rapifleX® MALDI PharmaPulse®

The rapifleX® MALDI PharmaPulse® accelerates the drug discovery process utilizing label-free mass spectrometry for uHTS.

High-Throughput Screening

Unique speed and specificity offered by label-free MALDI-TOF mass spectrometry

rapifleX® MALDI PharmaPulse®


rapifleX® MALDI PharmaPulse®

Less than a second per sample.
Maximum uptime in 24/7 operation and full automation.
Label-free mass spectrometry for lowest false discovery rates.
Enhancing performance for a wide range of screening applications.

rapifleX® MALDI PharmaPulse®

The all new rapifleX® MALDI Time-of-Flight mass spectrometer is the heart of the MALDI PharmaPulse®, it incorporates Brukers latest 10 kHz scanning laser technology and can read multiple samples per second. All components of the system work in concert for fully automatic HTS operation. The newly designed screening software suite supports HTS workflows and works in combination with a proprietary assay development module which empowers assay developer to accelerate label-free assay development for MALDI mass spectrometry. The latest ‚Synthesis Screening‘ software module of the rapifleX® MPP opens a new application space for e.g. monitoring of chemical reactions at high pace or analysis of binding assays at incomparable high throughput and specificity.

rapifleX® MALDI PharmaPulse®

rapifleX® MALDI PharmaPulse® (MPP) combs through large compound libraries of millions of substances

The use of mass spectrometry allows the measurement of unmodified substrates in primary screens to avoid false positives or false negatives, making confirmation screens redundant. The system is designed for fully automatic handling of 384 and 1536 sample plates to screen more than a million compounds in a week in support of drug discovery.

New standard for ultra-High-Throughput Screening Label-Free ‘Hit’ Identification

By combining the speed of Bruker’s patented smartbeam 3D laser technology with the direct-detection capability of mass spectrometry, the rapifleX® MPP delivers unprecedented screening capability for ultra high-throughput screening of biochemical and cellular assays. It allows you to screen through large and diverse compound libraries at a pace of over a million compounds a week, epitomizing the perfect balance of automation and miniaturization.

rapifleX MALDI PharmaPulse

Automated Sample Preparation for uHTS – with Courtesy of Analytik Jena (https://www.analytik-jena.com/industries-solutions/solutions/maldi-tof-ms/)

rapifleX MALDI PharmaPulse

rapifleX® MALDI PharmaPulse® integrated into an HighRes biosolutions (https://highresbio.com/) uHTS system at Pivot Park Screening Centre, Oss, Netherlands (https://www.ppscreeningcentre.com)

rapifleX MALDI PharmaPulse

Fully automatic exchange of 1536 MALDI Plates at Pivot Park Screening Centre.

We are very proud to be the first CRO having integrated Bruker’s rapifleX® mass spectrometer as read-out technology into our uHTS system. Mass spectrometry allows the direct measurement of label-free assays and reduces the number of false positives and false negatives in our screen, which makes the hit to lead phase of our drug discovery program more time and cost effective.

Steven van Helden, PhD, Chief Technology Officer at Pivot Park Screening Centre, Oss, Netherlands
rapifleX® MALDI PharmaPulse®

Robustness to analyze 2-3 million samples without intervention

  • New source and ion optical design
  • No source/ion optic cleaning even within primary screens
  • Easy and fast cleaning if required

Compatible with CyBio®-Well vario with 384 or 1536 channel simultaneous pipettor for high precision and ultra-fast sample plate preparation.

