Agilent G3212 GC-APCI Source

Agilent G3212 GC-APCI Source Quick Start Guide Where to find information 2 Getting Started 3 Step 1. Start the Data Acquisition program for the GC and the Q-TOF 3 Step 2. Prepare the GC and Q-TOF for data acquisition 4 Step 3. Acquire data with the GC and Q-TOF instrument 5 To optimize your system for performance 6 GC-APCI Ionization Theory 8 Use this guide for your first steps with the Agilent G3212A GC-APCI source used with the 6500 Series Quadrupole Time-of-Flight LC/MS system, and as a road map for your user information. Agilent Technologies

Where to find information Where to find information Online Help Press F1 To get more information about a pane or dialog box, place the cursor on the pane or dialog box of interest and press F1. Help menu From the Help menu, access How-to help and reference help. Documents The Installation and the Quick Start manuals are available for the G3212A GC-APCI Source hardware. GC-APCI Quick Start Guide Use this guide to learn to use the GC-APCI Source. Installation Guide This guide is for the Agilent customer engineer to install the hardware and software, configure the instrument, and verify performance. A separate installation guide is available for the 6500 Series Q-TOF LC/MS System and the 6224/6230 TOF. 2 GC-APCI Source Quick Start Guide

Getting Started Step 1. Start the Data Acquisition program for the GC and the Q-TOF Getting Started This procedure assumes that the installation verification procedure has been completed. Do not continue if the installation procedure is not complete. Make sure that the Q-TOF is tuned and calibrated using the Dual ESI Source or the Agilent Jet Stream source. The Q-TOF must be in the 1700-amu mass range to acquire data at the fastest possible acquisition rates. Make sure that the GC-APCI source is installed and that the necessary hardware in the desolvation assembly is installed. Step 1. Start the Data Acquisition program for the GC and the Q-TOF 1 Start the ChemStation program. 2 Start the MassHunter Data Acquisition program. 3 Load the appropriate method for the GC. 4 Load the appropriate method for the Q-TOF. 5 Wait for both systems to equilibrate and stabilize before you acquire data. GC-APCI Source Quick Start Guide 3

Getting Started Step 2. Prepare the GC and Q-TOF for data acquisition Step 2. Prepare the GC and Q-TOF for data acquisition 1 If pre-existing methods are not available, use the following set points for the GC as a starting point: Injector Temp: 290 C Injection Type: Pulsed Splitless Oven start temperature and ramp: 50 C, ramp to 280 C at 40 C/minute Aux Zone 2 (GC/APCI Transfer Line): 320 C 2 In the GC ChemStation program, save the method with an appropriate name. 3 Use these set points as beginning values for the source on the Q-TOF: drying gas = 5 L/min drying gas temp = 365 C Vcap = 1000 V Current = 1.0 µa Fragmentor = 150 (starting value which can be adjusted lower) MS scan range = 60 to 500 amu MS Acquisition = 10 scans per second MS Mode MS/MS Acquisition = No less than 8 MS/MS Spectra/sec 4 In the MassHunter Data Acquisition program, save the method with an appropriate name. 4 GC-APCI Source Quick Start Guide

Getting Started Step 3. Acquire data with the GC and Q-TOF instrument Step 3. Acquire data with the GC and Q-TOF instrument 1 After the GC and Q-TOF methods are created, type in the desired sample information in the GC ChemStation sequence table. 2 Export the sequence table using the Export Sequence to CSV command. 3 Import the CSV file using the Import Worklist feature in the MassHunter Acquisition software. 4 Change Worklist features as needed. Make sure that Worklist start is set to External. 5 Start the Worklist in the MassHunter Acquisition software. 6 Start the Sequence in the GC ChemStation software. The run now starts in the GC ChemStation and the sample is injected. When the sample is injected, the Q-TOF starts acquiring data. After the run completes, any automated data analysis starts and the next sample is injected. GC-APCI Source Quick Start Guide 5

