Mass Spectrometry-Based Differential Proteomics
Mass spectrometry-based differential proteomics is a comprehensive analysis of protein expression that involves comparing distinct proteomes, such as cells, tissues or cell lines that are normal, diseased or treated.
This type of analysis works best for defining differences between groups or treatments and for the initial "discovery" of potential biomarkers. For this service, the Proteomics Core currently employs the label-free approach and the stable isotope labeling by amino acids in cell culture (SILAC) approach.
The label-free approach uses one sample per gel lane and works on any type of material — assuming sufficient protein concentrations — from which proteins can be extracted.
The SILAC approach, most commonly done with cell lines, uses labeled media to metabolically incorporate an isotopic-labeled amino acid — lysine, arginine or both — into all proteins within the cell culture. Proteins from the SILAC culture are equally mixed with proteins from a corresponding unlabeled culture, with unlabeled-to-labeled protein abundance reported.
Prospective users should contact the Proteomics Core to obtain a project request form. The completed form will be reviewed by core staff and a follow-up meeting will be scheduled.
Before project approval, it is important to ensure that everyone involved has a complete and clear understanding of the project. The core also encourages users to consult with a biostatistician for guidance on both study design and data analysis.
The cost of a differential proteomics project can vary greatly depending on sample size, number of agreed-upon gel sections and analysis difficulty. A cost estimate is provided to clients prior to starting a project.
Read more about the label-free and SILAC approaches:
For more information or to initiate a service or project request, email the Proteomics Core.
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