What s New in Empower 3

Transcription

1 What s New in Empower 3 Revision A Copyright Waters Corporation 2010 All rights reserved

2 Copyright notice 2010 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF AMERICA AND IN IRELAND. ALL RIGHTS RESERVED. THIS DOCUMENT OR PARTS THEREOF MAY NOT BE REPRODUCED IN ANY FORM WITHOUT THE WRITTEN PERMISSION OF THE PUBLISHER. The information in this document is subject to change without notice and should not be construed as a commitment by Waters Corporation. Waters Corporation assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Waters Corporation be liable for incidental or consequential damages in connection with, or arising from, its use. Trademarks Waters is a registered trademark of Waters Corporation, and Empower and THE SCIENCE OF WHAT S POSSIBLE. are trademarks of Waters Corporation. Other registered trademarks or trademarks are the sole property of their owners.

3 Customer comments Waters Technical Communications department invites you to tell us of any errors you encounter in this document or to suggest ideas for otherwise improving it. Please help us better understand what you expect from our documentation so that we can continuously improve its accuracy and usability. We seriously consider every customer comment we receive. You can reach us at Contacting Waters Contact Waters with enhancement requests or technical questions regarding the use, transportation, removal, or disposal of any Waters product. You can reach us via the Internet, telephone, or conventional mail. Waters contact information Contacting medium Internet Telephone and fax Conventional mail Information The Waters Web site includes contact information for Waters locations worldwide. Visit From the USA or Canada, phone HPLC, or fax For other locations worldwide, phone and fax numbers appear in the Waters Web site. Waters Corporation 34 Maple Street Milford, MA USA iii

4 Empower 3 software Safety information See the operator s guides of the instruments or devices associated with this software product for information on how to safely operate and maintain them. Intended use Use the Waters Empower 3 software for acquiring, processing, reporting, and managing your chromatographic information. Audience and purpose This guide addresses novice and experienced Empower users. It explains in detail Empower 3 features that were not included in earlier versions of Empower software. It is intended as a supplement to the Empower 3 online Help. iv

5 Table of Contents Copyright notice... ii Trademarks... ii Customer comments... iii Contacting Waters... iii Empower 3 software... iv Safety information... iv Intended use... iv Audience and purpose... iv 1 Process-only sample sets Overview Process-only sample set privileges Creating a process-only sample set Process-only sample set editor considerations Altering process-only sample set information Acquiring a new sample set based on process-only sample sets Reporting process-only sample sets Process-only sample set considerations Saving process-only sample sets Copying and deleting process-only sample sets Custom fields Audit trail and revision history comments Audit trail records Table of Contents 1

6 2 Calculating USP, EP, and JP signal-to-noise ratio Calculation method Calculating the signal-to-noise ratio using a blank value Mass spectrometry Ion ratio processing (Peak ratio processing) Using the Peak Ratios (MS Ion Ratios) tab Entering peak ratio tolerances and reference injections Peak ratio results Peak Ratio view in Review and QuickStart Peak Ratio (MS Ion Ratio) Report groups Target Mass Using the sample table and a single method to process multiple base masses Configuring the MS Processing method Using the Include the Uncorrected Target or Base Mass option Specifying base masses according to the expected mass injection Specifying the Ionization mode Using the Percentage of Base Peak field Reporting expected mass results MS library changes Fraction Collection with WFC III Collecting fraction data Adding and updating fraction data Viewing fraction data Viewing fraction data in Review Viewing fraction data in the Project window Table of Contents

7 Formatting fraction data in Review Reporting fraction data Method validation Accuracy profile capability Reporting Accuracy Profile Plot information Linearity of the Method Linearity processing steps Linearity and Linearity Comparison report groups Limits of Quantitation ACQUITY UPLC Enhancements ecord data in the Empower 3 database Adding ecord data to the database Updating ecord data Viewing and managing ecord data Reporting ecord data Deleting ecord data from the Empower database ACQUITY UPLC sample loop support ACQUITY UPLC sample queue functionality Auto-addition Fixed vials Column selection Post Run Report group Post Run Report group Table of Contents 3

8 4 Table of Contents

9 1 Process-only sample sets This chapter describes the process-only sample set feature, which you can use to create sample sets from previously acquired data. Contents Topic Page Overview 1-2 Process-only sample set privileges 1-3 Creating a process-only sample set 1-4 Acquiring a new sample set based on process-only sample sets 1-6 Reporting process-only sample sets 1-7 Process-only sample set considerations

