MEDICINAL CHEMISTRY APPLICATIONS BOOK

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1 MEDICINAL CHEMISTRY APPLICATIONS BOOK

2 Introduction...3 The Role of LC and MS in Medicinal Chemistry...5 SCREENING System Management for a High Throughput Open Access UPLC/MS System Used During the Analysis of Thousands of Samples OpenLynx Open Access...15 CONFIRMATION New Tools for Improving Data Quality and Analysis for Chemical Library Integrity Assessment...23 PURIFICATION Scaling a Separation from UPLC to Purification Using Focused Gradients...29 Purification Workflow Management...33 Making a Purification System More Rugged And Reliable...39 Application of MS/MS Directed Purification to Identification of Drug Metabolites in Biological Fluids...45 Evaluating the Tools for Improving Purification Throughput...51 A Novel Approach for Reducing Fraction Drydown...57 PROFILING ProfileLynx Application Manager for MassLynx Software: Increasing the Throughput of Physicochemical Profiling...63 An Automated LC/MS/MS Protocol to Enhance Throughput of Physicochemical Property Profiling in Drug Discovery...65 OPTIMIZATION Synthetic Reaction Monitoring Using UPLC/MS...71 ACQUITY UPLC System: and Cost Savings in an Open Access Environment...73

3 The Role of Liquid Chromatography and Mass Spectrometry in Medicinal Chemistry Medicinal chemistry is a scientific discipline at the intersection of chemistry and pharmacy involved with designing, synthesizing, and developing pharmaceutical drugs. Medicinal chemistry involves the identification, synthesis and development of new chemical entities suitable for therapeutic use. Wikipedia.com The objective of medicinal chemistry is to design and discover compounds that offer the potential to become beneficial and profitable therapeutic drugs. Confidently confirming the identity and quality of these new chemical entities is a major challenge, particularly when labs are asked to maximize throughput and efficiency and to manage all the data generated by a variety of systems and users. Medicinal chemistry is also an iterative process that demands rapid turnaround times. High throughput liquid chromatography/ mass spectrometry (LC/MS), together with advanced data-handling software, has become the standard technique for drug discovery compound identification and purification, addressing needs for high throughput screening, optimization, and physicochemical property profiling. Waters UltraPerformance LC (UPLC ) technology is providing a sea change in capacity for medicinal chemistry labs. UPLC uses subtwo-micron column particle sizes to produce faster, more sensitive and high-resolution separations. Our UPLC systems are available with fast-scanning detectors, both optical and mass, and can be easily controlled by software that facilitates sample analysis in open-access laboratory environments. In this applications book, we look at a variety of system solutions that address the unique challenges of medicinal chemists in five key areas. n In Screening, we will demonstrate the use of high UPLC throughput and fast-scanning MS to obtain high quality and comprehensive data about compounds in the shortest possible time. n For Compound Confirmation, we will show how an open access interface, used with UPLC technology and advanced detection, enables chemists with minimal instrument training to determine the identities of known compounds, to rapidly identify unknowns, and to characterize complex sample components. n In Purification, we provide several examples on how chemists can use UPLC along with efficient time-saving techniques to dramatically increase throughput. n In Compound Profiling, we illustrate an automated UPLC/MS/ MS protocol that not only allows for automated MS method development and data acquisition, but also allows data generated from multiple assays to be automatically processed by a single processing method. n In Optimization, we will show how chemists were able to quickly and easily monitor their reactions, noting the relative amounts of starting materials and products by using a walkup UPLC/MS system. 3

4 THE ROLE OF LIQUID CHROMATOGRAPHY AND MASS SPECTROMETRY IN MEDICINAL CHEMISTRY Darcy Shave, Paul Lefebvre, and Marian Twohig Waters Corporation, Milford, MA, U.S. INTRODUCTION Confirming the identity and quality of new chemical entities is a major challenge facing the pharmaceutical industry. Maximum efficiency is essential for laboratories challenged by throughput requirements and the management of data from a variety of systems and users. Liquid chromatography with mass spectrometry has become the standard technique for confirming the identity and purity of drug discovery compounds to support high throughput screening (HTS), optimization, and physicochemical property profiling of these compounds. Medicinal chemistry is an iterative process and requires rapid turnaround times. High throughput solutions together with advanced data handling software must be employed. In this application note, we look at various solutions, including sub-2 µm column particle sizes, fast scanning mass spectrometers, and new software to assist the medicinal chemist in five key areas: n Screening n Confirmation n Purification n Compound profiling n Optimization METHODS AND DISCUSSION Screening It is important to verify the identity and purity of a compound before early activity studies. Chemists need to be sure they have synthesized the expected compound. Large numbers of compounds may be created, so it is necessary for this screening to be high throughput. Because only a small amount of material is synthesized, the screening must also consume as little material as possible, while generating a diverse amount of information. Figure 1. The ACQUITY SQD with the Sample Organizer plus PDA and ELS detectors. Samples were analyzed on a Waters ACQUITY UPLC System with a Sample Organizer. The column was an ACQUITY UPLC BEH C 18 (1.7 µm, 2.1 x 50 mm) run at 30 C. The injection volume was 5 µl. Compounds were separated using a generic water/acetonitrile gradient that was 1.1 min long. Detection was done with an ACQUITY UPLC Photodiode Array (PDA), ACQUITY UPLC Evaporative Light Scattering (ELS), and SQ Mass Detector with an ESCi source for ESI/APCI switching. Plates were logged into and processed with the OpenLynx Open Access Application Manager for MassLynx Software. By using an ACQUITY UPLC System with the Sample Organizer, we were able to analyze 3840 samples in under 7 working days on a single column. On a traditional HPLC system, this would take approximately 27 working days, assuming a 10-minute run time. The ESCi source on the mass spectrometer allowed the chemist to gather data in both electrospray and APCI (with positive/negative switching) modes during the same injection. In this way, the maximum amount of data was generated with a minimal amount of sample.