Single digit cost per sample

  • No LC solvents, no waste, no labeling
  • 0.025 to 1 μL sample volume
  • Low cost disposable sample plates

Fully automatic 1536 sample plate change

  • New ultra-fast autoloader seamlessly integrable with common robot systems
  • Rugged design tailored for uHTS operation

New disposable MALDI HTS sample plates

  • Fulfills all requirements for reliable MALDI ionization
  • Suitable for 384, 1536, 3072 or 6144 geometries

rapifleX MALDI PharmaPulse

CyBio Well vario for uHTS– with Courtesy of Analytik Jena (https://www.analytik-jena.com/industries-solutions/solutions/maldi-tof-ms/technology-maldi-sample-preparation/)
rapifleX® MALDI PharmaPulse®

The rapifleX® MPP assists assay development, accelerates HTS and uHTS hit finding, and supports hit confirmation and lead optimization

The MPP system allows for the measurement of unmodified substrates in primary biochemical screens, and offers several advantages:

  • It effectively eliminates confirmatory assays typically required of traditional fluorescence-based screening techniques
  • Saves costs for developing specific fluorescence probes or antibodies
  • Doesn’t require expensive solvents or consumables for continuous operation
  • Allows sample volume down to 25 nL

PharmaPulse® Solution

The PharmaPulse® Solution is based on Bruker´s advanced MALDI-TOF technology and on a dedicated software package. Ease of use and time to result were key drivers during the development resulting in an intuitive but yet powerful software solution to measure and analyze millions of samples in full automation. Two workflows guide the user from adapting an assay to MALDI mass spectrometry to readily exported results for further analysis in LIMS systems.

rapifleX® MALDI PharmaPulse®

New software module supports synthesis screening and binding assays

In biochemical screening experiments, the rapifleX® MPP determines the rate of conversion in a biochemical assay when performed in the presence of potential inhibitors. In such a screen, a distinct MS peak ratio comparing product and substrate intensities is monitored throughout large numbers of sample spots, where each spot represents the same biochemical conversion reaction, but measures the effectiveness of a different inhibitor molecule.

In addition to this screening functionality, the new MPP software module supports “Synthesis Screening”, a methodology that requires more flexibility with regard to m/z values to be targeted by MALDI-TOF MS. Here, m/z values of interest may vary from spot to spot as each sample may represent a different chemical reaction. Accordingly, the new MPP “Synthesis Screening” software module allows scientists to screen for a large number of compounds per individual sample spot. This new MALDI-TOF based high-throughput analysis workflow could, therefore, enable highly time-efficient surveying of chemical reactivity landscapes at previously unseen mapping depth.

rapifleX MALDI PharmaPulse Lead Generation Support

rapifleX® MPP in support of lead optimization
rapifleX® MALDI PharmaPulse®

rapifleX® MPP – the universal tool for drug discovery

rapifleX MALDI PharmaPulse

Full library screens

The rapifleX® MPP is the only mass spectrometer for large primary screens of millions of compounds with high diversity. Full automation supports screening of more than one million compounds per week, avoiding time-consuming confirmatory screens. [1]


rapifleX MALDI PharmaPulse

MALDI PharmaPulse® assay development module to support assay development for HTS

Focused library screens

The quality of data obtained with rapifleX® MPP meets the requirements of secondary and confirmatory screens and makes it the ideal detector for focused library screens, such as the identification of kinase inhibitors of a target protein from a smaller subset of the library. [2]

Fragment screening

The mass range and resolution accessible by MALDI-TOF mass spectrometry enables screening of fragments and other low molecular weight compounds. [3]


[1] Winter, M.; Ries, R.; Kleiner, C.; Bischoff, D.; Luippold, A. H.; Bretschneider, T.; Buettner, F. H.; Automated MALDI Target Preparation Concept: Providing Ultra-High-Throughput Mass Spectrometry–Based Screening for Drug Discovery. SLAS Technology 2018, https://doi.org/10.1177/2472630318791981
[2] Beeman, K.; Baumgartner, J.; Laubenheimer, M.; Hergesell, K.; Hoffmann, M.; Pehl, U.; Fischer, F.; Pieck, J.C.; Integration of an In Situ MALDI-Based High-Throughput Screening Process: A Case Study with Receptor Tyrosine Kinase c-MET. SLAS Disc. 2017, 22, 1203–1210.
[3] VanderPorten, E.; Scholle, M.; Sherrill, J.; et al. Identification of Small-Molecule Noncovalent Binders Utilizing SAMDI Technology. SLAS Discov. 2017, 22(10):1211-1217.


