AB SCIEX QTRAP 5500 Hybrid Triple Quadrupole Linear Ion Trap Mass Spectrometer with Shimadzu Prominence UFLC XR System

Overview

The AB SCIEX QTRAP 5500 is a hybrid triple quadrupole–linear ion trap mass spectrometer engineered for high-sensitivity quantitative analysis and structural characterization in complex biological and environmental matrices. Unlike conventional triple quadrupole platforms, the QTRAP 5500 integrates a linear ion trap (LIT) with triple quadrupole architecture—enabling both high-efficiency multiple reaction monitoring (MRM) quantification and information-rich MSⁿ experiments (including MS³) in a single acquisition cycle. Its core operational principle leverages radiofrequency (RF) and direct current (DC) fields in Q0, Q1, Q2, and the LIT to perform precursor selection, collision-induced dissociation (CID), and sequential ion trapping/fragmentation. This dual-capability design supports rigorous regulatory workflows in clinical research, pharmaceutical development, food safety, and environmental monitoring—particularly where orthogonal confirmation (e.g., MRM + neutral loss or precursor ion scanning) and retrospective data mining are required.

Key Features

• Hybrid architecture combining triple quadrupole precision with linear ion trap sensitivity and MSⁿ flexibility
• AcQuRate™ pulse-counting detector delivering high dynamic range and low detection limits across wide concentration spans
• Turbo V™ source platform supporting electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), and dual-mode ionization (DuoSpray™) without hardware reconfiguration
• TripleTrap™ scan mode enabling simultaneous MRM quantification and triggered MS/MS identification within one duty cycle
• Enhanced pMRM (predicted MRM) method generation for rapid assay development in metabolite profiling and biomarker verification
• Integrated SelexION™ differential mobility spectrometry option (hardware-ready) for gas-phase ion mobility separation prior to mass analysis
• Robust vacuum system including integrated low-vacuum pump and turbomolecular pumping stages optimized for continuous LC-MS operation

Sample Compatibility & Compliance

The system is validated for use with liquid chromatography interfaces—including Shimadzu Prominence UFLC XR modules (LC-20AD XR pump, SIL-20AC XR autosampler, CTO-20AC column oven, DGU-20A3R degasser, CBM-20A system controller)—ensuring stable gradient delivery at flow rates from 5 µL/min to 2 mL/min. It accommodates reversed-phase, HILIC, ion-exchange, and SEC separations with compatible mobile phase chemistries (e.g., aqueous/organic gradients with volatile buffers). All instrument control and data handling comply with analytical data integrity requirements: Analyst® software provides full 21 CFR Part 11 functionality—including electronic signatures, role-based access control, and immutable audit trails. The system meets ISO/IEC 17025 documentation standards for calibration, performance verification, and maintenance records. Routine qualification includes mass accuracy verification (< 0.1 Da at m/z 556.277), resolution assessment (unit resolution at 0.7 Da FWHM), and MRM sensitivity validation (sub-femtogram on-column LOD for reserpine).

Software & Data Management

Data acquisition and processing are managed through SCIEX’s Analyst® 1.7.2 platform—certified for regulated environments and fully compatible with Windows 10/11 LTSB editions. Analyst supports method templating, automated calibration, real-time peak integration, and batch processing with customizable reporting templates. Complementary applications include:

• MultiQuant™ v3.0.3 for high-throughput targeted quantitation with internal standard normalization and matrix effect correction
• LightSight™ v2.1 for untargeted metabolite identification using retention time alignment, isotopic pattern recognition, and in silico fragmentation prediction
• MRMPilot™ for rapid MRM transition optimization and scheduled method generation without synthetic standards
• Cliquid™ v2.1 for comprehensive LC-MS/MS workflow automation in food residue and environmental contaminant screening

All software packages operate under centralized license management and support raw data export in open formats (mzML, mzXML) for third-party reprocessing.

Applications

The QTRAP 5500 excels in multi-tiered analytical strategies requiring both quantitative rigor and qualitative depth. Key application domains include:

• Pharmaceutical ADME studies: Quantitative analysis of drug candidates and metabolites in plasma, urine, and tissue homogenates with confirmatory MS³ spectra
• Biomarker verification: Targeted SRM/MRM assays for candidate proteins/peptides in discovery-to-validation pipelines, accelerated via MIDAS™ workflows
• Food safety: Multi-residue pesticide screening using neutral loss scanning (e.g., phosphorothioate cleavage at m/z 97) coupled with MRM confirmation
• Clinical toxicology: Simultaneous quantification and structural confirmation of opioids, benzodiazepines, and novel psychoactive substances in forensic specimens
• Environmental analysis: Trace-level detection of perfluoroalkyl substances (PFAS), brominated flame retardants, and endocrine disruptors in water and soil extracts

FAQ

Is this unit refurbished or used—and what verification has been performed?
This is a pre-owned QTRAP 5500 system with documented 4-year operational history. It underwent full functional testing at SpectraLab Scientific, including vacuum integrity checks, mass calibration stability over 24 h, detector linearity assessment (1–1000 pg/µL reserpine), and LC-MS interface synchronization validation.
Does the system include original manufacturer documentation and service history?
Yes—complete set of SCIEX factory manuals (hardware, software, safety), Shimadzu UFLC XR operation guides, and a verified maintenance log covering all major service events during prior ownership.
Can the system be upgraded to support newer software versions or optional hardware modules?
The QTRAP 5500 firmware supports Analyst® v1.7.2 and later; upgrade paths to Analyst® v1.8+ require SCIEX-certified service engineer deployment. SelexION™ and NanoSpray III™ modules are field-installable if not already present.
What level of technical support is included post-purchase?
Buyers receive 6 months of remote diagnostics and method troubleshooting support from certified SCIEX application scientists, plus priority access to firmware patches and security updates distributed via SCIEX Connect.
Are consumables and spare parts available through your inventory?
We maintain stock of critical spares—including Turbo V source components, LIT lens assemblies, detector replacement kits, and Shimadzu LC fluidic seals—ensuring minimal downtime during routine maintenance cycles.