Quantitative Proteomics to Label or not to Label

To label or not to label?

Qualitative proteomics can compare relative quantities of individual proteins in complex samples using a label-free approach or incorporate the use of protein or peptide labels.Workflow for protein identification.Proteins are extracted and can be fractionaled,enriched or separated on a gel followed by digestion with protease into small peptides between 8 and 30 aminoacids. These peptides can first be enriched or fractionaled followed by a clean-up and then separated using chromatography and detected by mass spectrometry and fragmented. The data is then analyzed using Peaks 10.0 software and compared to protein databases which leads to protein identification.

Discovery-based Quantitative MS methods

Quantitative Proteomics to Label or not to Label

Targeted Quantitative Proteomics MS Methods

MSF LFQ Service: Requirements and Deliverables

Label-free quantitation (LFQ): Normalization is completed based on overall sample intensity (i.e., total ion chromatogram), or an internal standard (spiked-in or “housekeeping” proteins).

Label-based quantitation: Proteins or peptides are labelled to allow for multiplexing and more precise relative quantitation between samples. Instrument time and technical variation can be reduced (vs. LFQ), but reagent costs are higher.

TMT labelling