The New Workhorses in Proteomics Research - Q-TOFs and Orbitraps

The New Workhorses in Proteomics Research - Q-TOFs and Orbitraps

Changes in the competitive and technological landscape of proteomics research can take a long time to take hold. Core instruments in translational research for biomarkers and drug targets, such as mass spectrometers (MS), may be replaced or upgraded in a laboratory only once every ten to fifteen years. Many proteomics core labs at universities and research centers still rely on manufacturer-discontinued MS systems, though reinforcements in the lab have been conspicuous in recent years. New MS technologies, representing upgrades both in performance and versatility, now challenge the traditional workhorse mass spectrometer of proteomics, the linear ion trap (LIT). Competing for share in the high-resolution MS market segment, hybrid time-of-flight (TOF) and Orbitrap instruments have become fixtures in proteomics research. The strength of these instrument types is in the production and conversion of richly complex discovery proteomics data into high-throughput targeted analyses needed to advance new drug targets and biomarkers.

Time-of-flight (TOF) mass spectrometry technology is integral to modern proteomics research with a long-held advantage in mass resolution over ion trap and triple quadrupole instruments, high mass range, and amenability to soft MALDI ionization. These characteristics suit the technology well to intact protein identification and characterization. An added quadrupole to a TOF analyzer allows for more diverse ionization and dissociation or fragmentation options; pure TOF or TOF/TOF is generally limited pulsed ionization such as MALDI. Resultant quadrupole-TOF (Q-TOF) instruments provide more controllable fragmentation for peptide sequencing and have acquisition speeds that unlock data-independent acquisition (DIA) methods such as SWATH (AB Sciex) and LC/MSE (Waters).

Q-TOF instruments represent nearly 20% of the installed mass spectrometer base in proteomics research - representing a significant increase from Kalorama Information’s previously estimated market share for the instrument of 10%. The fortunes of Q-TOF technology have risen with the development of DIA and labs’ need for a versatile workhorse instrument able to participate in proteomics workflows from global discovery to targeted analysis and quantintation.  Data-independent acquisition provides thorough, highly complex, post hoc searchable peptide maps; the method also allows researchers to perform targeted searches later at a workstation for peptides of interest and initial relative quantitation. Added scan information is provided by the ion mobility separation (IMS) capability of many Q-TOF instruments. The feature allows instruments to separate and differentiate ions by their drift time, which is a product of their cross section or structure. The high-resolution, accurate data generated by DIA can provide the basis for targeted quantitative analyses such as multiple reaction monitoring (MRM). One market leader for MS in proteomics research, AB Sciex, markets its Q-TOF for applications in biomarker verification on the basis of its MRM capability, instrument speed, and improved sensitivity.

Orbitrap mass spectrometry was rolled out roughly a decade ago by Thermo Electron (now part of Thermo Fisher Scientific) and has since earned broad acclaim by capturing the unparalleled resolution of Fourier transform (FT-ICR) MS systems within a lower footprint and at a lower price. Orbitraps use ion trapping with an electrical field, rather than a magnetic field (eliminating the need for a bulky, expensive magnet). Unique Orbitrap capabilities arise from its hybrid coupling with another mass analyzer, most often an ion trap or quadrupole. The instrument has had astonishing success in the proteomics research market space over the past 10 years - today Orbitraps represent over 25% of the installed MS base in proteomics labs.

Similar to TOF-based instruments, Orbitrap-based instruments have high mass range and an array of ionization and dissociation options (HCD, CID, ETD) needed to handle intact protein characterization. As a non-destructive mass analysis method, ion trapping in an Orbitrap also allows MSn or the repetition of fragmentation and mass analysis to provide more sequential information for peptides. Orbitraps offer researchers the capability to perform high-performance qualitative analyses needed to characterize drug targets and biomarker candidates. The high acquisition speed of hybrid Orbitrap instruments enables various acquisition and scanning modes including DIA and advanced data-dependent acquisition (DDA), the latter using parallel MSn acquisition in the LIT and full MS spectrum scans in the Orbitrap. Orbitraps also facilitate targeted quantitative analyses such as pseudo selected reaction monitoring (pSRM)/parallel reaction monitoring (PRM).

Orbitrap and Q-TOF mass spectrometry uniquely address the proteomics research market by combining high resolution (or a high level of performance in context to the discovery of biomarker and drug target candidates in complex samples) with the versatility to address experiments along the proteomics workflow from discovery to verification. Overall, Thermo Fisher’s Orbitraps have taken an upper hand on Q-TOF in the proteomics research market based upon recent placements.

Kalorama Information will release a new title in proteomics research this month, including the markets for mass spectrometry, liquid chromatography and electrophoresis instrumentation in translational research for the discovery and validation of protein biomarkers and drug targets.