Explore the proteome in greater depth
As a cost-effective alternative to isotopic labeling approaches, label-free quantitation (LFQ) 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).
 Orbitrap Eclipse Tribrid Mass Spectrometer |  Orbitrap Exploris 480 Mass Spectrometer |  Orbitrap Exploris 240 Mass Spectrometer | |
| Advantages | Obtain maximum insights on your most complex molecules and biological systems, from whole proteome profiling and quantitation, structural characterization to multiplexed single-cell proteomics. With new innovations that deliver the ultimate flexibility in experimental scope, it accelerates your path to new, impactful results, so you can drive your science beyond today’s discovery. | Obtain maximum quantitative insights from untargeted proteome profiles to targeted proteomics experiments with industry leading single-cell sensitivity and extraordinary accuracy, precision and simplicity. With curated workflows that deliver greater usability, it accelerates your path to large-scale studies, delivering proven high data quality and time savings, so you can go beyond faster to actionable outcomes. | Expand your capabilities from small- to large-scale studies across a variety of applications from protein identification, quantitation, to multiplexing proteomics studies. With optimized methods, it delivers a fast turnaround of sample to results with operational simplicity. Best-in-class performance, all within a compact footprint, so you can go beyond with everyday versatility. |
| Resolving Power | 7,500-500,000 FWHM at m/z 200 (1M option) | 480,000 at m/z 195 | Up to 240,000 FWHM at m/z 200 |
| Scan Speed | Up to 40Hz | ||
| Mass Range | 50 to 6,000 (Up to 8,000 with HMRn) | 40 to 6,000 m/z (up to 8,000 m/z with the BioPharma option) | |
| Dynamic Range | >5000 with a single OTMS spectrum | >5000:1 | |
| Mass Accuracy | Internal <1 ppm RMS; External: <3 ppm RMS | ||
Obtain broad peptide coverage
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 system offers operational simplicity and high performance, while the UltiMate 3000 RSLCnano system features versatility and superior precision.
The Thermo Scientific FAIMS Pro Duo interface enhances precursor selectivity, improving qualitative and quantitative results for most peptide and protein applications while reducing time-consuming sample preparation steps. The FAIMS Pro Duo interface increases analytical performance through gas-phase fractionation and selective enhancement of peptidic compounds, reducing the complexity of the MS spectra, and improving the analyte signal-noise ratio. The end result is greater proteome coverage, enhanced sensitivity and more accurate quantitation.
Software for label-free quantitation
Discover novel protein biomarkers
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.
Label-free quantitation workflow
Two different LFQ approaches to identification data acquisition
In a LFQ DDA approach, the ions for a given m/z range are individually isolated and fragmented. The quantitation involves extracting peptide chromatograms (MS
In traditional data-dependent workflows, consistent precursor and thereby protein quantitation can be challenging to achieve due to the stochastic sampling nature of the mass spectrometer. Innovations in software algorithms now extract LC-MS peaks in the raw data files and map them to identified spectra, detecting these features across LC-MS data files using retention-time alignment and feature linking, minimizing "missing data points" and maximizing quantitative insights.
In a LFQ DIA approach, a precursor mass range is selected and then divided into a series of relatively wide isolation windows: for example, 25 m/z each. Chimeric MS/MS data is acquired from all detected precursor ions in the first isolation window and then repeated for each consecutive, adjacent isolation window until the entire precursor mass range is covered. MS/MS spectral libraries are used to identify peptides of interest from the acquired data.
DIA significantly increases coverage and reproducibility by acquiring MS/MS data from all detected precursor ions; it also makes retrospective data analysis possible. LFQ DIA involves extracting peptide chromatograms (MS