10 Overview The process-only sample set feature helps you create a sample set from previously acquired injections, channels, or sample sets. The data in a process-only sample set is a copy of the original data. Changes you make to process-only sample sets do not affect the original sample sets. You create a process-only sample set by selecting existing raw data from the Project window or the QuickStart application and bringing it into the Process-Only Sample Set Editor, where you can rearrange the order of the data, add function lines, split replicate injections from one row into multiple rows, and combine replicate injections from multiple rows into a single row. Reviewing and processing process-only sample set data You review and process process-only sample sets in the same way that you process regular sample sets. Locked channels are not processed when a process-only sample set containing those channels is processed. You cannot export process-only sample set data. While you can preview results created from a process-only sample set, you cannot preview the process-only sample set itself (raw, unprocessed data). Viewing process-only sample set data The Sample Set Type column in the Sample table on the Project Window s Sample Set tab indicates the sample set type. The software sets the field to Acquired, for regular sample sets, and Process Only, for process-only sample sets. When you copy a process-only sample set to another project, the software sets the sample set type to Copied Process Only. When viewing information relating to process-only sample sets in the Project Window or QuickStart interface, bear in mind these restrictions: You cannot use the View As functionality to view a process-only sample set as injections or channels. You see process-only sample set information only in the Sample Set, Result Set, and Results views. When you view sample sets as injections or channels, you cannot view the injections or channels related to the process-only sample set. If process-only sample sets are among the rows selected, only conventional sample sets appear as injections or channels. You cannot view the generated results of process-only sample sets as injections or channels. If multiple results are selected, only results generated from regular sample sets appear as injections or channels. 1-2 Process-only sample sets

11 The Number of Process Only Sample Sets field tracks the number of times each injection or channel is associated with a process-only sample set. You can access this field from the following areas in the Empower 3 interface: Injection view Channel view Review Reports Process-only sample set privileges The Manage Process Only Sample Set privilege controls user access to process-only sample set functionality. You can view and copy process-only sample sets in the Project Window and QuickStart Sample Set view even if you do not have the Manage Process Only Sample set privilege. Nevertheless, you must have the privilege to perform actions relating to creating a process-only sample set. To delete process-only sample sets, you must have both the Manage Process Only Sample Set privilege and the Delete Data privilege. To enable or disable the Manage Process Only Sample Set privilege: 1. In the Configuration Manager tree, click User Types. 2. Select the user type for which you want to grant process-only privileges, right click, and then select Properties. 3. In the User Type Properties dialog box, click the Methods tab. 4. In the list of properties, select or clear the check box Manage Process Only Sample Set. 5. Click OK. 6. Supply a comment and a password, if required, and then click OK. Process-only sample set privileges 1-3

12 Creating a process-only sample set A process-only sample set is comprised of existing injection, channel, or sample set data you select from the Project window or the QuickStart application. You can mix any sample types in a process-only sample set. When you create a process-only sample set, the Empower 3 software makes a copy of the original data. The injection ID of the data in the process-only sample set is the same as the injection ID of the native data. However, the vial IDs of the data in the process-only sample set are different from the vial IDs of the native data. Built-in sample information fields such as Node and System Name are populated when the information is relevant to all data within the process-only sample set. Otherwise, these fields are blank. To create a process-only sample set: 1. In the Project window or the QuickStart application, select the injections, channels, or sample sets you want to include in the process-only sample set. 2. Click Tools > Create Process Only Sample Set. 3. In the Name Sample Set dialog box, enter a name for the sample set. Tip: The name you select also becomes the name of the process-only sample set s sample set method. Restriction: The name Untitled is not a valid process-only sample set name. 4. Click OK. Result: The process-only sample set editor appears and searches for duplicate entries and for sample lines that can be split into individual sample lines. 5. If you selected replicate injections that share the same vial ID, the software prompts you to merge the injections into one sample line. To merge the injections, click Yes. To bring the injections into the editor individually, click No. 1-4 Process-only sample sets

13 6. Add or rearrange data in the Process-Only Sample Set Editor window as follows: To add data to the process-only sample set, in the Project Window or the QuickStart interface, select the injections, channels, or sample sets you want to add to the process-only sample set and drag them into the process-only sample set editor. If you add injections generated from the same vial, the editor prompts you to merge them into one sample line. To add a function to the process-only sample set, select a row in the process-only sample set editor, and then select Edit > Insert Row. The row is added to the process-only sample set above the row you selected. To delete a row from the process-only sample set, select the row you want to delete, and then select Edit > Delete Row. Deleting an item from a process-only sample set does not delete the item from the original sample set or from the project. To merge sample lines, select the lines you want to merge, right-click, and then select Merge Sample Lines. To rearrange rows, select a row and then drag it to the desired position. You can select and move one or more rows at the same time. 7. Select File > Save to save the process-only sample set. Important: Be sure the process-only sample set is configured as desired before you save it. After you save the sample set, you cannot reopen the process-only sample set editor. You must make all subsequent changes to the process-only sample set using the Alter Sample function. Process-only sample set editor considerations You cannot create new sample lines in the editor. You must bring existing injections, channels, or sample sets into the editor. The Auto Fill, Add Row, Insert Rows, and Delete Rows functions exactly as they do in the Alter Sample editor. The Copy, Paste, and Cut menu items and their corresponding key combinations are not supported in the process-only sample set editor. Use the drag-and-drop function to rearrange items in the editor. You cannot change injection volumes in the process-only sample set editor. Creating a process-only sample set 1-5