Getting Started To optimize your system for performance To optimize your system for performance If you get poor peak shape and sensitivity, do these steps to optimize your system. 1 Replace the septa in the split/splitless GC inlet. The red, high temperature silicon septa provide the best performance. 2 Make sure that the injector liner is correct for the application. Use the liner that was used for performance verification (p/n 5181-3315). 3 Make sure that the column is installed no more than 5 mm past the ferrule. 4 When injecting dirty samples, replace the gold seal at the bottom of the injection port on a weekly basis. Extremely dirty samples can require daily replacement of the gold seal. 5 When installing a new column, condition the GC column at the maximum allowable temperature for the column. Make sure that the GC and Q-TOF are not coupled together during the conditioning step. 6 For a used column, remove 1 meter of column length from the inlet side of column. Reinstall the column correctly into the injection port. 7 Use MS-compatible thin film columns (0.1-mm film thicknesses suggested). The use of 0.1-mm film columns leads to lower sample loading and also lower bleed from the column itself. 8 Use smaller injections to avoid overloading the thin film columns. Smaller injections provide the best performance. 9 Make sure that the column is cut squarely on the inlet and outlet ends of the column. Use a diamond blade capillary cutter (p/n 5183-4620). 10 Make sure that the column is extended no more than 4 mm from the end of the transfer line. 11 For better sample precision, use the gas-tight 10 µl syringe with the PTFE plungers (p/n G4513-80203) for injection volumes of less than 1 µl. 12 For best mass accuracy, use no more than two reference mass ions. For single point Internal Reference Mass correction, use the background ion C 16 H 32 O 2, with mass of m/z 257.2475. 13 Calibrate the Q-TOF before acquiring data with the GC-APCI source. Rinse the desolvation assembly using Acetonitrile, Isopropanol, and then Methanol. Never use modifiers, such as Formic Acid. Do not spray any liquid down the capillary of the Q-TOF. 14 When the GC and the Q-TOF are not coupled together, the GC-APCI source must be covered with a piece of foil to protect the instrument from 6 GC-APCI Source Quick Start Guide

Getting Started To optimize your system for performance unwanted particles in the air. These particles can contaminate the ion optics of the instrument, which leads to requiring more frequent cleaning. 15 When the GC and the Q-TOF are not coupled together, the transfer line safety cover must be used. Otherwise, the transfer line can cause accidental burns. 16 The Q-TOF acquisition rate must be set to 8 to 10 spectra per second. Acquisition rates slower than eight spectra per second results in poor peak shape recorded by the Q-TOF. 17 If the background count of the Q-TOF exceeds the expected range of 5,000 to 10,000 abundance counts in the real-time spectral profile window, remove the PTFE spray chamber exhaust hose from the plastic waste bottle. Observe the background. Choose the configuration that is lower in counts. GC-APCI Source Quick Start Guide 7

GC-APCI Ionization Theory GC-APCI Ionization Theory The GC-APCI uses the Atmospheric Pressure Chemical Ionization (APCI) process. This process uses a corona discharge to generate both electrons and ions inside a large open chamber coupled to a mass spectrometer vacuum inlet. The APCI ionization process generates approximately 99.9% stable even electron type ions. These ions consist of the addition of a proton to yield a following ion, [M+H] +. The APCI processes uses a small amount of residual water vapor from within the ionization chamber to assist in chemical reaction with the vapor phase analyte molecule [M] 0, to form the [M+H] + ion. As the vapor phase neutral molecule that exit from the GC column pass near the small spatial region of the corona discharge, the neutral molecules go through several chemical reaction processes as shown in Equation 1 through Equation 4, to form the even electron species [M+H] +. The GC-APCI process ionizes all types of vapor phase compounds which have a Proton Affinity (PA) that is equal to or greater than the PA of water. There are a few type classes of compounds for which the proton affinity is low and other processes can be required. The typical mechanisms for chemical ionization (CI) are: H 2 O 0 + e - H 2 O +. + 2e - (1) H 2 O + + H 2 O 0 H 3 O + + OH - (2) M 0 v + H 3 O+ [Μ+Η] + + H 2 O 0 (3) H 2 O 0 + H 3 O + [2H 2 O+H] + (4) Equation 1 shows the first step for the APCI using the water present in the environment with the free electrons generated by the corona needle to form a radical cat ion, [H 2 O] +. Equation 2 shows the reaction of radical cat ion with neutral water gas phase water molecules to form the reagent Hydronium [H 3 O] +. 8 GC-APCI Source Quick Start Guide

GC-APCI Ionization Theory Equation 3 is the most important equation. The gas phase analyte neutral molecule M 0 elutes from the end of the GC column and reacts with the [H 3 O] + Hydronium ion to form the very stable even electron ion, [M+H] +. Equation 4 shows the reaction between the H 3 O + and additional water. This reaction occurs when the water concentration is higher than necessary to use APCI process. Figure 1 Diagram of the gas phase chemistry occurring in the GC-APCI ion chamber with all the reactants. Figure 2 shows the resulting mass spectrum obtained from GC-APCI system when the concentration of water is at a very high level, 1% or more. The APCI reactions are dominated by the concentration of the reagents involved in the chemical ionization processes. This example shows the results when one of the reagents or analytes are overly concentrated by 100 to 1000 times. Equation 4 shows these effects. GC-APCI Source Quick Start Guide 9

GC-APCI Ionization Theory Figure 2 more. The resulting mass spectrum when the concentration of water is at 1% or 4 mm Figure 3 tip. The GC column positioned 4 to 5 mm extended beyond the transfer-line exit 10 GC-APCI Source Quick Start Guide

GC-APCI Ionization Theory GC-APCI Source Quick Start Guide 11

www.agilent.com In this Book The Quick Start Guide presents first steps to use the GC-APCI Source. Agilent Technologies, Inc. 2011 Printed in USA Revision A, July 2011 *G3212-90001* G3212-90001 Agilent Technologies