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PerkinElmer FLEXAR SQ 300 MS User Manual

Chromera chromatography data system
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Summary of Contents for PerkinElmer FLEXAR SQ 300 MS

  • Page 1 ® Chromera Chromatography Data System...
  • Page 3 Chromera and Flexar SQ 300 MS User’s Guide...
  • Page 4 The information contained in this document is subject to change without notice. Except as specifically set forth in its terms and conditions of sale, PerkinElmer makes no warranty of any kind with regard to this document, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose.

  • Page 5: Table Of Contents

    Contents Introduction ........................5 Starting .......................... 7 Overview ..........................8 Flexar SQ 300 MS Status LEDs ....................9 LED Functionality ......................9 Starting the SQ 300 MS Detector ................... 10 Checking the Position of the ESI Probe ................. 11 Starting Chromera ......................13 Configuring Chromera ......................
  • Page 6 Flexar SQ 300 MS User’s Guide Chromatogram Smoothing ....................98 Chromatogram Peak Detection ..................98 Manual Peak Detection ....................98 Automatic Peak Detection .................... 99 Evaluating Mass Spectra .................... 103 Evaluating Acquired Mass Spectra ..................104 Creating an Average Mass Spectrum ..................106 Using the Left Mouse Button Command .................

  • Page 7: Introduction

    The Flexar SQ 300 MS combined with Chromera provides fast and reliable analysis of chemical samples by liquid chromatography mass spectrometry. The system consists of the Flexar SQ 300 MS, LC Pump, and Autosampler; and allows the addition of a column oven and alternate detector, such as a UV/VIS, fluorescence or PDA if desired.
  • Page 8 Flexar SQ 300 MS User’s Guide...

  • Page 9: Starting

    Starting...

  • Page 10: Overview

    The start-up instructions provided in this chapter assume that Chromera and the SQ 300 MS Driver software, the Flexar SQ 300 MS instrument, and the PC have been correctly installed by a representative of PerkinElmer.

  • Page 11: Flexar Sq 300 Ms Status Leds

    Starting. 9 Flex ar SQ 300 M S Status LEDs The Flexar SQ 300 MS detector status is displayed on the upper front panel through the following indicator lights. Power On Ready/Error Vacuum Green Green/Red Green/Red LED Functionality Power On LED...

  • Page 12: Starting The Sq 300 Ms Detector

    CAUTION! Do not move the instrument with the power on as this may damage the vacuum pumps. To start the Flexar SQ 300 MS system: 1. Switch the Power ON/OFF switch to position On (located on the right side panel). The Power lamp should light.

  • Page 13: Checking The Position Of The Esi Probe

    Starting. 11 7. Check the vacuum status displayed in the Status screen. When ready, the Lamps (Power, Vacuum, and Ready) should all be green. The Vacuum lamp changes from flashing to steady light at this stage. NOTE: The vacuum state light will take several hours to become ready and the system will not be able to load a Tune file.
  • Page 14 Flexar SQ 300 MS User’s Guide 12 .

  • Page 15: Starting Chromera

    Starting Chrom era...

  • Page 16: Configuring Chromera

    Flexar SQ 300 MS User’s Guide 14 . Configuring Chrom era The LC/MS system is configured in Chromera through the Chromera Manager; this acts as a control panel for the system. Closing Chromera Manager will not affect data acquisition or processing on a running instance of the Chromera.

  • Page 17: Creating An Lcms Instrument

    Starting Chromera. 15 4. Click the Create Database button and observe the progress bar as the system database is created. 5. Upon successful completion, the next step is to configure “an instrument” for the system. In Chromera, an instrument is defined as a collection of devices. For example, individual Devices such as Flexar or Series 200 autosamplers, pumps and detectors are combined to create an instrument.
  • Page 18 4. Click on the drop-down button in Device Name box, and device choices appear. Select the appropriate devices (modules) for the Instrument you are creating. In this example, select Flexar SQ 300 MS Detector. The Flexar SQ 300 MS Detector automatically fills in the Port Name field with COM DLL.
  • Page 19 Starting Chromera. 17 5. Select your LC Pump from the Device Name drop-down list. In this example, the Series 275 HRes Binary pump. 6. To determine a correct Port Name for the pump, open the Edgeport Configuration Utility from the Start button > All Programs > Digi USB > Edgeport Configuration Utility. 7.
  • Page 20 Flexar SQ 300 MS User’s Guide 18 . 10. Select your LC Autosampler from the Device Name drop-down list. In this example it is the Series 225/275 autosampler. 11. Select the Port Name for the autosampler. If your autosampler is plugged into Port 2 on the Edgeport the corresponding COM port is COM5.