5 The open access interface allowed the user to log in the sample plates while providing a minimal amount of information. A series of methods, each including gradient conditions, MS conditions, and processing parameters, was designed by the system administrator. The user simply chose a method from this list, imported their sample lists, and placed their microtitre plates in the indicated positions. The samples were then analyzed and the data was processed. Once processing was finished, the data was automatically copied to a file storage PC. From here the users could do further processing, if desired. A report file was also generated from the processed file and converted to pdf. This facilitated storage of the results in a database. Confirmation Exact mass experiments permit elemental composition determinations of unknowns or confirmation of a suspected elemental composition. This allows the medicinal chemist to confirm identities of known compounds, to rapidly identify unknowns, and to characterize complex sample components. Samples were analyzed on an ACQUITY UPLC System. The column was an ACQUITY UPLC BEH C 18 (1.7 µm, 2.1 x 50 mm) run at 30 C. The injection volume was 5 µl. Compounds were separated using a generic water/acetonitrile gradient that was 1.1 min long. Detection was done with an ACQUITY UPLC PDA and an LCT Premier XE Mass Spectrometer with an ESCi source for ESI/APCI switching. Samples were logged into the system using OpenLynx Open Access and processed with MassLynx OpenLynx with i-fit exact mass processing. Figure 2. OpenLynx OALogin plate login wizard. A fast generic liquid chromatographic method was designed to provide excellent selectivity without compromising either chromatographic resolution or speed of analysis. To obtain such an analytical method, UPLC in conjunction with oa-tof MS detection was employed. With this analytical system, identification of the anticipated samples, isomers, and possible impurities with mass accuracy deviations less than 5 ppm from the actual were obtained using LockSpray. With such high accuracy data, the calculation of elemental compositions for each of the analytes was possible. Subsequent elemental composition results were produced using the i-fit algorithm, which takes into account the distribution of the spectral isotopes for the compounds of interest and employs novel data interpretation to simplify results lists returned. The Open Access interface allowed the medicinal chemist to log in the samples while providing a minimal amount of information. The results, including a pdf report showing the most probably elemental compositions, were then made available to the chemist. 6

6 Purification Having a pure building block is important for controlling the synthetic reactions and successfully making a pure target. A pure target is critical for understanding the results of screening and building quality structure/activity relationship (SAR) information. Reverse-phase HPLC has been successfully applied to the different aspects of the medicinal chemist s process. It is capable of purifying milligrams to multiple grams in a single system, and can be configured to automatically process hundreds of samples. The results can provide high purity and recovery of the desired compounds with minimal user intervention. Samples were analyzed on a Waters AutoPurification System, including a 2545 Binary Gradient Module, 2767 Injector, and Collector, and a System Fluidics Organizer (SFO). The compounds were purified on an XBridge Prep C 18 ODB column (5 µm, 19 x 50 mm) run at room temperature. Detection was done with 2996 PDA, ELS, and 3100 mass detectors. Fraction collection and processing was done with the FractionLynx Application Manager. Compounds were separated using 5-minute gradients that were chosen by the AutoPurify functionality of FractionLynx. A rapid LC/MS method was developed for the analysis of a medicinal chemistry library. The MS data confirmed the presence of the target compound and its retention time from a high resolution LC separation with a 1-minute cycle time. The retention time corresponded to a percent organic solvent at which the compound eluted. Based on this correspondence, a focused purification method for a 19 mm I.D. column with 5 micron particles was selected to maintain the analytical resolution. The isolated target was then separated by LC. The original analytical methodology was then used to determine the new purity for each compound collected. By logging in their samples just once, the medicinal chemists were able to get a purified product along with reports showing the initial and final purities. Compound profiling In an effort to avoid clinical failures, there is an emphasis across the pharmaceutical industry on examining pharmacokinetic and safety profiles earlier in the drug discovery process. Assays are developed in order to select compounds with the highest probability of becoming successful drugs based on preferred pharmacological properties. This step includes extensive testing for the absorption, distribution, metabolism, excretion, and toxicity (ADMET) and physicochemical properties of a compound. Samples were analyzed on an ACQUITY UPLC System with a Sample Organizer. The column was an ACQUITY UPLC BEH C 18 (1.7 µm, 2.1 x 50 mm) run at 30 C. The injection volume was 5 µl. Compounds were separated using a generic water/acetonitrile gradient that was 1.1 min long. Detection was done with an ACQUITY UPLC PDA, a ACQUITY UPLC ELS and a Quattro Premier XE Mass Spectrometer with an ESCi source for ESI/APCI switching. MS conditions were optimized using the QuanOptimize Application Manager. The samples were processed using the ProfileLynx Application Manager. Properties analyzed included solubility, logp, microsomal stability, and CHI. Figure 3. MS and UV chromatograms showing targeted mass and impurities. 7