14 Altering process-only sample set information After you save a process-only sample set, you cannot edit it in the process-only sample set editor. You must make all changes using the Alter Sample function. Use Alter Sample to edit the process-only sample set in the same way that you modify native sample sets. Because the data within a process-only sample set is a copy of the original data, altering the process-only sample set does not alter the original data and vice versa. When you modify sample or sample set information in a full audit trail project that contains a process-only sample set, the software generates sample/sample set history information, starting from the point of process-only sample set creation. Acquiring a new sample set based on process-only sample sets Empower 3 software allows you to reacquire a sample set based on process-only sample sets, in the same manner as regular sample sets. There are two ways to acquire process-only sample sets. Tip: Ensure that the system configuration used for all samples in the sample set are compatible. To acquire a process-only sample set from the Run Samples window: 1. In the Empower 3 Pro window, click Run Samples. 2. In the Run Samples dialog box, select the chromatographic system on which you want to run samples, and then click OK. 3. In the Run Samples window, select File > Load Samples. 4. In the Load Sample dialog box, select Reinject samples from a previously run sample set, and then click OK. 5. In the Project window, click the Sample Sets tab, and then select the process-only sample set. 6. Click the Load into Run Samples button. 7. Run the samples as you would run a regular sample set. 1-6 Process-only sample sets

15 To run a process-only sample set from the Project window: 1. In the Project window, click the Sample Sets tab, right-click the process-only sample set, and then select View as > Sample set methods. 2. Right-click the sample set method, and then select Method Properties. 3. In the Method Properties dialog box, select the method, and then click Save as current. 4. Click OK. The software saves the process-only sample set as a sample set method, which now appears in the Methods tab in the Project window. 5. Run the process-only sample set as a normal sample set method. Reporting process-only sample sets You can create reports only by using results or result sets that were generated from process-only sample set. You cannot print the process-only sample set (the raw, unprocessed data) or bring it into Preview or Report Publisher. Results and result sets generated from process-only sample sets are reported in the same manner as native Empower results. Process-only sample set considerations This section provides details about how Empower 3 software behaves with process-only sample sets. Saving process-only sample sets When you save a process-only sample set, the software behaves as follows: Generates a new sample set method associated with the sample set. For Full Audit Trail projects, removes existing sample history of the data within the process-only sample set. The sample history remains with the original sample set. Assigns the same date and time to the sample set s start and end dates. Reporting process-only sample sets 1-7

16 Stores the name of the user who created the sample set in the Acquired By column. Sets the System and Node names of the process-only sample set to empty, unless the System and Node information is the same for all data included in the process-only sample set. Copying and deleting process-only sample sets When you copy a process-only sample set to another project, the software generates a regular sample set by cloning associated injections, vials, and methods. The copied sample set, indicated by the Copied Process Only sample set type, behaves like a conventional sample set in the destination project. Before deleting individual injections or channels that are associated with a process-only sample set, you must delete any associated process-only sample sets. Custom fields Empower 3 software populates process-only sample sets with sample set type custom field data as follows: When you create a process-only sample set from... Injections or channels Multiple sample sets Empower 3 software Does not copy sample set custom field information. Copies only the sample-set-level custom fields from the first selected sample set to the new, process-only sample set. Custom fields from other sample sets are ignored. Sample type custom field information is retained when you create a process-only sample set. To supply or edit custom field values in process-only sample sets, use the Alter Sample function. 1-8 Process-only sample sets

17 Audit trail and revision history comments When you create, alter, or delete a process-only sample set, the Comment dialog box allows you to enter comments for the process-only sample set and underlying sample set method. These comments are separate from and in addition to audit trail comments. When you save a process-only sample set, the software prompts you for the revision history reason and the audit trail reason based on the sample object comment setting or the method object comments setting, as follows: Both settings Silent The software requests neither sample history reason nor audit trail reasons. The software does not enter default comments into the audit trail. Both settings not Silent The software requests reasons for both sample revision history and audit trail. Either setting Restricted The software considers audit trail commenting as restricted and the Save dialog box displays the audit trail strings associated with the Sample and/or Method objects in the Default Comments area of the dialog box. If no default string is available, then the software prompts you to enter comments. Either setting Unrestricted, with neither setting set to Restricted The software considers the audit trail commenting as unrestricted, and the Save dialog box allows you to use the Default Comments drop down list or the comments area of the Save dialog box to create comments. The audit trail record and the sample/method revision history record comments share these comments description. Audit trail records Process-only sample sets have the following audit trail records types: Record type Created Process Only Sample Set Action Records the creation of a process-only sample set. The details section of this audit trail record shows all injection IDs associated with the process-only sample set, the sample set ID, the sample set method ID, and an audit trail reason. Process-only sample set considerations 1-9