  • Page 21: Setting The Operate Method

    Starting Chromera. 19 Upon successful connection, the Run Time screen displays: Setting the Operate M ethod At this time you must assign an Operate method. The Standby method not selectable; all you have to do is apply it when necessary. NOTE: When you close Chromera you lose the Operate method settings.
  • Page 22 Flexar SQ 300 MS User’s Guide 20 . 2. Select and open the ESI folder. 3. Select Operate method and click Open. 4. Look at the Manual Control section of the Run Time screen. 5. To verify the methods work with Chromera, in the Standby row click Apply.
  • Page 23 Starting Chromera. 21 6. Next, in the Operate row click Apply. Observe that in the Status Panel, the MS Detector State displays Operate. 7. Leave the SQ 300 MS Detector in the Operate mode.

  • Page 24: Auto Tune On The Sq 300 Ms Detector

    Auto Tune on the SQ 300 M S Detector Tuning the Flexar SQ 300 MS sets ion source and ion lenses parameters to obtain optimal resolution and sensitivity, and involves adjusting the probes. The Flexar SQ 300 MS instrument is tuned at the factory and it will be checked and re-tuned if necessary during installation.

  • Page 25: Preparing The Calibration Vials For Auto Tuning

    Starting Chromera. 23 P reparing the Calibration Vials for Auto Tuning There are two calibration vials as shown below. Typically use Vial 1 for Positive Ion Tune mix and Vial 2 for a Negative Ion Mix. 1. To remove calibration Vial 1, reach in and unscrew the left side calibration vial as shown below. Vial 1 Vial 2 Calibration Vials on the SQ 300 MS...

  • Page 26: Run An Auto Tune

    Flexar SQ 300 MS User’s Guide 24 . Peak Tubing coming from the calibration compartment Finger tight Peak Fastener Sprayer Probe Run an Auto Tune 1. Click Method to open the Chromera Method screen. 2. Select Create/Edit MS Method/Tune from the File menu.

  • Page 27: Running Auto Tune From The Calibration Vials

    Starting Chromera. 25 3. If an Acquisition Method displays, close the displayed Acquisition Method. Running Auto Tune from the Calibration Vials If you are tuning in positive ion mode open the tune Autotune_pos Tune or if you are tuning in the negative ion mode open Autotune_neg Tune.
  • Page 28 Flexar SQ 300 MS User’s Guide 26 . Select Auto Tune from the Tune menu. The Auto Tune dialog displays. 4. In the Auto Tune dialog, select a tuning compound reference file by clicking on Restore. This displays the Load Calibration Parameters screen.
  • Page 29 Starting Chromera. 27 6. Select Vial 1 (with the Positive Ion Tune Mix) for the Analyte Source from the drop-down menu. Analyte Source 7. Click on the Sample Prime button and the Tune Setup dialog displays. Start Pumping Button 8. Type in the System Name and the User Name. Note that the Syringe Pump selections are grayed out.
  • Page 30 Flexar SQ 300 MS User’s Guide 28 . A steady TIC is achieved in around 30 seconds Mid-Range Mass 10. While viewing the Mid-Range Mass, you can adjust the source position by turning the indicated controls for maximum sensitivity. Depth of probe adjustment for maximum sensitivity.
  • Page 31 Starting Chromera. 29 Set the source horizontal position so that the horizontal probe marking is positioned 10  spaces to the right side of the scale as shown below: Horizontal Set the Probe Tilt position as shown below:  Set Tilt Position Here 11.
  • Page 32 Flexar SQ 300 MS User’s Guide 30 . The Status light on the Auto tune page will turn yellow and displays Status: Executing auto tune and the Autotune Report screen displays. As Auto Tune runs in the positive ion mode, it creates the following three master tunes: pos_1k, pos_5k, and pos_10k upon completion.
  • Page 33 Starting Chromera. 31 12. After auto tune is complete, click on Check Tune. The Status light will turn yellow and Status: Executing check tune displays. If a significant amount of time passes between the completion of Auto Tune and the execution of Check Tune, click the “Sample Prime” button to get the calibration mixture flowing again.
  • Page 34 Flexar SQ 300 MS User’s Guide 32 . 13. The Check Tune results above show that the tuning masses all passed the evaluation criteria. NOTE: I f check tune fails the Status light will turn red and display Status: Auto tune FAI LED: m asses –...