7 Optimization Once a hit is generated through library screening, optimization of the compound of interest takes place. This step involves multiple repetitions of chemical modification of the hit to develop compounds with desired properties. Chemists need to know as soon as possible that these reactions are proceeding as desired. Samples were analyzed on an ACQUITY UPLC System with a Sample Organizer. The column was an ACQUITY UPLC BEH C 18 (1.7 µm, 2.1 x 50 mm) run at 30 C. The injection volume was 5 µl. Compounds were separated using a generic water/acetonitrile gradient that was 1.1 min long. Figure 4. ProfileLynx browser showing results of solubility experiment. Early screening of physicochemical properties (PP) is an integral process for modern drug discovery. Typical PP profiling practices include properties such as solubility, stability (ph and metabolic), permeability, integrity, etc. The critical factor to consider in PP profiling is throughput. The bottlenecks to throughput include MS method optimization for a large variety of compounds and data management for the large volume of data generated. Detection was done with an ACQUITY UPLC PDA, ACQUITY UPLC ELS and an SQ Mass Detector with an ESCi source for ESI/APCI switching. Single samples were logged into the system using OpenLynx Open Access and processed with the OpenLynx Application Manager. An automated UPLC/MS/MS protocol was developed that not only allowed for automated MS method development and data acquisition, but also allowed data generated from multiple tests to be processed by a single processing method, all in an automated fashion. As a result, the physicochemical profiling process was significantly simplified and throughput increased. The column manager bypass channel allowed users to easily switch to direct flow injection analysis for compound optimization without sacrificing one of the column positions. Chemists can choose the optimal conditions and chemistry for their compounds as the column manager is a thermostat-controlled oven with temperature regulation from 10 to 90 C and has automated switching for four columns. Figure 5. Chromatograms from various times during a 60-minute reaction. During the compound optimization stage of a discovery cycle, medicinal chemists are not only interested in determining the key structural features responsible for activity and selectivity, but also what structural changes need be made to improve these characteristics. Because the reactions necessary to bring about these changes may take a long time, chemists need to be sure they are progressing as expected. 8

8 By using a walk-up UPLC/MS system, chemists were able to quickly and easily monitor their reactions, noting the relative amounts of starting materials and products. They were also able to note the formation of any side products and make the necessary alterations to minimize these in their reaction protocol. CONCLUSION We were able to increase throughput and data quality by combining UPLC with a variety of detection techniques and software solutions. n Screening: By combining the speed of the ACQUITY UPLC System with the capacity of the Sample Organizer, we were able to nearly quadruple the screening throughput of the lab, without sacrificing data quality. n Confirmation: With the Open Access interface, medicinal chemists were able to confirm the elemental composition of their compounds, with minimal instrument training. The i-fit algorithm simplified the final exact mass determination by reducing the number of possible elemental formulas. n Purification: We were able to use analytical LC/MS data to tailor the purification method to maintain the analytical resolution. n Compounds profiling: The determination of physciochemical properties was simplified with the use of the ProfileLynx Application Manager, which automated the calculations of solubility, logp, metabolic stability, and CHI. The combination of the Column Manager and QuanOptimize facilitated the development of optimal MS/MS method. n Optimization: Chemists were able to quickly and easily log in their samples to determine the progress of the reaction. They were able to see the results of the analyses within minutes. Waters, ACQUITY UPLC, UPLC, and ESCi are registered trademarks of Waters Corporation. AutoPurification, AutoPurify, FractionLynx, i-fit, LCT Premier, LockSpray, MassLynx, ODB, OpenLynx, ProfileLynx, Quattro Premier, QuanOptimize, XBridge, and The Science of What s Possible are trademarks of Waters Corporation. All other trademarks are the property of their respective owners Waters Corporation. Printed in the U.S.A. June EN LB-KP Waters Corporation 34 Maple Street Milford, MA U.S.A. T: F:

9 SCREENING

10 SYSTEM MANAGEMENT TOOLS FOR A HIGH-THROUGHPUT OPEN ACCESS UPLC/MS SYSTEM USED DURING THE ANALYSIS OF THOUSANDS OF SAMPLES Darcy Shave, Warren Potts, Michael Jones, Paul Lefebvre, and Rob Plumb Waters Corporation, Milford, MA, U.S. INTRODUCTION Many compound libraries contain compounds that were synthesized several years prior or obtained from outside resources. It is important that the expected composition of each compound be confirmed. LC/ MS has become the standard technique for confirming the purity and identification of a compound that has demonstrated activity in a biological screen. If the library store is not routinely checked, false positives in an activity screen are highly possible. This will lead to wasted time, effort, and money on compounds that should not advance in the discovery process. Because these libraries may contain thousands, if not millions, of compounds, an Open Access UltraPerformance LC (UPLC )/MS system was investigated for high-throughput library quality control. Enhancements to HPLC and LC/MS technologies have provided useful tools to improve the throughput and accuracy of these assays. Throughput can be substantially increased with the use of UPLC/ MS, which makes use of small column particles (sub-2 μm) and high operating pressure (>10,000 psi). This can result in an up to 10-fold increase in throughput along with a three-fold increase in sensitivity. Due to the large number of samples analyzed and data generated during this testing, a new software package has been created that facilitates administration of this Open Access system. It created new project directories for the users and moved the resulting project data (such as raw data files) across the network as it was created. Data processing could then be done on a separate dedicated computer. The software also monitored the instrument PC, providing on-the-fly information about its status and the status of its sample queue from a centralized location. The ACQUITY UPLC System with the ZQ Mass Detector for open access laboratories. EXPERIMENTAL All experiments were conducted using the Waters ZQ Mass Detector, equipped with an ACQUITY UPLC System with a Sample Organizer, Photodiode Array (PDA) Detector, cooled Autosampler and Column Heater. The ZQ was equipped with an ESCi source, running in the ES+ ion mode. The instrumentation was controlled by MassLynx 4.1 Software with OpenLynx and OpenLynx Open Access Application Managers. Samples were run on a 1 min gradient from 5 to 95 organic at 0.8 ml/min. The column was a 1.7 µm, 2.1 x 50 mm ACQUITY UPLC BEH C 18 Column. The PDA was set to analyze a wavelength range from 210 to 400 nm. The mass detector analyzed a mass range from 100 to 500 amu with a dwell time of 100 ms and an interscan delay of 50 ms. Eight microtitre palates, each containing 96 pharmaceutical samples, were logged onto the system using OpenLynx Open Access. The first and last samples in each plate were used for quality control.

11 RESULTS AND DISCUSSION By using an ACQUITY UPLC System with the optional Sample Organizer, we were able to analyze 3840 samples in under seven working days on a single column. On a traditional HPLC system, this would take approximately 27 working days, assuming a 10-minute run time. The Open Access interface allowed users to log in the samples while providing a minimal amount of information. A series of methods, each including gradient conditions, MS conditions, and processing parameters, was designed by the system administrator. The users simply chose a method from this list, imported their sample lists, and placed their microtitre plates in the indicated positions. The samples were then analyzed and the data was processed. Once processing was finished, the data was copied to a file storage PC. From here the users could do further processing if desired. As well, a report file was generated from the processed file and converted to.xml format. This facilitated storage of the results in a database. Instrumentation Throughput was increased by using UPLC. This technique made use of 1.7 μm column particles and high operating pressure (12,000 psi). These properties resulted in a five-fold increase in throughput. Sensitivity was not investigated. Due to the large number of samples being run, an ACQUITY UPLC Sample Organizer was also used. This thermally-conditioned sample storage compartment extended the capacity of the system by adding space for seven deep-well microtitre plates (or 21 shallow-well plates). Total sample capacity was increased from 192 samples (two plates) to 768 samples (eight plates) when using 96-well plates. If using 384-well plates, maximum capacity would be 8064 samples. An added advantage of the Sample Organizer in an open access environment is the ability to add samples to the system without pausing the sample queue. When the door to the Sample Manager is opened, any movement whether of the sample plate or of the needle is paused for safety. This pause does not occur when loading the Sample Organizer. Software administration tools The Open Access software allowed chemists to walk up to a terminal and log in samples onto an instrument, inputting the minimum of information needed for the sample run. It also allowed the system administrator to maintain control over the Open Access systems and to track the performance of each system. It facilitated batch processing and reporting of results. The administrator selected the fields that appeared when remote users logged in samples. The administrator designated fields as mandatory so that login would not proceed unless the remote users entered values for these fields. They also defined upper and lower limits for the values of numeric fields. In addition, the administrator defined the format for text that remote users entered in the text fields. The Open Access Toolkit (OAToolkit) service ran on the Acquisition PC and copied open access users batch files and raw data to remote locations once their samples were run. The information about these users, and the locations to where their data was to be sent, is contained within the administration tool. This information is uploaded to the service on the Acquisition PC. The illustration in Figure 1 and following procedure describe the order of events during typical operation. 1. The administrator uses the Administration Tool to create a user. 2. The administrator uses the Administration Tool to add extra information about the OALogin user, for example, that the raw data of any of the user s samples should be moved to the File Storage PC whenever a user s sample is processed. 3. The administrator uploads the user information to the OALogin PC. This adds the user s name to the drop-down list in the login screen on the OALogin PC. 4. The administrator uploads the user information to the OAToolkit service on the Acquisition PC. The service now contains the instructions of how to proceed if the OALogin user logs in a batch. 5. The OALogin user logs in a sample using the OALogin terminal as normal. 6. oalogin logs the sample with MassLynx. 12