18 Record type Altered Process Only Sample Set Deleted Process Only Sample Set Action Records the modification of a process-only sample set in the Alter Sample editor. The details section of the audit trail record shows the sample set name and ID, sample set method name and ID, and an audit trail reason. Records the deletion of a process-only sample set. The details section of this audit trail record shows the sample set name and ID and an audit trail reason. Injection IDs are not listed in this entry because actual injections are not deleted Process-only sample sets

19 2 Calculating USP, EP, and JP signal-to-noise ratio This chapter describes USP, EP, and JP signal-to-noise calculations that are new or changed in Empower 3. Contents Topic Page Calculation method 2-2 Calculating the signal-to-noise ratio using a blank value

20 Calculation method The software calculates signal-to-noise ratio according to the latest US, European, and Japanese pharmacopeias, as shown by this equation s/n = 2h/h n where h = the height of the peak corresponding to the component h n = the difference between the largest and smallest noise values observed over a distance equal to at least five times (USP) or 20 times (EP and JP) the width at the half-height of the peak and, situated equally around the region of the peak of interest in a blank injection. You can specify whether to calculate USP, EP, and JP s/n using the Calculate USP, EP, and JP s/n (formerly Calculate EP s/n) check box on the processing method s Suitability tab. You also can specify whether to calculate USP s/n, EP s/n, and JP s/n using noise values calculated from the peak regions centered on a blank injection. Noise regions are unique to each peak. You determine noise regions by means of a corresponding blank injection that centers the noise region at the retention time of each peak. You define the noise region by specifying the half-height multiplier parameter. USP s/n The new suitability peak field USP s/n is implemented using the signal-to-noise (s/n) formula in the US Pharmacopeia. USP s/n is calculated as 2 height/(noise/scaling) where: height = the absolute value of the height of the peak noise = the peak's noise value (peak-to-peak noise) scaling = the scale to µv value By default, the software reports the USP s/n value to a precision of 6, not in scientific notation, and with no units. 2-2 Calculating USP, EP, and JP signal-to-noise ratio

21 The noise value used to calculate USP s/n is determined according to the state of the Use noise centered on peak region in blank injection option: When you select this option, the software calculates a noise value for each peak using the peak-to-peak noise determined in the blank injection. The value is calculated for a region in the same channel in a separate blank injection. This region is centered around the peak's retention time and has a width equal to the peak s width at half height the Half Height Multiplier for USP Noise Region value. The software reports this noise value in the result as USP Noise. By default, the software reports the value to a precision of 6, not in scientific notation, and with the units Plot Units. When you clear the option, the software uses the result's peak-to-peak noise value; noise is not calculated using the blank injection. You specify the start and end times of this region on the processing method s Noise and Drift tab. The Half Height Multiplier for USP s/n Noise Region field, located on the processing method s Suitability tab, has a range of 1 to 99 and defaults to 5. The field is inactive when you clear the option Use noise centered on peak region in blank injection and when the pharmacopoeia choice is JP or EP. EP s/n The EP s/n suitability peak fields are implemented using the signal-to-noise (s/n) formula in the European Pharmacopoeia. The EP s/n is calculated as 2 (height - (0.5 noise/scaling))/(noise/scaling) where: height = the absolute value of the height of the peak noise = the peak's noise value (peak-to-peak noise) scaling = the scale to µv value By default, the software reports the EP s/n value to a precision of 6, not in scientific notation, and with no units. Calculation method 2-3

22 The noise value used to calculate EP s/n is determined according to the state of the Use noise centered on peak region in blank injection option: When you select this option, the software calculates a noise value for each peak using the peak-to-peak noise determined in the blank injection. The value is calculated for a region in the same channel in a separate blank injection. This region is centered around the peak's retention time and has a width equal to the peak s width at half height the Half Height Multiplier for EP Noise Region value. The software reports this noise value in the result as EP Noise. By default, the software reports the value to a precision of 6, not in scientific notation, and with the units Plot Units. When you clear the option, the software uses the result's peak-to-peak noise value; noise is not calculated using the blank injection. You specify the start and end times of this noise region on the processing method s Noise and Drift tab. The Half Height Multiplier for EP s/n Noise Region field, located on the processing method s Suitability tab, has a range of 1 to 99 and defaults to 20. The field is inactive when you clear the option Use noise centered on peak region in blank injection and when the pharmacopoeia choice is JP or USP. JP s/n The new JP s/n suitability peak field is implemented using the signal-to-noise (s/n) formula in the 16th JP Pharmacopoeia. The JP s/n is calculated as 2 (height - (0.5 noise/scaling))/(noise/scaling) where: height = the absolute value of the height of the peak noise = the peak's noise value (peak-to-peak noise) scaling = the scale to µv value By default, the software reports the JP s/n value to a precision of 6, not in scientific notation, and with no units. 2-4 Calculating USP, EP, and JP signal-to-noise ratio