  • Page 35: Running Auto Tune Using The Built-In Syringe Pump

    Starting Chromera. 33 Running Auto Tune Using the Built-in Syringe P um p Running Auto tune using the built-in syringe pump is very similar to running Auto Tune using the Calibration vials except that the syringe parameters and flow rate must be input as demonstrated in the following screen: 1.
  • Page 36 Flexar SQ 300 MS User’s Guide 34 .

  • Page 37: Initial Process To Configure An Optimal Tune And Method On The Sq 300 Ms Detector

    I nitial P rocess to Configure an Optim al Tune and M ethod on the SQ 300 M S Detector...

  • Page 38: Process Overview

    Flexar SQ 300 MS User’s Guide 36 . Process Overview Once the SQ 300 is tuned and calibrated, the next step is typically to create a Method specific to the analytes(s) that are to be measured or identified. The following pages describe a detailed process for accomplishing this, specifically so that the operator will understand why the process is conducted and how it will provide the best possible results.

  • Page 39: Setting Up A Sample Infusion

    Initial Process to Configure an Optimal Tune and Method on the SQ 300 MS Detector. 37 Setting up a Sam ple I nfusion Infusion is easy to accomplish using the SQ 300 MS Detector’s built in syringe pump. Typically, there are two options for accomplishing this: infuse the standard at a low flow rate directly into the MS, or infuse it into the LC stream running at a typical flow rate so as to also optimize “flow dependent”...

  • Page 40: Creating A Peak Detection Mini-Method

    Flexar SQ 300 MS User’s Guide 38 . Creating a P eak Detection M ini-M ethod The SQ 300 MS Driver software allows the creation of simple data evaluation routines called mini-methods. Creating this routine will facilitate data evaluation for the process being described here, as well as for many future evaluations.
  • Page 41 Initial Process to Configure an Optimal Tune and Method on the SQ 300 MS Detector. 39 4. Select Open Tune from the File menu. The Open Tune dialog displays. pos_1k tune file and click OK to open it. 5. Select the most recent The above example shows selecting pos_1k_29_OCT_2010_14h30m as the tune file.
  • Page 42 Flexar SQ 300 MS User’s Guide 40 . In Global Variables: Set the Scan from 100 to 700 • • High Turn off the Cal flow: Set Cal Gas Valve and Cal Gas Valve 2 On to: • False (off) Set Cal Sample 1 and 2 On to: •...
  • Page 43 Initial Process to Configure an Optimal Tune and Method on the SQ 300 MS Detector. 41 8. To download to the SQ 300 MS all the changes made to the Tune, we must “Apply the Tune” by selecting Tune from the Apply menu. This will start the syringe flowing at the specified rate. 9.
  • Page 44 Flexar SQ 300 MS User’s Guide 42 . 11. Close the Mass data evaluation screen. 12. Left-click and drag a box over the TIC area as shown below. 13. When you release the mouse button, select Average Spectra from the drop-down list.
  • Page 45 Initial Process to Configure an Optimal Tune and Method on the SQ 300 MS Detector. 43 The Mass data evaluation screen appears. 14. Left mouse click and drag a box around the reserpine protonated molecular ion cluster at z 609 and select Zoom X-Y Axis from the drop-down list.
  • Page 46 Flexar SQ 300 MS User’s Guide 44 . 16. A peak detection data evaluation mini-method will now be created to facilitate data evaluation for this and all future analyses. Select Peak Detect... from the Evaluation menu. The Mass Spectrum Peak Detect dialog box displays.
  • Page 47 Initial Process to Configure an Optimal Tune and Method on the SQ 300 MS Detector. 45 18. Select Save from the Evaluation menu and the Save Spectrum Evaluation Method dialog box displays. 19. Type Peak Detect to name the method, then click OK. 20.