12 7. When MassLynx has finished running the sample, the OAToolkit service reads the batch file (.olb), and registers that it is from a recognized user. 8. The OAToolkit service moves the raw information to the specified location on the File Storage PC Acquisition PC File Storage PC Mass Spectrometer Figure 2. OpenLynx browser report. Figure 1. Data from the mass spectrometer is captured by the Acquisition PC, then is managed by the system administrator or accessed by the individual user via the OALogin tool. The raw data is also backed up to a File Storage PC. Reporting OAToolkit Administration PC OAToolkit Administration PC The Open Access software allowed the administrator to define how samples were processed. Once all the data for a sample set had been collected, the OpenLynx Application Manager automatically processed the data and created an OpenLynx Browser report (.rpt). The browser report (Figure 2) presented a summary of results as a color-coded map (found/not found/tentative) for easy visualization of analysis results. Users accessed and reviewed the data by simply pointing and clicking on the sample location of interest. Chromatograms, spectra, sample purity, peak height, peak area, retention time, and other information can easily be reviewed within the browser. The browser report was created in the report folder of the current project. A secondary report location could have been specified, but was not. The toolkit service also allowed for a copy of the report to be sent over the network to another location. That location was specific to each user a folder on their office PCs. The users no longer had to access the Acquisition PC to view their reports. In addition, the raw data folders were moved across the network to each user s PC and the users were able to reprocess it with a process-only version of MassLynx. Finally, the OAToolkit service was used to automatically convert the browser reports to.xml format. This was accomplished using the included.xml import and.xsl export schema. This data can then be easily incorporated into a database or shared with colleagues. System monitoring On the Administration PC, the Remote Status Monitor (RSM) monitored the status of the Open Access Acquisition PC, along with other Acquisition PCs on the network and wrote that monitoring information to an.xml file. The information could then be read and interrogated remotely in a browser (Figure 3). 13

13 CONCLUSION Figure 3. Status of the Open Access Acquisition PC. More detailed information about an instrument can be displayed by clicking anywhere in the instrument row (Figure 4). Waters Open Access systems give chemists the ability to analyze their own samples close to the point of production by simply walking up to the LC/MS system, logging in their samples, placing their samples in the system as instructed, and walking away. As soon as the analysis is completed, sample results are ed or printed as desired. System configuration and setup is enabled through a system administrator who determines login access, method selection, and report generation. OpenLynx OAToolkit enables administrators to manage open access users from a central point, assigning detailed configuration information and attributes for these users, and then exporting these details to multiple OALogin PCs and Acquisition PCs. OpenLynx OAToolkit also enables administrators and users to remotely monitor the status of Acquisition PCs. Figure 4. Detailed view of instrument status. Waters, ACQUITY UPLC, ESCi, UltraPerformance LC, and UPLC are registered trademarks of Waters Corporation. MassLynx, OpenLynx, ZQ, and The Science of What s Possible are trademarks of Waters Corporation. All other trademarks are the property of their respective owners Waters Corporation. Printed in the U.S.A. June EN LB-KP Waters Corporation 34 Maple Street Milford, MA U.S.A. T: F:

14 OPENLYNX OPEN ACCESS OVERVIEW Maximum efficiency is essential for LC/MS labs challenged by throughput requirements and the management of data from a variety of systems and users. Analyzing routine samples and returning the results to chemists can easily consume an analyst s entire day, leaving them with little time to focus on tasks that require their expert attention. Walk-up open access systems allow chemists to analyze their own samples, freeing up analysts time for more challenging analyses without compromising the quality of the final results. The Waters OpenLynx Open Access Application Manager for MassLynx Software offers the power of chromatography and mass spectrometry to chemists who are not analytical instrumentation specialists. To minimize the learning curve for instrument operation, OpenLynx Open Access leads chemists through sample submission, method selection, and reporting options. The system is maintained by a system administrator who predefines the system configuration, available experimental methods, processing criteria, and reporting options. By allowing chemists to submit their own samples, routine analyses can be performed more efficiently, leaving instrumentation experts more time to focus on advanced analyses. OpenLynx Open Access offers comprehensive capabilities: n Simplified sample submission process A single page login or a step-by-step, wizard-enabled process allows users to enter their name and sample information, and select pre-determined experimental methods and processing criteria n Exact mass measurement utilization For use with the appropriate mass spectrometers n Summary report generation Reports are automatically printed, ed, and viewed via the OpenLynx browser, containing sample found/not found information, purity, probable elemental composition (with exact mass MS), chromatograms, and spectra n Walk-up optimization of MS/MS methods and quantification of compounds of interest Combines OpenLynx Open Access with QuanOptimize and QuanLynx Application Managers n Advanced search Spectral library generation and searching n Automation of routine system administration tasks Through the use of OpenLynx Open Access Toolkit (OAToolkit) SOFTWARE SETUP Defining parameters INTRODUCTION Open access LC/UV, LC/MS, LC/MS/MS, and GC/MS The OpenLynx Open Access Application Manager is designed to allow chemists to walk up to a terminal and log in samples onto an instrument, while inputting the minimum of information needed for the sample run. OpenLynx Open Access allows the system administrator to maintain control over the open access systems and to track the performance of each system. It also facilitates batch processing and reporting of results. OpenLynx Open Access allows remote users to run samples on the acquisition computer. For OpenLynx Open Access users to be successful, the administrator defines (via the OpenLynx method) the sample information that users must provide when running samples. An intuitive OALogin setup wizard simplifies the system configuration and administration workspace to include only the analytical features the administrator uses.

