Stable isotope labeling with amino acids in cell culture (SILAC) is a powerful and widely used method for identifying and quantifying relative changes in complex protein samples. It can be applied to complex biomarker discovery and systems biology studies as well as to isolated proteins and protein complexes.
SILAC involves the labeling of protein samples in vivo by substituting an isotopically heavy form of an amino acid for the naturally occurring light form. Because labeled and unlabeled samples are combined during the initial steps of sample preparation, SILAC minimizes the quantitative error inherent in handling separate samples in parallel. In addition, the mixing of samples permits a variety of enrichment techniques, including immunoprecipitation. These techniques can improve the detection of abundance changes for both low-abundance proteins and posttranslational modifications such as phosphorylation or glycosylation.
Reverse phase separation on Thermo Scientific™ low flow systems can be seamlessly integrated into label-free quantitative workflows and combined with Thermo Scientific Orbitrap mass spectrometers. The Thermo Scientific Vanquish Neo UHPLC System is the system of choice for label-free quantitative proteomics. The Vanquish Neo UHPLC system combines an unrivaled degree of innovation to deliver 24/7 reproducible separations of complex mixtures at maximum performance for a variety of high-sensitivity LC-MS workflows.
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Precursor ion-based quantitation techniques like SILAC require mass spectrometers that provide HRAM without compromising scan speed and spectral quality. The Thermo Scientific Orbitrap Exploris™ 480 mass spectrometer combines an HRAM, ultra-high-field Orbitrap analyzer with high performance quadrupole precursor ion selection to deliver unsurpassed speed while maintaining the sensitivity needed for SILAC experiments. System resolutions of up to 480,000 enable discrimination of co-eluting isobaric ions that can interfere with accurate quantitation.
In SILAC, proteins are identified using accurate-mass precursor information combined with HCD, CID, ETD, and/or EThcD fragmentation data. The relative peak intensities of multiple distinct peptides derived from each protein are averaged to determine their overall relative abundance (and fold change) between experimental and control conditions. Peptide SILAC ratios can be calculated using the Precursor Ions Quantifier node and Quantification Method included within the Thermo Scientific Proteome Discoverer Software. Custom quantification methods can also created by editing the SILAC duplex and triplex methods.
Learn how to prepare and metabolically label cultured cells using standard heavy or NeuCode amino acids for SILAC applications using mass spectrometry.