  • Page 48: Ramping Parameters- Optimizing The Capillary Exit Voltage

    Flexar SQ 300 MS User’s Guide 46 . R am ping Param eters- Optim izing the Capillary Ex it Voltage The SQ 300 MS driver SW allows you to ramp certain Tune parameters to determine the best settings for those parameters. However, the Auto Tune routine has eliminated the need to do this except for the one parameter that is “compound dependent”, the Capillary Exit voltage.
  • Page 49 Initial Process to Configure an Optimal Tune and Method on the SQ 300 MS Detector. 47 Set the following Ramp values: Start Value: 50 • End Value: 300 • Step Size: 2 • • Spectra: 3 Note: The settings above are used to show the process in greater detail than is typically required.
  • Page 50 Flexar SQ 300 MS User’s Guide 48 . 10. Position the cursor at the apex of the 609 peak (the cursor turns to a hand) and right-click. 11. Position the cursor at the apex of the 195 ion (the cursor turns to a hand) and right-click. The 195 ion is a known fragment of reserpine, which will appear with higher capillary exit values.
  • Page 51 Initial Process to Configure an Optimal Tune and Method on the SQ 300 MS Detector. 49 13. On the green curve, move the cursor to the apex of the highest point (it turns to a hand) and left-click. The Mass data evaluation window displays.
  • Page 52 Flexar SQ 300 MS User’s Guide 50 . 14. Select Tune from the View menu. Look at the Capillary Exit (Volts) value (the window below shows Single=152). This means that the value of the Capillary Exit voltage at the cursor position, which was the maximum of the curve, was equal to 152 volts.
  • Page 53 Initial Process to Configure an Optimal Tune and Method on the SQ 300 MS Detector. 51 16. Now we wish to examine our reserpine fragment ion a bit. In the BIC screen, click on the red line (194 to 196 Amplitude – Peak Detect). This makes the red line a solid line.
  • Page 54 Flexar SQ 300 MS User’s Guide 52 . z 195 fragment ion, a Capillary Exit This indicates that to produce the maximum intensity voltage of ~250 volts should be used. 19. Select Ramp from the Tune menu to deselect it.

  • Page 55: Creating Methods And Sequences

    Creating M ethods and Sequences...

  • Page 56: Creating An Ms Method

    Flexar SQ 300 MS User’s Guide 54 . Creating an M S M ethod The foundation for an optimal MS Method is starting with a mass calibrated Tune (with a date/time stamp). These are created every time Auto Tune is completed and under normal operating conditions, they can remain stable and usable for months .
  • Page 57 Creating Methods and Sequences. 55 3. Select New from the File menu. The following dialog displays. 4. Select Method then click OK. The following method screen displays. to expand the method row and display Periods. 5. Click the plus sign...
  • Page 58 Flexar SQ 300 MS User’s Guide 56 . 6. Give the method a name by selecting Save as from the File menu. In this example, the method name is MS Method 1. 7. Click on the green Time Period dot and set the run Duration to equal that in the Chromera HPLC method.
  • Page 59 Creating Methods and Sequences. 57 10. Select the most recent pos_1k tune file (with a date/time stamp), then click OK. This example shows pos_1k 29 Oct 2010 is selected as the most recent pos_1k tune file. 11. In the Global Variables section, click on Acquisition Function, select SIM from the drop-down list, and then press Enter.
  • Page 60 Flexar SQ 300 MS User’s Guide 58 . NOTE: This is a pre-determined value known to be optimal for the compound used in this example. The alternative selection for Capillary Ex it (Step Function…) uses a calculated value for the mass selected that is derived from the optimal values determined for the masses in the calibration mix during the Auto Tune procedure.
  • Page 61 Creating Methods and Sequences. 59 NOTE: This is a quick way to build a Method requiring multiple acquisition experiments. Simply copy previously defined Tunes as this minimizes the number of changes required for each Tune in the Method. 20. Click on the top Sim blue dot and change it to Scan in Acquisition Function of the Global Variables section.
  • Page 62 Flexar SQ 300 MS User’s Guide 60 . 24. Click on Capillary Exit (Volts) and from the drop-down list select Step Function Calibrated to Q1 m/z. 25. Left-click on Capillary Exit again to set this value. 26. Select Save from the File menu.