15 Figure 1. OpenLynx method showing some of the OpenLynx Open Access input fields. Figure 2. Administrator-set OpenLynx Open Access options. The administrator selects the fields that appear when remote users log in samples using OpenLynx Open Access via the Walk-up tab of the OpenLynx method (Figure 1). They can designate fields as mandatory so that login will not proceed unless the remote users enter values for these fields. They can also define upper and lower limits for the value of numeric fields. In addition, the administrator can define the format for text that remote users enter in text fields. Setting options for users Using the administrator mode of OpenLynx Open Access, the administrator defines how users login samples via a number of options (Figure 2). Login setup ranges from changing the window appearance to allowing users to create their own user name. Notification of users via can be enabled, as can barcode support. OALogin can be configured for use with either OpenLynx (sample processing) or AutoPurify (fraction processing). Setting file options The administrator sets several file options. These include specifying the location where the OpenLynx methods, OpenLynx status file, and HPLC files are located. The administrator can set which methods are visible to users, along with the format needed for the text fields. Configuring quality control runs The administrator can configure OpenLynx to check that the LC and MS instrumentation are working correctly, thus ensuring the consistency of the data. The quality control feature (Figure 3) allows users to run a standard and have it compared to the results of the same standard that was run at an earlier time. Values that can be used to confirm system operational performance include peak retention time, peak area, the presence of specific masses or wavelengths, and spectral intensity.

16 Figure 4. OpenLynx Toolkit Administrator Tool. Figure 3. OpenLynx Open Access quality control options. Before a QC comparison can be run to check the system, there must be an OpenLynx method that contains the expected results from a standard. The QC run acquires data from a sample with a known retention time and peak intensity and then compares the results to the values defined in the OpenLynx method. Figure 5. Remote Status Monitor. OpenLynx Open Access Toolkit (OAToolkit) OpenLynx OAToolkit allows the creation and administration of OpenLynx Open Access users. It can push user information to OpenLynx Open Access PCs across the same network, as well as gather existing OpenLynx Open Access user information from OpenLynx Open Access PCs. It can create new project directories for the OpenLynx Open Access users and can move the resulting project data (such as raw data files) as it is created. The software can monitor numerous instrument PCs, providing on-the-fly information about their status as well as the status of their batch queues all from a central location. It ensures confidence in analytical results with password protection for open access users. The OpenLynx OAToolkit includes the following key features: n Administration Tool (Figure 4) Enables an administrator to create and manage all OpenLynx Open Access users from a single PC, and replicates that information to multiple OpenLynx Open Access PCs and Acquisition PCs n OAToolkit Service Runs in the background on one or more Acquisition PCs, monitors sample batches submitted by OpenLynx Open Access users that were uploaded from the Administration Tool n Remote Status Monitor (Figure 5) Enables any user to monitor the status of Acquisition PCs and their batch queues from a single PC

17 Additionally, the OpenLynx OAToolkit Service: n Relocates data produced during the processing of an OpenLynx Open Access user s batch of samples n Creates new project folders in which to store the processing data on a timed basis n Converts report files to different formats (XML, HTML, or text) LOGGING SAMPLES Login samples window Running samples using OpenLynx Open Access (Figure 6) involves entering sample information to correctly identify the samples and loading the samples into the autosampler. The methods available to the users depend on selections made by the administrator. Figure 6. OpenLynx Open Access window. If the administrator enables user passwords (using OpenLynx OAToolkit), the user must enter their designated password before they can login samples (Figure 7). If they enter an incorrect password, an error message appears and they cannot continue until the correct password has been entered. Single-page log-in vs. wizard OpenLynx Open Access displays the wizard for sample login by default. However, the administrator can allow OpenLynx Open Access users to use a single-page dialog box (Figure 8) for single shot samples. Users can enter multiple samples in this way. OpenLynx Open Access views the samples logged in as a single job. Figure 7. Entering user password.

18 PROCESSING SAMPLES Processing data automatically The administrator determines how OpenLynx processes the Open Access results. To configure OpenLynx Open Access to process data automatically, the administrator must create an OpenLynx method that defines the processing parameters. Figure 9. With the wizard, walk-up users enter their name, choose a method, enter sample information, and place the sample in the autosampler. The single-page login contains most of the selections on the wizard pages (Figure 9) necessary to schedule samples. The benefit of the single-page login is the speed of entering information for a single sample in a single dialog box, rather than through a wizard. This wizard is beneficial when logging in larger sample sets. The administrator must define the integration parameters for the type of data they want to process: n MS+ data For positive ions (total ion chromatogram (TIC), base peak intensity (BPI), and mass chromatograms) n MS data For negative ions (TIC, BPI, and mass chromatograms) n Analog data For up to four channels of analog chromatograms n DAD data For total absorbance chromatogram (TAC), BPI, and wavelength chromatograms Specifying how peak detection occurs involves selecting the integration algorithm and parameters that control peak detection, enabling smoothing (if desired), and setting the smoothing parameters and setting threshold values. Loading samples into the autosampler There are two ways to load samples into the autosampler. The system administrator designates each plate in the autosampler as either single shot or whole plate login. If a plate is designated for single shot login, the user enters data for their samples manually or imports data from a tab-delimited text file. OpenLynx assigns available positions for the samples on existing plates. If a plate is designated for whole plate login, the user prepares data in a spreadsheet or as a text file and imports it into OpenLynx Open Access. This is useful if the user needs to run a large number of samples in one run. OpenLynx reserves the entire plate for samples and the user selects the sample locations. Typically, a system with multiple plates will have both single shot and whole plate login available. Figure 10. Chromatogram integration window. When setting the integration and peak detection parameters (Figure 10), the administrator can specify which integration algorithm (standard or ApexTrack ) to use; how the baseline will be treated for valleys, peak tailing, and drift; and how peak separation for fused

