Proudly serving laboratories worldwide since 1979 CALL for Refurbished & Certified Lab Equipment

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1 Proudly serving laboratories worldwide since 1979 CALL for Refurbished & Certified Lab Equipment Applied Biosystems QStar Pulsar i Features of the API QSTAR Pulsar i The API QSTAR Pulsar i Hybrid LC/MS/MS Quadrupole TOF system delivers sensitivity, selectivity, and reproducibility while providing unrivaled performance for the following applications: Characterization of proteins and peptides in the life sciences. Analysis of drug metabolite information from small quantities of metabolites. Identification of products, by-products, and contaminants in combinatorial chemistry. Features of the API QSTAR Pulsar i mass spectrometer include: Curtain gas technology prevents any impurities from getting between the analyzer and your sample, ensuring minimal operator intervention. New ion optics routinely ensure the lowest limits of detection in all biological matrices. Trouble-free, continuous operation with no daily cleaning or calibration required to maintain performance. omaldi can be adapted for high-throughput and auto-sampling. Rugged ionization sources allow for maximum performance across the widest range of flow rates and mobile phase composition. Precision-machined, gold-plated ceramic quadrupole rods with low thermal expansion coefficient. Single-phase power and air-cooled ceramic bearing turbo pumps reduce operating costs year after year. Accommodation of multiple sources including the orthogonal Matrix Assisted Laser Desorption Ionization (MALDI) source which is easily installed by removing the interface. (For more information, see MALDI Source on page 15.) Mass Spectrometry Techniques The API QSTAR Pulsar i mass spectrometer is a versatile and reliable system for performing liquid chromatography mass spectrometry (LC/MS) analysis on liquid sample streams to identify, quantify, and examine polar compounds. API QSTAR Pulsar i uses the following mass spectrometry techniques to analyze samples: Two modes of single mass spectrometry (MS): Quadrupole-based single mass spectrometry (for Q1 calibration only) Time of flight-based single mass spectrometry Two modes of tandem mass spectrometry (MS/MS):

2 Product ion mass spectrometry Precursor ion mass spectrometry Single Mass Spectrometry (MS) Single mass spectrometry (MS) is used to analyze charged molecules in order to determine the molecular weight and amount of detected ions. Individual ions detected by MS can indicate the presence of a target analyte. Quadrupole-Based Single Mass Spectrometry (Calibration Only) In a quadrupole-based single mass spectrometry (Q1 MS) scan, API QSTAR Pulsar i functions as a traditional quadrupole mass spectrometer. In this mode, API QSTAR Pulsar i generates single mass spectrometric information using the first quadrupole (Q1) section of the instrument. Time of Flight-Based Single Mass Spectrometry In a time of flight-based single mass spectrometry (TOF MS) scan, API QSTAR Pulsar i generates mass spectrometric information by pulsing ions into a flight tube and recording their precise arrival time at the detector. Ions with a greater mass-to-charge ratio take longer to travel the flight tube. Tandem Mass Spectrometry (MS/MS) The technique of MS/MS is well suited to mixture analysis because the characteristic product ion spectra can be obtained for each component in a mixture without interference from the other components, assuming that the product ions have a unique m/z ratio. You can use MS/MS for targeted analysis by monitoring specific precursor/ product ions while the sample is eluting. This type of analysis is more specific than single MS, which only discriminates on the basis of the mass-to-charge ratio. Product Ion Mass Spectrometry In a product ion scan, Q1 selects a precursor ion which fragments in Q2 (a collision cell), generating product ions which are detected in the time of flight section. Product ions can provide information on the molecular structure of the original (precursor) ions. Precursor Ion Mass Spectrometry In a precursor ion scan, API QSTAR Pulsar i detects precursor ions which generate a specific product ion. The instrument uses Q1 in mass resolving mode to scan over the mass range of interest, while the TOF section records product ion spectra for each precursor ion. The Q1 mass spectrum shows all precursor ions which produce the product ion of interest. Hardware Overview The API QSTAR Pulsar i mass spectrometer is a complex instrument with many different systems all working together to analyze the composition of your samples. This chapter includes information on the various systems inside API QSTAR Pulsar i. Sample Introduction System Vacuum System Ion Path Chamber