  • Page 63: Creating A Chromera Method

    Creating Methods and Sequences. 61 Creating a Chrom era M ethod After creating the MS method, open Chromera to create a Chromera method. The Chromera method will define all the operating requirements for all the other components in the Chromera configuration. To create a Chromera method: 1.
  • Page 64 Flexar SQ 300 MS User’s Guide 62 . This example shows a Method Name of Demo Method and a Group of Reserpine Group. 4. Select Save Method from the File menu. 5. Enter your instrument parameters by clicking on each instrument.
  • Page 65 Creating Methods and Sequences. 63 The Select Method dialog displays. 9. Select the method you created in the SQ 300 MS driver, then click Open. This example shows MS Method 1.sqm 10. Select Save Method from the File menu.

  • Page 66: Creating A Chromera Sequence

    Flexar SQ 300 MS User’s Guide 64 . Creating a Chrom era Sequence After creating a Chromera method, create a simple Chromera Sequence to run the method. To create a Chromera sequence: 1. Click Sequence to open the sequence screen.
  • Page 67 Creating Methods and Sequences. 65 5. Enter the Sequence Parameters. Select the Sample Type from the drop-down list. This example shows Sample. • Type a Sample Name. This example shows Reserpine. • Type the number of Injections. This example shows 1 injection. •...
  • Page 68 Flexar SQ 300 MS User’s Guide 66 .

  • Page 69: Starting Data Acquisition

    Starting Data Acquisition...

  • Page 70: Preparing For An Analysis

    Flexar SQ 300 MS User’s Guide 68 . Preparing for an Analysis Prepare the system with the mobile phase, column, and sample listed below for the analysis. The analysis conducted for the example shown on the following pages utilizes an isocratic HPLC method, which is delivered from a single mobile phase reservoir (“A”...

  • Page 71: Equilibrate The System

    Starting Data Acquisition. 69 Equilibrate the System Before running an analysis, the LC system must be equilibrated to achieve a stable chromatographic baseline and to properly condition the LC column. To equilibrate the system: 1. In Chromera click Run Time then click Manual Control for the Control Mode. 2.
  • Page 72 Flexar SQ 300 MS User’s Guide 70 . 4. Make sure the chromatographic tubing is connected between the LC system and the SQ 300 MS detector. 5. Enter your Pump Settings (0.4 mL/min and 100% A). 6. Click the Apply button to start the pump.

  • Page 73: Running A Sequence

    Starting Data Acquisition. 71 R unning a Sequence Once the system has reached equilibration, you can load and run the sequence. To run a sequence: 1. Click Sequence for the Control Mode. 2. Select Open Sequence from the File menu. The Data Selector –...
  • Page 74 Flexar SQ 300 MS User’s Guide 72 . 5. Click Open to open this sequence. The sequence displays and is ready to run, indicated by the green Start button. 6. Click on the green Start button. The sequence starts to run.
  • Page 75 Starting Data Acquisition. 73 The running sequence is displayed as a green line. Observe the two chromatographic traces. The Total Ion Chromatogram or TIC, which is the sum of intensities for all ions observed in each scan is is displayed as a black line, and the SIM of z 609.3 is displayed as a blue line.
  • Page 76 Flexar SQ 300 MS User’s Guide 74 . When the run completes the display clears. You can review the results in Post Run.

