During label-free relative quantitation workflows, digested peptides are separated by LC prior to MS. RP separation on Thermo Scientific low-flow systems integrates well with label-free quantitation workflows and combines seamlessly with Thermo Scientific Orbitrap mass spectrometers. The Thermo Scientific EASY-nLC 1200 System and UltiMate 3000 RSLCnano System are the LC systems of choice; the EASY-nLC 1200 offers operational simplicity and high performance, while the UltiMate 3000 RSLCnano features versatility and superior precision.
Explore the proteome in greater depth
As a cost-effective alternative to isotopic labeling approaches, label-free analysis enables relative quantitation of protein samples from any origin. Samples are tested individually using advanced software with chromatographic features that align the various runs. The biggest advantage of this approach is that the number of sample comparisons is not limited. Additionally, peptide identification can be performed with any fragmentation method (CID, ETD, EThcD, and/or HCD).
The Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer has the highest resolving power (up to 500,000 at m/z 200) of all available Orbitrap technology, enabling accurate label-free precursor-based quantitation without compromising fast data acquisition, sensitive precursor peak detection, and discrimination between co-eluting isobaric ions that can skew results. With the Orbitrap Fusion Lumos, peptide identification is not restricted by fragmentation type; CID, ETD, EThcD and/or HCD can be applied, offering peptide coverage overlap that results in better identification.
The Thermo Scientific Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer combines HRAM ultra-high-field Orbitrap analysis with high-performance quadrupole precursor ion selection to deliver the speed and sensitivity needed for label-free experiments. A resolution of up to 240,000 enables discrimination not only between co-eluting isobaric ions that can interfere with accurate quantitation, but also between peptide signals and noise for low abundance peptides. High scan speed (17,500 @ m/z 200) reduces analysis time spent during label-free relative quantitation.
Thermo Scientific Proteome Discoverer Software, with its new label-free quantitation node, provides an easy-to-use automated solution for evaluating large amounts of LC-MS data generated by label-free experiments. The label-free quantitation node also features a full suite of quantitative capabilities previously only available for isotopically labeled workflows. The combination of label-free quantification workflows with the scaling, normalization, and study management features of Proteome Discoverer software offers a powerful means for analyzing highly complex data.