3 Sample Introduction System The sample introduction system manages the introduction of a sample into the API QSTAR Pulsar i instrument and the conversion of the sample into ions which you can analyze in the quadrupole and time of flight (TOF) sections of the instrument. The sample introduction system uses three methods of sample ionization: Atmospheric Pressure Chemical Ionization (APCI), IonSpray, and Matrix Assisted Laser Desorption Ionization (MALDI). The API QSTAR Pulsar i sample introduction system offers the following choice of components: LC Pump or Integrated Syringe Pump (standard) IonSpray Sources (optional) omaldi Source (optional) Ion Source Interlocks Vacuum Interface LC Pump or Integrated Syringe Pump The liquid sample stream is pumped to the ion source by a liquid chromatography (LC) pump or a syringe pump, with flow rates determined by the inlet requirements or dictated by the chromatography or by the volume of sample available. If introduced by an LC pump, the sample may be injected through a loop injector with a separation column (LC) or without (flow injection analysis or FIA). It is important that you apply the appropriate analytical procedures and practices to minimize dead volumes. Proper procedures help ensure chromatographic integrity and analytical reproducibility. It is also important that samples are sufficiently pre-filtered so that the capillary tubing in the inlets is not blocked by particles or precipitated samples or salts. IonSpray Sources The IonSpray sources generate gas phase ions which are representative of the molecular composition of the sample with minimal fragmentation. The ionspray sources include the following benefits: Allows direct observation of the inlet through plexiglass windows. Provides convenient access to the vacuum interface (quickly and easily removed without tools). Includes the following external connections: High voltage connection Gas 1 and Gas 2 connections Collision (CAD) gas connection LC inlet and splitter outlet connection Samples are normally introduced to the API QSTAR Pulsar i instrument in a flowing liquid stream when using LC sources. All five LC ion sources operate at atmospheric pressure to produce gas phase ions. These gas phase ions are subjected to mass spectrometric analysis by the instrument. The API QSTAR Pulsar i instrument uses the following LC ion sources:

4 IonSpray converts liquid phase ions into gas phase ions Samples which are introduced through the IonSpray probe are nebulized by a jet of gas and sprayed through a high-voltage sprayer, creating a mist of small highly-charged droplets. The ions in the droplets evaporate from the droplet surface in the ion source by a process termed ion evaporation. TurboIonSpray variant of the IonSpray source The TurboIonSpray uses an IonSpray inlet with an additional probe blowing hot (for example, 400 C) dry gas orthogonally to the plume of charged droplets from the sprayer. The heated gas increases the efficiency of the ion evaporation resulting in increased sensitivity (i.e., produces higher ion intensities) and the ability to handle higher liquid sample flow rates. MicroIonSpray ions in solution are emitted into the gas phase without the application of heat MicroIonSpray (µionspray) extends the capabilities of the conventional IonSpray source by greatly reducing the sample introduction flow rates, thus providing long analysis times for very small sample volumes. MicroIonSpray is based on NanoSpray technology developed by Mann and Wilm at the EMBL in Germany, but the process does not require special conductive coatings. Heated Nebulizer produces ions by nebulizing the liquid sample in a heated tube which causes the finely dispersed sample drops to vaporize. This process leaves the molecular constituents of the sample intact. These molecules are ionized via the process of Atmospheric Pressure Chemical Ionization (APCI), induced by a corona discharge needle, as they pass through the ion source chamber into the interface region. NanoSpray allows extremely low flow rates (20-40 nl/min) and efficient sample utilization. For more information about NanoSpray contact Protana ( omaldi Source The API QSTAR Pulsar i will accommodate an orthogonal Matrix Assisted Laser Desorption Ionization (omaldi) source. When the API QSTAR Pulsar i is being used for omaldi applications, the interface is removed, giving direct access to the quadrupoles to introduce the sample. To ensure better fragmentation, the recommended CAD gas for use with omaldi sources is argon; for other ion sources, nitrogen is used. CAD gas is introduced in the API QSTAR Pulsar i using a separate connection so that the change in gas types can be made. When performing omaldi applications: Both sample and matrix are placed on a target surface. Matrix compound absorbs the laser light from a pulsed laser. Matrix in turn desorbs and ionizes the sample. Ions move down the quadrupoles and are orthogonally injected into the Time of Flight (TOF) chamber and are recorded. omaldi plates can hold multiple samples, with the position of the plate adjusted to let the stationary laser strike each sample as desired. omaldi analysis is generally quick and can be automated. While the omaldi source is in use, unused inter-connections are