23 The noise value used to calculate JP s/n is determined according to the state of the Use noise centered on peak region in blank injection option: When you select this option, the software calculates a noise value for each peak using the peak-to-peak noise determined in the blank injection. The value is calculated for a region in the same channel in a separate blank injection. This region is centered around the peak's retention time and has a width equal to the peak s width at half height the Half Height Multiplier for JP Noise Region value. The software reports this noise value in the result as JP Noise. By default, the software reports the value to a precision of 6, not in scientific notation, and with the units Plot Units. When you clear the option, the software uses the result's peak-to-peak noise value; noise is not calculated using the blank injection. You specify the start and end times of this region on the processing method s Noise and Drift tab. The Half Height Multiplier for JP s/n Noise Region field, located on the processing method s Suitability tab, has a range of 1 to 99 and defaults to 20. The field is inactive when you clear the option Use noise centered on peak region in blank injection and when the pharmacopoeia choice is USP or EP. Calculating the signal-to-noise ratio using a blank value You can use noise values calculated for a blank injection(s) to calculate USP, EP, and JP signal-to-noise ratios. When the software calculates the noise value from a blank injection(s), it behaves as follows: If the sample set includes a single blank injection, the software uses the injection to determine the peak-to-peak noise values for each peak in the sample set. If the software finds multiple blank injections in the sample set, it calculates multiple noise values for each blank injection (of the same channel), averages them, and then uses the average noise value. The s/n Blank Channel IDs field displays the IDs of the blank channels used to determine USP, JP, and EP noise, and subsequently USP, JP, and EP s/n. Calculating the signal-to-noise ratio using a blank value 2-5

24 Blank injections are defined by selecting the Blank check box in Run Samples, the sample set method editor, or Alter Sample. The blank injection(s) must occur in the same sample set and must be located before the injections for which USP, JP, and EP s/n is being determined. By default, this check box is cleared. Use the Calculate USP, EP, and JP s/n check box on the processing method s Suitability tab to specify whether to calculate USP s/n, EP s/n, and JP s/n. Use the Use noise centered on peak region in blank injection check box on the processing method s Suitability tab to specify whether to calculate USP s/n, JP s/n, and EP s/n using noise values calculated from a blank injection. Use the USP Half Height Multiplier for Noise Region, EP Half Height Multiplier for Noise Region, and JP Half Height Multiplier for Noise Region to specify the noise region in the corresponding blank chromatogram. Empower determines the half height of each integrated peak in the chromatogram and uses a noise interval in the blank equal to a distance of the half height the multiplier specified in the processing method. The noise region is determined in the blank(s) and is centered around the retention time of each peak of interest. Tip: The Blank check box is also available for use in custom field formulas. When signal to noise is calculated with the Use noise centered on peak region in blank injection option selected, the noise value is either a noise value calculated from a single blank channel or an averaged noise value calculated from multiple blank channels. The new suitability result field s/n Blank Channel IDs holds the IDs (separated by spaces) of the blank channels used. The s/n Blank Channel IDs field is blank if USP s/n, JP s/n, and EP s/n are not calculated using noise values from blank channels. Rule: The blank channel must be placed earlier in the sample sequence than the channels that use it to calculate USP s/n, EP s/n and JP s/n. If you do not apply the noise from a blank injection(s), the software uses the peak-to-peak noise, as determined using the parameters specified on the processing method s Noise and Drift tab. The Peak to Peak Noise field is used as the noise value for USP s/n, EP s/n, and JP s/n only if you select Calculate USP, EP, and JP s/n but do not select Use noise centered on peak region in blank injection in the Processing method s Suitability tab. The noise region in the blank requires a minimum of five data points to determine noise. Ten or more are recommended. 2-6 Calculating USP, EP, and JP signal-to-noise ratio

25 To calculate signal to noise using a blank value: 1. Include one or more blanks in your sample set to inject before injection of the samples for which you want to calculate signal to noise. Select the Blank check box for the blank samples. 2. On the processing method s Suitability tab, select both Calculate USP, EP, and JP s/n, and Use Noise Centered on Peak Region in Blank. 3. Process the sample set with the processing method from step 2 or a method set that contains the processing method from step 2. Calculating the signal-to-noise ratio using a blank value 2-7

26 2-8 Calculating USP, EP, and JP signal-to-noise ratio

27 3 Mass spectrometry This chapter describes mass spectrometry functionality that is new or changed in Empower 3. Contents Topic Page Ion ratio processing (Peak ratio processing) 3-2 Target Mass 3-7 MS library changes