  • Page 77: Analyze Results In Post Run

    Analyze Results in P ost R un...

  • Page 78: Viewing The Results In Post Run

    Flexar SQ 300 MS User’s Guide 76 . View ing the R esults in Post R un Whether reprocessing existing data or acquiring new data, the completed samples will be displayed in the Post Run environment, and can be inspected by navigating through the Sample tree and interacting graphically with the chromatographic display.
  • Page 79 Analyze Results in Post Run. 77 You could also search for previously stored data by selecting Open Data from the File menu. This displays the Data Selector. Search and select the data you want to analyze then click Open. 2. Uncheck the pump pressure (BPump-1). 3.
  • Page 80 Flexar SQ 300 MS User’s Guide 78 . 5. Move the mouse pointer to the apex of the peak (it turns to a hand) at retention time ~1.2 min. and then right-click. 6. Select Examine Mass Spectra from the menu.
  • Page 81 Analyze Results in Post Run. 79 The spectrum from the selected retention time opens in the lower portion of the SQ 300 MS driver window, and a copy of the TIC is displayed in the top portion of the window. 609.3 peak (it turns to a hand) then right-click to 7.

  • Page 82: Importing Chromera Data And Methods

    Flexar SQ 300 MS User’s Guide 80 . I m porting Chrom era Data and M ethods To import the data into Chromera: 1. Select Import from the Tools menu then select Chromera Results… The Import Results dialog appears: 2. Click the browse button...
  • Page 83 Analyze Results in Post Run. 81 The Open dialog appears: 3. Navigate to the directory containing your data. 4. Select the data file then click Open. This example shows data file name (External std-results.chxb), that appears in the Select batches to import list.
  • Page 84 Flexar SQ 300 MS User’s Guide 82 . 5. Select External stds-UTM-2 then click the Import button. The progress bar shows the import progress. Upon completion, the message Import of results successful appears in the Messages box. 6. Click the Close button.

  • Page 85: Using The Data Selector

    Analyze Results in Post Run. 83 Using the Data Selector Now that data has been imported into Chromera you can open it using the Data Selector. To open a data file using the Data Selector follow this procedure: 1. Click on the Post Run button The Post Run environment opens: 2.
  • Page 86 Flexar SQ 300 MS User’s Guide 84 . 3. Click on the plus sign to expand the batch and choose one or more samples from a batch. The data are stored in Batches, which are, in turn, stored in groups. Use the Data Selector to choose data for guiding the method editing.

  • Page 87: Searching A Library To Identify Unknowns

    Analyze Results in Post Run. 85 Searching a Library to I dentify Unknow ns It is important to note that both electrospray (ESI) and atmospheric pressure chemical ionization (APCI) are very soft ionization techniques, especially when compared to more traditional techniques, like electron impact used for GC/MS analysis.
  • Page 88 Flexar SQ 300 MS User’s Guide 86 . 4. Select Save Spectrum to Library from the Evaluation menu. 5. Run a library search by selecting Run Library Search from the Evaluation menu. 6. The search results are then displayed.
  • Page 89 Analyze Results in Post Run. 87 Unknown Spectrum Unknown vs. Match Difference Best Library Match For additional information on library searching, refer to the NIST manual which should be installed on the hard drive and is also available on line.

  • Page 90: Viewing Spectra Results In The Sq 300 Ms Driver Window

    Flexar SQ 300 MS User’s Guide 88 . View ing Spectra R esults in the SQ 300 M S Driver W indow NOTE: Some of the following examples show data from a time-of-flight (TOF) mass spectrometer. However, the commands demonstrated may be applied to the quadrupole data generated by the SQ 300 MS detector.
  • Page 91 Analyze Results in Post Run. 89 3. The SQ 300 MS driver window displays a Total Ion Chromatogram (TIC) in the upper half of the window. If the mouse was right-clicked in the Chromera chromatogram (as in the first example above), the spectrum from that retention time will be displayed.