19 peaks and shoulders will be handled. By enabling smoothing, noise will be decreased by filtering data points. Smoothing types include Savitzky-Golay and mean. The threshold values are set for one or more of the four threshold parameters: relative and absolute height and relative and absolute area. This option is used to remove peaks whose height or area is less than a specified percentage of the highest peak. In addition to acquiring and processing data, quantitation and optimization can be performed through OpenLynx Open Access. Performing quantitation Open Access quantitation is a way for the user to run quantitation analysis through OpenLynx Open Access (Figure 11). OpenLynx stores the conditions required for a particular quantitation analysis in an OpenLynx method. OpenLynx Open Access users select the OpenLynx method during login. Using Open Access quantitation, OpenLynx Open Access users can quantify the results as data are acquired. The processing steps available include: n Integrating samples n Quantitating samples n Calibrating standards Using QuanOptimize with OpenLynx Open Access The optional QuanOptimize optimizes the acquisition and quantitation parameters for a particular experiment. Open Access QuanOptimize (Figure 12) generates MS and MS/MS parameters by optimizing the cone voltage, parent ion, and collision energy parameters. QuanOptimize then takes these MS methods and performs automated acquisition and processing using processing methods developed on the fly. It can quantify these results using specified methods. This technique is useful for high throughput screening. Figure 11. Open Access quantitation parameters. Figure 12. Open Access QuanOptimize parameters.

20 REPORTING Results reporting Reporting in Open Access systems is facilitated by the OpenLynx Application Manager. OpenLynx can report results using a flexible array of printed reports or through a results browser. The standalone OpenLynx browser (Figure 13) is an interactive tool for viewing OpenLynx results and can be run on any windows PC without requiring a full MassLynx installation. Chemists can use the browser on their desktop PC to view the results (.rpt file format) that had been automatically ed to them at the end of OpenLynx processing. The OpenLynx browser presents a summary of results as a colorcoded (found/not found/tentative) map for easy visualization of analysis results. Chemists can access and review the data supporting any found/not found/tentative assignment by simply pointing and clicking on the sample location of interest. Chromatograms, spectra, sample purity, peak height, peak area, retention time, and other information can easily be reviewed within the browser. Figure 13. OpenLynx browser.

21 Printing and distributing reports OpenLynx creates an OpenLynx browser report file (.rpt) after it finishes a run and processes the data. This file resides in the OpenLynx Open Access\Reportdb folder. The file is named with the job number followed by the extension.rpt when the user logs in to OpenLynx. OpenLynx report files may be exported in.txt,.tab,.csv, and.xml formats. The administrator can configure OpenLynx Open Access so remote users can find the reports that OpenLynx generates after running samples. Information such as where to store reports and what print report format to use can be specified. CONCLUSION The OpenLynx Open Access Application Manager provides comprehensive, easy, and flexible open access walk-up LC/UV, LC/MS, LC/MS/MS, and GC/MS systems operation management for laboratories that have chemists with varying levels of instrumental analysis experience. With customizable batch processing and results review to support the large amounts of data resulting from high throughput analyses, a highly productive environment is ensured for high-volume laboratories. Waters is a registered trademark of Waters Corporation. MassLynx, QuanOptimize, QuanLynx, ApexTrack, AutoPurify, OpenLynx, and The Science of What s Possible are trademarks of Waters Corporation. All other trademarks are the property of their respective owners Waters Corporation. Printed in the U.S.A. June EN LB-KP Waters Corporation 34 Maple Street Milford, MA U.S.A. T: F:

22 confirmation

23 N E W T OO L S FO R IM P ROV ING DATA QUA L IT Y A N D A NA LYSIS T IM E FOR CHEMICAL LIBRARY INTEGRITY ASSESSMENT Marian Twohig, Paul Lefebvre, Darcy Shave, Warren Potts, and Rob Plumb Waters Corporation, Milford, MA, U.S. INTRODUCTION The identity and purity of a candidate pharmaceutical is critical to the effectiveness of the drug screening process. LC/MS is employed extensively in drug discovery in order to exclude false positives and maintain the high quality of the product. This process can be time consuming and can potentially delay the progression of a drug through the discovery process. Thus, sample throughput is a critical issue in moving compounds from the hit to lead status. UltraPerformance LC (UPLC ) leverages sub-2 µm LC particle technology to generate high efficiency faster separations. When a photodiode array/evaporative light scattering/mass spectrometry (PDA/ELS/MS) detection scheme is used in conjunction with multiple-mode ionization, the potential for peak detection is greatly improved. Pharmaceutical chemical libraries often contain a great diversity of small molecules to cover a broad range of biological targets. 1 In this environment, the ability to obtain information pertaining to multiple MS acquisition modes, in addition to PDA and ELS, in a single injection is invaluable. Open Access software offers the power of chromatography and mass spectrometry to chemists who are not analytical instrumentation specialists. It allows them to quickly and easily know what they ve made and allows the experts to work on the difficult analytical problems. An Open Access UPLC/MS system was investigated for high throughput library QC. In this application note, we describe some of the enhancements to LC and LC/MS technologies that have generated useful tools that improve the throughput and accuracy of these assays. Figure 1. The ACQUITY SQD for open access. EXPERIMENTAL LC conditions LC system: Waters ACQUITY UPLC System Column: acquity UPLC BEH C 18 Column 2.1 x 30 mm, 1.7 µm Column temp.: 50 C Sample temp.: 8 C Injection volume: 2 µl Flow rate: 800 µl/min Mobile phase A: 0.1 Formic acid in water Mobile phase B: 0.1 Formic acid in acetonitrile Gradient: 5 to 95 B/0.70 min

24 MS conditions MS system: Waters SQ Detector Ionization mode: esi positive/esi negative, multi-mode ionization Capillary voltage: 3.0 KV Cone voltage: 20 V Desolvation temp.: 450 C Desolvation gas: 800 L/Hr Source temp.: 150 C Acquisition range: 100 to 1300 m/z Scan speed: 2500, 5000, and 10,000 amu/sec Sample login OpenLynx Open Access Application Manager for MassLynx Software is designed to allow chemists to walk up to a terminal and log in samples while entering the minimum information required to run the samples. A series of methods, each including gradient and MS conditions as well as processing parameters, are initially set up by the system administrator. The users choose an appropriate method from the list, importing their sample lists and placing their samples in the position designated by the software. Desired sample analysis is then performed by the configured system. The single page login window can be seen in Figure 2. Note: A low volume micro-tee was used to split the flow to the ELS and SQ. ELS conditions Gain: 500 N2 gas pressure: 50 psi Drift tube temp.: 50 psi Sampling rate: 20 points/sec PDA conditions Range: Sampling rate: 210 to 400 nm 20 points/sec Figure 2. OpenLynx Open Access single page login. RESULTS AND DISCUSSION Maximum efficiency is essential for labs challenged by throughput requirements and the management of data from multiple systems and users. The Waters Open Access suite of software streamlines the integration of analysis with data acquisition, processing, and reporting. The system and software are initially configured by a system administrator who defines login access, method selection, and reporting schemes. This allows users to analyze their own samples with minimal intervention from analytical support. Open access system Chromatographic separations were carried out using the ACQUITY SQD System coupled to detectors specialized for UPLC separations: the single quadrupole SQ Mass Detector, and PDA and ELS detectors that provided simultaneous signal collection. For additional flexibility, the UPLC system was configured with a Sample Organizer and a Column Manager. The sample capacity of the system totals twenty two 384-well plates, for 8448 library samples in total. This extends the overall walk-away time for the system. The column manager allows four UPLC columns to be installed, heated, and switched into line 24

25 based on the method requirements. This allows the chemist to take advantage of the broad range of stationary phases that encompass compound types, ranging from very hydrophilic to very lipophilic. Sample analysis Samples were analyzed using gradients less than one minute in length with a flow rate of 800 µl/min. When analyzing the narrow peaks generated by the UPLC/MS system, the data collection rate can compromise the number of points across the LC peak, resulting in a poor definition of the eluting peak and hence inaccurate results. The ability of the MS system to collect data at a high scan speed, 10,000 amu/sec, greatly improves chromatographic peak definition. This in turn facilitates the acquisition of a large number of individual acquisition modes in one run while maintaining adequate peak characterization. As can be seen from the data displayed in Figure 3, the result of operating at lower data collection rates can compromise the chromatographic resolution. To maintain chromatographic integrity, it is therefore advantageous to be able to scan at elevated scan speeds. The total cycle time of the method was 1 minute 20 seconds, facilitating increased sample throughput while still allowing generous washing steps to prevent sample-to-sample memory effects. Using a flow rate of 800 µl/min and a 2.1 x 30 mm column clears 9 column volumes/min. The spectral data quality of scanning experiments carried out from 2500 to 10,000 amu/sec were found to be comparable, thus providing confidence that operating at these rapid data collection rates does not compromise the spectral data quality. Figure 4 shows a comparison of an acquired spectrum with a software generated isotopic model. Isotope ratios of data collected at 10,000 amu/sec were within 1 of the isotopic model, again ensuring data fidelity is not compromised. In addition to obtaining mass confirmation by multiple MS modes, it is possible to add PDA and ELS detectors to obtain auxiliary information. A single run can then provide UV spectral information and an estimation of compound purity at low wavelengths amu/sec C17H20N2CIS Acquired Spectrum 10,000 amu/sec amu/sec C17H20N2CIS Isotope Model 10,000 amu/sec m/z Figure 3. Chromatograms shown at 2500, 5000, and 10,000 amu/sec. Figure 4. Spectrum for isotope model and for acquired spectrum. 25

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