28 Ion ratio processing (Peak ratio processing) Use the new ion ratio processing parameters to calculate ion ratio peak values for LC, PDA, GC, IC, CE, CIA and MS results. Ion ratio processing produces multi-channel results similar to cross channel internal standard processing. Ion ratios are available for native 2D channels, derived 2D channels, and 2D channels extracted from 3D data. Tip: Although the main function of this functionality is to determine MS ion ratios, you also can use it to determine peak ratios for non-ms data. Using the Peak Ratios (MS Ion Ratios) tab The LC Processing Method window includes the new Peak Ratio (MS Ion Ratios) tab. Use this tab to select a processing method component and enter the information necessary to complete cross-channel peak ratio calculations with acceptance tolerance checking on data related to an injection. The Peak Ratios (MS Ion Ratios) tab includes the following components: Components of the Peak Ratios tab: Component Description Primary Peak Table (Primary MS Ion Table) Secondary Peak Table (Secondary MS Ion Table) Enables you to specify one or more existing components and the primary channel. You can specify a channel by name or by description. You also can specify whether the software determines the peak ratio by area or height. Contains the secondary peaks for the component that you select in the Primary Peak table. This table can contain up to four secondary peaks. Peak Response field Enables you to specify determination of the peak (ion) ratio by peak area or peak height. 3-2 Mass spectrometry

29 Tips: In Review and QuickStart, you can specify the channel description by selecting it from the drop down list. The software does not store channel descriptions in the processing method. The purpose of channel descriptions is only to help you specify the appropriate channel name. When you create derived channels, ensure that each channel description is unique. The software requires unique channel names and descriptions when it loads data into the Peak Ratio Tab. Entering peak ratio tolerances and reference injections You can enter peak ratio acceptance tolerances for each peak ratio channel. The acceptance tolerances are percentages of the reference injection s peak value. For example, if peak ratio tolerance is 20, the peak ratio for the unknowns must be within 20% of the peak ratio for the same component in the reference injection. The system flags results outside of the specified peak ratio tolerance as faulted. A fault is a condition (detected by Empower software) that results during processing or acquisition when either a peak field value is outside the limits set in System Suitability, or the Internal Standard, RT Reference, Default, or Must peak is missing. Because the peak ratio fields exist only in the main results, the system flags only those results when peak ratio faults exist. See also: System Suitability Limit fields in the Empower 3 online information system. Although the Peak Ratio Tolerance field instructs the software to assess the peak ratios relative to a reference injection, you also can use the System Suitability Limits tab to define absolute limits on the four peak ratio value peak fields. To define the reference injection: 1. Open the sample set in the Run Samples sample table or the Alter Sample editor. 2. For each sample you want to designate as a reference injection, select the Peak Ratio Reference check box. When processing a sample set that contains more than one reference injection, the software processes the samples in the order specified in the sample set, Ion ratio processing (Peak ratio processing) 3-3

30 averaging the peak ratio(s) of the reference injections with those of previous reference injections, and applying this running peak ratio average for subsequent samples. Peak ratio results Peak ratio processing produces multi-channel results similar to those produced by cross-channel, internal standard processing. The multichannel result includes a main result that is quantitated or calibrated as in normal single channel processing, and a list of one or more sub results. The sub results include a result for each of the primary and secondary peak ratio channels for all the components listed in the Peak Ratio tab, unless one of the peak ratio channels is the same as the main result s channel. Main results are displayed in the Project window. To display sub results, bring the main result into Review, click the 2D Channels tab, and then select the Sub Results check box in the table. Tip: It is often helpful to display main and sub results in a stack plot. Results include: Peak Ratios (ion ratios) 1-4. Peak Ratio % Difference 1-4 (the difference between the peak ratio of the current result, as compared with the reference, expressed as a percentage). Peak Ratio Tolerance (the tolerance specified in the processing method). The software displays faulted results (results that are outside of the tolerance limit) in bold, red font. The software determines each Peak Ratio value by dividing the Peak Response of the appropriate primary channel by the Peak Response of the secondary channel. For example, to calculate a ratio when the Peak response is set to Height, the software uses the height of the peak in the primary channel as the numerator and the height of the peak in the secondary channel as the denominator. Both channels are always from the same injection. Peak Ratio Reference injections are used only under the following conditions: Peak Ratio Reference injections must be in the same Sample Set as the sample injections that refer to them. Peak Ratio Reference injection results must have been processed with the same processing method as the sample injections. 3-4 Mass spectrometry

31 Peak Ratio Reference injection results must have been processed before the sample injections. If a Peak Ratio Reference injection was processed multiple times, only the last saved (non-superseded) result for the injection is used. When Cross Channel Peak Ratio processing is performed in Review, the software ignores Peak Ratio Reference injection results unless they have been saved to the database. Tip: You must ensure that the Peak Ratio Reference injections are processed and the results saved to the data base before the non Peak Ratio Reference injections. When the software processes peak ratios for a Peak Ratio Reference injection, the Peak Ratio Reference values in the Peak Ratio Reference result s peaks are blank. The values are blank because a Peak Ratio Reference injection cannot reference another Peak Ratio Reference injection. Peak Ratio view in Review and QuickStart In Peak Ratio View mode, the Chromatogram plot displays the channels in the current result that are associated with the selected peak ratio peak. These channels include the main result channel and the sub results associated with the primary and secondary peak channels named in the component s peak ratio parameters. To turn on and turn off Peak Ratio mode: Perform one of the following steps: To turn on Peak Ratio mode, in the Chromatogram plot, right-click within a peak, and then select Show Peak Ratio (MS Ion Ratio) View. To turn off Peak Ratio mode, in the Chromatogram plot, right-click a peak, and then select Return from Peak Ratio (MS Ion Ratio) View. Peak Ratio (MS Ion Ratio) Report groups The Processing Method report group tree includes the new Peak Ratio Plot report group and Peak Ratio Table group. Use these groups to report peak ratio (MS ion ratio) parameters for all processing method types except GPC. Ion ratio processing (Peak ratio processing) 3-5