5 safely located on a blanking panel located on the frame inside the instrument. Traditional MALDI uses post-source decay to fragment ions for detection in the TOF section. With the API QSTAR Pulsar i, you control fragmentation and improve results by filtering and fragmenting the ions in the quadrupoles. Variety in thickness of the sample deposit on the plate does not affect mass accuracy in the TOF. Ion Source Interlocks The purpose of the ion source interlocks is to disable high voltages in the sample introduction system. WARNING! Do not rely solely on the interlocks to ensure safety from the instrument s high voltage. When performing routine maintenance, turn off the main circuit breaker and disconnect the main power supply. The ion source interlock system includes the following benefits: If a valid ion source is not installed or installed incorrectly, the high voltages to the ion source (both IonSpray voltage and the curtain plate voltage) are disabled and the quadrupole RF supplies are turned off. The TOF voltage supplies remain on. Detects the type of ion source for controlling the source exhaust system. When an omaldi source has been installed, the interlocks disable the laser system to prevent exposure to laser emissions, if the following occurs: the fiber optic cable is removed, the door is open, or vacuum pressure is not correct. Source Exhaust System All of the LC ion sources produce both sample and solvent vapors. These vapors represent a potential hazard to the laboratory environment. The source exhaust system is designed to safely remove and allow for the appropriate handling of the ion source exhaust products. WARNING! Take all necessary precautions to ensure the safe disposal of the source exhaust gases. The source exhaust system includes the following benefits: Draws vapors from the ion source using the Venturi system (a flow of gas through a Venturi tube). Provides an external connection to remove the exhaust from the laboratory, by fume hood or other venting system. Prevents operation of the instrument without the source exhaust system with the TurboIonSpray and Heated Nebulizer ion sources (these ion sources use large volumes of gas and heat to produce ions). NOTE: The source exhaust system slightly reduces the pressure in the ion source. The reduction in pressure has proven to be beneficial for the ionization performance of both the Heated Nebulizer and TurboIonSpray ion sources. Includes a pressure switch on the source exhaust pump for the following high-pressure scenarios: With the TurboIonSpray and Heated Nebulizer ion sources, shuts down the instrument. With the IonSpray ion source, shuts down the source exhaust pump and displays a warning ( The source exhaust pump is not operating )

