of PRISM and acquires data from mass spectrometers, collects laboratory information, and tracks and controls the intermediate data processing. The MTS, also a Web-based subsystem of PRISM, is responsible for identifying potential mass and time tags from SEQUEST results and confirming and validating accurate mass and time tags using ICR-2LS peak results.

This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

Download document detailing PRISM (4/7/04)

DMS functions

  • Capture raw spectra files from mass spectrometers.
  • Process raw spectra files into analysis results files.
  • Store and track data files.
  • Collect and manage lab information (samples, experiments, protocols, etc.).
  • Allow users to locate and access data files.

MTS functions

  • Manage the lists of peptides identified in MS/MS data by analysis software (e.g. SEQUEST).
  • Compare the peptides with features identified in mass spectrometry data to generate lists of peptides and proteins observed for a set of analyses.
  • Allow users to browse and export the peak matching results.