  • Page 92: About The Total Ion Chromatogram (Tic)

    Flexar SQ 300 MS User’s Guide 90 . About the Total I on Chrom atogram (TI C) The TIC is a chromatogram where each data point represents the sum of intensities of all ions detected for each scan. Consequently, each data point in a TIC has a scan associated with it. The TIC mirrors a typical chromatogram displayed in an LC analysis where the amplitude is UV absorbance.

  • Page 93: Creating An Extracted Ion Chromatogram (Eic)

    Analyze Results in Post Run. 91 Creating an Ex tracted I on Chrom atogram (EI C) The EIC is a form of a limited mass range TIC. An EIC is extracted from scan data, and typically used where specific ion(s) of interest, or small mass ranges are being searched for. It is possible to display several mass ranges in the same EIC chromatogram.
  • Page 94 Flexar SQ 300 MS User’s Guide 92 . 7. For the Range Selection, select Full Range, Time Range or Spectrum Range. 8. Select how to display the created EIC. NOTE: An EIC cannot be displayed in the same window as a TIC.

  • Page 95: Creating A Base Ion Chromatogram (Bic)

    Analyze Results in Post Run. 93 Creating a Base I on Chrom atogram (BI C) The BIC is a form of a limited mass and time range ion chromatogram where mass, peak intensity/area and resolution are displayed as a function of time or spectrum number. A BIC can be generated in two ways: •...
  • Page 96 Flexar SQ 300 MS User’s Guide 94 . 8. In the Range Selection section, select to display Full Range, Time Range, or Spectrum Range. If you select Time Range, enter the number of the first and last spectrum. • If you select Spectrum Range, enter the number of the first and last spectrum.

  • Page 97: Processing Of Ion Chromatograms

    Analyze Results in Post Run. 95 Processing of I on Chrom atogram s To zoom in: 1. Left-click and drag a box around the area of interest, release button and select Zoom X-axis. The zoomed area appears. 2. Left-click and drag a box somewhere in the chromatogram, release the button and select Zoom Out.

  • Page 98: Displaying Statistics

    Flexar SQ 300 MS User’s Guide 96 . Displaying Statistics Left-click and drag a box around a peak of interest, release the button and select Display  Statistics. About Right M ouse Click M enus Each graph view contains a graphical package which includes functions to modify and export graphs.

  • Page 99: Setting The Chromatogram Noise Calculation Preferences

    Analyze Results in Post Run. 97 NOTE: An increased Baseline segment value will flatten the baseline. A decreased value may lead to a baseline which interferes with the peaks. 4. The level of the calculated baseline is found in the Peak Information box when Manual peak detection is used.

  • Page 100: Chromatogram Smoothing

    Flexar SQ 300 MS User’s Guide 98 . 2. Enter a Threshold value and decide if the ion chromatogram will be subtracted with this value. 3. The threshold can be hidden or displayed with the Threshold from the Chromatogram View menu.

  • Page 101: Automatic Peak Detection

    Analyze Results in Post Run. 99 Data points appear on the peaks. 2. Move the cursor to a data point until the "hand" displays. 3. Click the right-mouse button and display peak detect results in the Peak Table. NOTE: The S/N value is calculated using the centroid amplitude. Autom atic Peak Detection 1.
  • Page 102 Flexar SQ 300 MS User’s Guide 100 . 3. Under Search Method, select Full Chromatogram or Partial Chromatogram. If partial, enter a range in seconds. 4. Under Selection Criteria, enter a signal-to-noise limit. 5. Under Retention Time, select Peak Top or Centroid.
  • Page 103 Analyze Results in Post Run. 101 9. Select Print from the File menu in Microsoft Excel to print the table.
  • Page 104 Flexar SQ 300 MS User’s Guide 102 .

  • Page 105: Evaluating Mass Spectra

    Evaluating M ass Spectra...