32 Peak Ratio Plot group Use the Peak Ratio Plot group to report, in plot format, a component and its peak ratio results. Each plot reports only one component overlaid in a single or stack plot. This group includes the following sub-groups: Overlay Chrom All Peaks Overlay peak Ratios You can use the Peak Ratio Plot properties dialog box to specify whether to plot one peak and its ratio peaks per plot, or to plot the entire chromatogram and any associated chromatograms that contain ratio peaks related to the peaks in the main result. For example, consider a result that contains two peaks, Component A and Component B, each with one associated peak ratio. If you overlay one peak per plot, the result produces two plots, one for Component A and its associated ratio peaks, and another plot for Component B and its associated peaks. The plots show only the peaks. They do not show full chromatograms. If you overlay chromatograms, the result produces two plots, one for Component A, and another plot for Component B. Each plot shows full chromatograms for the main peak and related peak ratios. To report and customize Peak Ratio Plot information: 1. In Report Publisher, perform one of the following procedures: Create a Peak Ratio Plot report group method. Open a report method that includes a Peak Ratio Plot report group. 2. Right-click the Peak Ratio Plot group, and then select Peak Ratio Report Properties. 3. In the Peak Ratio Plot Properties dialog box, use the Peak Ratio Plot tab to select one of the following: Overlay Peak Ratio (1 peak/plot) Overlay chromatogram with All Peak Ratios 4. Use the tabs on Peak Ratio Plot Properties dialog box to customize the Peak Ratio Plot report. 3-6 Mass spectrometry

33 Peak Ratio Table group Use the Peak Ratio Table group to report, in tabular format, a peak and its peak ratio results. Each table reports information for only one peak and its associated peak ratio results. To report and customize Peak Ratio Table information: 1. In Report Publisher, perform one of the following procedures: Create a Peak Ratio Table report group method. Open a report method that includes a Peak Ratio Table report group. 2. In the report, right-click the Peak Ratio Table group, and then select Peak Ratio Table Properties. 3. In the Peak Ratio Table Properties dialog box, use the tabs to select customization options. Target Mass Using the sample table and a single method to process multiple base masses In previous versions of the Empower software, you can enter only one target mass per processing method. To target a different base mass, you must use a different processing method and reprocess the same data. In Empower 3 software, you can enter as many as five target masses in the sample table together with a method set containing the corresponding processing method. As a result, you can use the same processing method to process multiple target masses in one sample or different target masses in different samples. Enter target mass information when you use Run Samples, QuickStart, or Open Access to acquire data. You also can use the Alter Sample function to add or modify masses to data that has already been acquired. When the sample table contains target masses, and the target mass functionality is enabled in the processing method, the software calculates target masses. You also can specify a target mass in the processing method, in the same way that you did in previous versions of Empower. Target masses Target Mass 3-7

34 specified in the sample table supersede the single base mass specified in the processing method. To enable the Target Mass functionality: 1. Ensure that the Mass Spectrometry option is enabled in the project. 2. Add the target masses to the samples. 3. As in Empower 2, configure the MS processing method for injection-based expected mass processing. 4. As in Empower 2, add the processing method to the Expected Mass dialog in the Method Set Editor. (To open the Expected Mass dialog box, click the Expected Mass button.) Configuring the MS Processing method To accommodate multiple base masses, the MS processing method includes the following additions and changes. New MS processing method additions and changes: Addition/Change Include the Uncorrected Target or Base Mass in the list of expected masses option (new functionality) Expected Mass Injection-based base processing (changed functionality) Injection-based Base Mass and Intensity fields (changed functionality) Ionization Mode (new functionality) Description If selected, uses only the adduct-corrected target or base masses in the list of expected masses. If you do not select this option, the software includes the target or base mass and also the adduct-corrected target or base mass in the list of expected masses. Enables you to specify expected mass injection-based base masses in either the MS processing method or the sample table. Accept blank input. Specifies the ionization mode (positive or negative) of the channel that contains the adduct. You can leave this field blank. 3-8 Mass spectrometry