6 on the applications computer. WARNING! The source exhaust system is necessary for samples containing toxic or highly volatile chemicals or solvents. Applied Biosystems/MDS SCIEX recommends you maintain at least 20% positive oxygen flow into the laboratory. Vacuum System The vacuum system which controls the pressure in the interface and the ion path chamber is critical to the operation of the API QSTAR Pulsar i instrument. High voltage to the ion source, the mass filters and associated ion optics, TOF and the detector are shut down if the vacuum system pressure is too high. The vacuum system includes the following components: Vacuum interface Vacuum control system NOTE: When using the omaldi source, the interface is removed and the sample is introduced directly into the Q0 rods from the source. Vacuum Interface The vacuum interface separates the low pressure ion path chamber from atmospheric pressure in the ion source. This allows the transfer of ions from the ion source to the mass spectrometer while restricting sample, solvent, and ambient air from entering the ion path chamber. This is accomplished using a gas curtain of dry nitrogen. The vacuum interface system includes the following components: Gas curtain interface Differentially-pumped interface Entrance optics Gas Curtain Interface The gas curtain interface is a small volume chamber at atmospheric pressure which is flushed with a pure, inert curtain gas (ultra high purity % nitrogen). Features of the gas curtain interface include: Provides a region for ion declustering: sample ions collide with the gas molecules, creating collisional energy which breaks down ions clusters and separates sample ions from solvent molecules. Pumps curtain gas into the interface at a rate ranging from 0 to approximately 3.0 L/min (at a maximum inlet pressure of 60 psi). Maintains a curtain gas flow of approximately 700 ml/min through the orifice plate into the differentially-pumped interface (the remainder flows back into the ion source through the aperture in the curtain plate). Allows you to control the curtain gas flow rate from the applications computer and is physically controlled by a gas flow controller. The gas line is connected to the gas curtain interface through a quick coupling on the bottom of the vacuum interface. If the curtain gas pressure falls below 40 psi, the instrument shuts down. Differentially-pumped Interface The differentially-pumped interface is the first low pressure stage in the

7 transition from the atmospheric pressure ion source to the low pressure ion path chamber. Features of the differentially-pumped interface include: Maintains pressure at approximately 1 to 2 torr using the rotary vane pump located outside of the main console. Controls the flow of ions with the following sequence: a) Draws curtain gas and ions from the gas curtain interface into the differentially pumped interface using the pressure differential across the orifice plate. b) Draws ions further into the differentially pumped interface using the difference in voltage between the orifice plate and the skimmer. c) Focuses ions into the ion path chamber through the aperture in the skimmer. For MS/MS experiments, feeds N2 gas to the collision cell (in the ion path chamber) as CAD gas. For MALDI applications, recommended CAD gas is argon, to ensure better fragmentation. NOTE: API QSTAR Pulsar i CAD gas is provided through a separate external connection to accommodate a different CAD gas. Entrance Optics You can control the flow of ions by modifying the voltage on any of the elements that constitute the entrance optics. Some entrance optics elements have an associated state file parameter that you can use to control the voltage from the applications computer. The entrance optics consist of the following elements: For a list of operational voltage ranges, see Appendix B: Generic Parameters. Entrance Optics Elements Element Function Curtain plate Separates the sample flow from the curtain gas flow Maintains a fixed voltage (not computer-controlled) For NanoSpray, includes toggle switch to connect curtain plate to the ring voltage, ensuring ring and curtain plate have the same voltage Orifice plate (OR) Provides a division between atmosphere and the approximately 1.2 torr pressure in the differentially-pumped interface Includes a 254 µm orifice Electrically isolated* Focusing ring (RNG) Focuses the ions through the skimmer into the ion path chamber Electrically isolated* *The orifice plate and the focusing ring are electrically isolated so that a variable declustering voltage of -350 to +375 V can be obtained between them. Vacuum Control System The vacuum control system is fundamental to the safe and reliable operation of the instrument. A stable ion path chamber pressure must be maintained to perform mass spectrometric analyses. This is accomplished using a staged pumping system. Features of the vacuum control system include: Automatically pumps down the ion path chamber when you start up the

8 instrument. Disables the instrument s analytical components until it can maintain a stable operating pressure. Continually monitors the pressure and several physical interlocks to determine the vacuum status. If the vacuum integrity is breached, shuts down the instrument's high voltages until the vacuum operating conditions are restored. The vacuum control system includes the following components: Pumping system Vacuum gauges Gas control system Proudly serving laboratories worldwide since 1979 CALL for Refurbished & Certified Lab Equipment