rapifleX® MALDI PharmaPulse®

Target evaluation and hit confirmation

Thorough understanding of enzyme biochemistry and kinetics is essential to develop and validate robust HTS assays. rapiflex® MPP assists assay development and hit confirmation with linearity tests, substrate selection, Ki measurements and IC50 determination.

rapifleX MALDI PharmaPulse

Linearity test: Enzyme titration curve based on 3 technical replicates indicates high level of reproducibility provided by the MALDI-TOF based assay method.

rapifleX MALDI PharmaPulse

Time course studies performed for two different enzymes (kinases) applied at high and low concentration. Resulting Z´of >0.9 indicates outstanding robustness of the MALDI-TOF based assay. Validated by radiometric measurements (33P).

rapifleX MALDI PharmaPulse

MALDI PharmaPulse® software supporting easy setup of screening experiments. Color coded spots indicate QC positions for Z´ calculation.


rapifleX MALDI PharmaPulse

MALDI PharmaPulse® software interface enabling instant display of screening results
rapifleX® MALDI PharmaPulse®

IC50 determination of inhibitors

Half-maximal inhibitor concentration (IC50) is a key parameter in the drug discovery process. MALDI PharmaPulse® software supports assay development by featuring a dedicated method development module. Optimal assay conditions obtained using the method development module are applied during MALDI-TOF screening, for example aiming for IC50 determination, which is set up and executed in the software´s dedicated screening module.

rapifleX MALDI PharmaPulse

Comparison of MALDI-TOF-based IC50 data with values obtained from AlphaScreen technology reveals high level of consistency (Winter, M.; Bretschneider, T.; Kleiner, C.; Ries, R.;Hehn, J.P.; Redemann, N.; Luippold, A. H.; Bischoff, D.; Büttner, F. H.; Establishing MALDI-TOF as Versatile Drug Discovery Readout to Dissect the PTP1B Enzymatic Reaction. SLAS Discov. 2018, 10, 1-13.)

rapifleX MALDI PharmaPulse

Dose-response curves obtained from rapifleX® MPP measurements. IC50 curves are shown for selected enzymes (kinases): 50 μM substrate, 45 μM ATP and 3 nM enzyme. Validated by radiometric measurements (33P).
rapifleX® MALDI PharmaPulse®

rapifleX® MPP – for primary screening

Drug discovery workflow with rapifleX MALDI PharmaPulse®


A million samples per week with rapifleX® MALDI PharmaPulse®

The new rapifleX® MPP is the result of Bruker’s innovative development of MALDI mass spectrometers. It reflects our passion for and knowledge about this technology and its unique applications. The time-of-flight mass spectrometer (TOF MS) of the rapifleX® MALDI PharmaPulse® monitors up to 30 masses in HTS mode: from small molecules to large proteins. The improved resolution and sensitivity of the rapifleX® TOF MS allows e.g. the monitoring of acetylcholine (ACh) and choline to identify acetylcholinesterase (AChE) inhibitors out of millions of substances. An ingenious detector design delivers significantly improved signal to noise ratios for enhanced sensitivity across the mass range. A completely new HTS software suite supports easy set-up of HTS screens, and the proprietary assay development module ensures fast adaption of label-free assays for MALDI mass spectrometry.

Automation of rapifleX® MALDI PharmaPulse®

The rapifleX® MALDI PharmaPulse® is designed to seamlessly integrate with laboratory automation systems to perform fully automatic screening campaigns. The MALDI PharmaPulse® software solution offers an open interface to control parts of its operation from external scheduling software (e.g. Analytik Jena lab automation, HighRes Biosolutions, Beckman Coulter, Thermo Scientific automation). The new high-speed autoloader of the rapifleX® MPP works hand in hand with robot systems for quick loading and unloading of sample plates.

Correlation between MALDI Mass Spectrometry with SPE Mass Spectrometry

Correlation between MALDI mass spectrometry (1536 plate geometry) with SPE mass spectrometry (384 plate geometry). Haslam, C. et al., The Evolution of MALDI-TOF Mass Spectrometry toward Ultra-High-Throughput Screening: 1536-Well Format and Beyond. J. Biomol. Screen. 2015, 1-11.