35 New MS processing method additions and changes: (Continued) Addition/Change Percentage of Base Peak column in the Injection-based Adduct table (new functionality) Description When the Include the Uncorrected Target or Base Mass option is selected, enables you to specify, in the Injection-based Adduct table, the percentage of base peak for the adduct. The software faults the adduct's expected intensity value in the peak when the value, as a percentage of the peaks's Expected Intensity 1 value, is less than the value that you specify here. See also: The Expected Mass Tab topic in the Empower 3 online information system. Using the Include the Uncorrected Target or Base Mass option The Include the Uncorrected Target or Base Mass option includes the uncorrected target or base mass in the list of expected masses. By default, in existing MS processing methods, this option is selected. In new MS processing methods, by default, this option is not selected. Enabling the Include the Uncorrected Target or Base Mass option If you select the Include the Uncorrected Target or Base Mass option, you can enter a maximum of four adducts of the same ionization mode provided that you observe the restrictions in the following table. Allowable entries when Include Uncorrected Target or Base Mass is selected: Condition Only positive adducts Only negative adducts Positive and negative adducts No positive or negative adducts Allowable entries Maximum of four positive adducts Maximum of four negative adducts Maximum of four positive adducts plus a maximum of four negative adducts Maximum of four unspecified (blank) adducts Target Mass 3-9

36 Allowable entries when Include Uncorrected Target or Base Mass is selected: (Continued) Condition Positive and blank adducts Negative and blank adducts Allowable entries Maximum of three positive and one blank adducts Maximum of three negative and one blank adducts Additionally, the software allows the adduct table to remain empty. To enable the Include the Uncorrected Target or Base Mass option: 1. Create an MS processing method, or open an existing MS processing method in the processing method editor. 2. On the MS Expected Mass tab, select the Include the Uncorrected Target or Base Mass in the list of expected masses check box. 3. Make other desired changes to the processing method, and then save it. Clearing the Include the Uncorrected Target or Base Mass option If you clear the Include the Uncorrected Target or Base Mass option, you can enter a maximum of five adducts provided that you observe the restrictions in the following table. Allowable entries when Uncorrected Target or Base Mass is cleared: Condition Only positive adducts Only negative adducts Positive and negative adducts No positive or negative adducts Positive and blank adducts Negative and blank adducts Allowable entries Maximum of five positive adducts Maximum of five negative adducts Maximum of five positive adducts plus a maximum of five negative adducts Maximum of five unspecified (blank) adducts Maximum of four positive and one blank adducts Maximum of four negative and one blank adducts Rule: You must add at least one adduct to the table Mass spectrometry

37 To clear the Include the Uncorrected Target or Base Mass option: 1. Create an MS processing method, or open an existing MS processing method in the processing method editor. 2. On the MS Expected Mass tab, clear the Include the Uncorrected Target or Base Mass in the list of expected masses check box. 3. Make other desired changes to the processing method, and then save it. Specifying base masses according to the expected mass injection You can specify base masses according to the expected mass injection in both the MS processing method and sample table. You can add an expected mass processing method to a Method Set via the Expected Mass Processing button in the Method Set editor. This function is available for all MS detectors. When processing an MS scan channel with a method set containing an expected mass processing method, if the sample table contains target masses, the software creates an MS Result for each target mass. If the sample table contains no target masses, the software creates an MS result for the base mass in the processing method. Tip: The target masses that you specify in the sample table supersede the single-base mass listed in the processing method. If you select Include the Uncorrected Target or Base Mass in the List of Expected Masses, the target or base mass is the first mass in the list of expected masses. If you clear Include the Uncorrected Target or Base Mass in the List of Expected Masses, the target or base mass is not included in the list of expected masses. To specify expected base masses in the processing method: 1. Create an MS processing method, or open an existing MS processing method in the processing method editor. 2. On the MS Expected Mass tab, select Injection-Based Processing. 3. Select or clear the Include the Uncorrected Target or Base Mass in the list of expected masses check box. Target Mass 3-11

38 4. Enter a base mass in the Base Mass box. Alternative: Enter the base mass in the Target Mass 1-5 fields in the Sample Table. 5. In the Adduct table, enter an adduct delta mass value, in Daltons, and then enter an adduct intensity in percent. 6. Make other desired changes to the processing method, and then save it. Specifying the Ionization mode Use the Ionization mode option to match the mode of the adducts of the MS data. To specify the Ionization mode: In the Expected Mass tab of the MS Processing Method for injection-based processing, use the Ionization mode field in the Adduct table to set the Ionization mode for the adduct. If the adduct's Ionization mode is Positive, the adduct is applied only to positive Ionization Mode 3D MS channels. If the adduct's Ionization mode is Negative, the adduct is applied only to negative Ionization Mode 3D MS channels. If the adduct's Ionization mode is blank, it is applied to all 3D MS channels. Using the Percentage of Base Peak field When the Include the Uncorrected Target or Base Mass in the List of Expected Masses option is selected, use the Percentage of Base Peak field to specify a percent value used to fault an adduct's expected intensity value in the peak. The the adduct's percentage of base peak is defined as the adduct's expected intensity value as a percentage of the peaks's Expected Intensity 1 value. If the percentage of base peak is less than this entered value, then the adduct's expected intensity value is faulted Mass spectrometry