  • Page 106: Evaluating Acquired Mass Spectra

    Flexar SQ 300 MS User’s Guide 104 . Evaluating Acquired M ass Spectra 1. As demonstrated earlier, moving the mouse pointer to a point on the chromatogram in Chromera and then right-clicking and selecting Examine Mass Spectra from the drop-down list will open the SQ 300 processing window.
  • Page 107 Evaluating Mass Spectra. 105 spectrum from that retention time will be displayed. If no point in the chromatogram is selected, then the first spectrum from the acquisition is displayed. When a data file is opened a TIC window and a Mass spectrum window will be displayed.

  • Page 108: Creating An Average Mass Spectrum

    Flexar SQ 300 MS User’s Guide 106 . Creating an Average M ass Spectrum Below is an example of how to analyze the TIC peak. Using the Left M ouse Button Com m and 1. Left-click and drag a box around the peak of interest.
  • Page 109 Evaluating Mass Spectra. 107 5. Decide how to display the mass spectra in the Display section. NOTE: Average spectra are not displayed in the same window as single spectra. 6. Click OK. 7. The Mass spectrum will be updated to an average Mass spectrum.

  • Page 110: Creating An Eic And Bic From A Mass Spectrum

    Flexar SQ 300 MS User’s Guide 108 . Creating an EI C and BI C from a M ass Spectrum To create an EIC: 1. Left-click and drag a box around a peak of interest in the Mass spectrum. The width of the box will be the set range.
  • Page 111 Evaluating Mass Spectra. 109 To create a BIC: 1. Left-click and drag a box around a peak of interest in the mass spectrum. The width of the box will be the set range. 2. Release the button and select Display BIC from the menu. 3.

  • Page 112: Processing Of Mass Spectra

    Flexar SQ 300 MS User’s Guide 110 . Processing of M ass Spectra NOTE: In some functions the ability to select "undo" is not available. We recommend creating spectra in a new window before using functions like subtract baseline, subtract threshold, and smoothing. Otherwise, a new spectrum has to be generated in order to revert to the original display.

  • Page 113: Displaying Statistics

    Evaluating Mass Spectra. 111 Displaying Statistics To display statistics: 1. Left-click and drag a box around the area of interest. Release the button and select Display Statistics. Using R ight M ouse Click M enus The application obtains a graphical package which includes functions to modify and export graphs. Individual functions can be selected or the Customization Dialog can be used.

  • Page 114: Setting Spectrum Noise Calculation Preferences

    Flexar SQ 300 MS User’s Guide 112 . 3. Enter shortest Baseline Segment Size, and Baseline Noise Window. NOTE: An increased Baseline segment value will flatten the baseline. A decreased value may lead to a baseline which interferes with the peaks.

  • Page 115: Setting The Mass Spectrum Threshold

    Evaluating Mass Spectra. 113 Setting the M ass Spectrum Threshold To set the mass spectrum threshold: 1. Select a mass spectrum 2. Select Threshold from the MS Evaluation menu. 3. Enter a threshold value and decide if the mass spectrum will be subtracted with this value. M ass Spectrum Sm oothing To smooth mass spectra: 1.

  • Page 116: Mass Spectrum Peak Detection

    Flexar SQ 300 MS User’s Guide 114 . M ass Spectrum Peak Detection M anual Peak Detection 1. To display data points, select the right mouse button command Mark Data Points. This makes it easier to see the individual data points in the spectrum.
  • Page 117 Evaluating Mass Spectra. 115 3. In the Search Method section, select Full Spectrum or Partial Spectrum. If partial is selected, enter a Start and End range. 4. In the Selection Criteria section, enter a signal to noise limit. Peaks with a S/N lower than the entered value will be excluded. m / z Assignment section, select Peak Top or Centroid.
  • Page 118 Flexar SQ 300 MS User’s Guide 116 . The following example shows a default peak annotation. The following example shows an enhanced peak annotation. 12. To print the table from Microsoft Excel, select Print from the File menu.
  • Page 120 PerkinElmer 710 Bridgeport Avenue Shelton, CT 06484-4794, U.S.A. Internet: http://www.perkinelmer.com email: info@perkinelmer.com PerkinElmer is a registered trademark of PerkinElmer, Inc.

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