Shotgun qunatitation

Quantify more proteins from smaller amounts within larger sample cohorts

Developed to meet the demands of sample limitations and throughput

Quantitative workflows are one of the cornerstones of quantitative proteomics. It is essential to the proper understanding of biological assemblies or for biomarker panels discovery experiments. The unique combination of speed, selectivity, sensitivity and robustness delivered by Bruker’s proteomics solutions allow users to obtain reliable and quantitative information for more proteins while working from limited amount and/or short gradient times.

PASEF-LFQ: get the best from two worlds

In non-targeted protein quantitation are the cycle time (defining the chromatographic peak resolution), the uniqueness of the ion(s) chosen to evaluate a peptide amount (selectivity) and the system sensitivity (quantitation of low-abundance compounds). MS-based approaches provide comprehensive quantitative results but  overlapping ions reduce the selectivity of these workflows. MS/MS (DIA) based quantitation provides excellent selectivity at the cost of reduced sensitivity.
TIMS-PASEF based Label-Free Quantitation (PASEF-LFQ) combines the best of both approaches. TIMS provides both an additional dimension of separation, greatly increasing selectivity, while the preconcentration effect of the TIMS cell provides greater sensitivity. The PASEF cycle time is compatible with narrow nano-uHPLC peaks while its speed (>100 Hz MS/MS) greatly improves the reproducibility of parent ion selection compared to traditional DDA approaches, while sensitivity is higher than with traditional DIA approaches.

Label-free quantitation
Label-free quantification outcome of a three-proteome mixture. The total protein load is 150ng, separated with a 90min gradient. MaxQuant is used for processing.

Stepping into the future: introducing diaPASEF

In diaPASEF, the DIA acquisition is multidimensional leveraging mobility and mass to charge (m/z).  The correlation between molecular mass and mobility is advantageous in selecting the densest region of target peptides. The extra dimension results in increased selectivity, increased sensitivity and shorter cycle times. for more information read our LC-MS157 application note

Enter the 4th dimension

Reproducible Collisional Cross Section determination (mobility) enables 4D- Where Match Between Runs (MBR) maximizes the number of proteins quantified from Label Free Quantification experiments while maintaining the highest level of confidence even while using challenging short gradients. The 4D MBR approach is supported by PeaksX™and MaxQuant. Read our corresponding LC-MS154 application note

Proteomics pic
Label-free quantification outcome of a three-proteome mixture.The total protein load is 150ng, separated with a 60min gradient. PeaksX is used for processing, Perseus for display.
PASEF
Powered by PASEF

Get ready for high-throughput clinical research

The unique ability of the timsTOF Pro to deliver sustainable performance over hundreds of injections combined with the enhanced LFQ performance make the system an ideal platform for high-throughput clinical research.
Data processing is key for protein quantitation and the PASEF-LFQ approach is already supported by some of the most powerful software suites.

PEAKS data processing

PEAKS Studio is powered by high performance feature extraction from PASEF data files, obtaining high quality results in Peptide-based protein identification, label-free quantitation and DeNovo sequencing. Multiple sophisticated visualization and exporting capacities allow users  to review, share or refine results from multiple proteomics analyses.

MaxQuant data processing

MaxQuant, the popular, powerful, open-source software fully supports PASEF-LFQ data enabling advanced quantitation, visualization and reporting.

clinical proteomics
EvosepOne/timsTOF Pro coupling for clinical proteomics: reproducibility and performance level of100 consecutive injections of 50 ng of an Hela Cell digest separated with a 6 min gradient (200 samples/day method. Left: intensities correlation for the 100 runs. Middle: Illustration of LFQ outcome. Right: reproducible measurement of species with various concentration levels.

Increased advanced software support

An increasing number of advanced proteomics processing Software packages now directly read the timsTOF Pro raw data: this includes Skyline™, GeneData™, the complete proteins metrics suite, Mascot Distiller™.

For Research Use Only. Not for Use in Clinical Diagnostic Procedures.