Analyst software

This technical note describes a rapid and sensitive analysis of a comprehensive panel of forensic compounds in human urine using the ExionLCTM AC HPLC system and the QTRAP®/Triple Quad™ 4500 LC-MS/MS system. This forensic panel contains 93 compounds, and a total of 212 MRM transitions (including internal standards) are monitored. Some compounds ionize preferentially in positive mode, while others ionize preferentially in negative mode; therefore this method takes advantage of rapid polarity switching. The total LC runtime is 6.5 minutes, which can be further accelerated for a smaller panel of compounds. Sample preparation is based on enzymatic hydrolysis and a simple “dilute and shoot” methodology.

With the new Scheduled MRM™ Algorithm offered in the Analyst® software version 1.5, MRM transitions of the targeted analytes are monitored only around the expected retention time. Thus, automated MRM scheduling decreases the number of concurrent MRM transitions, allowing both the cycle time and the dwell time to be optimized for highest sensitivity, accuracy, and reproducibility. In addition Scheduled MRM™ allows the monitoring of many more MRM transitions in a single acquisition or to speed up the analysis by the use of UHPLC or to combine both concepts without compromising data quality.

This document outlines the 6 easy steps to upgrade a basic Multiple Reaction Monitoring (MRM) acquisition method to utilize the Scheduled MRM™ Pro algorithm to improve quantitative data quality and to automatically include Enhanced MS/MS scanning to increase confidence in compound identification and confirmation.

LC-MS/MS instruments operating in Multiple Reaction Monitoring (MRM) are widely used for targeted quantitation and screening on triple quadrupole and hybrid triple quadrupole linear ion trap (QTRAP® ) systems because of their well known selectivity and sensitivity. However, the current limit of a few hundred transitions per chromatographic run limits the number of analytes that can be monitored per injection. In this application note, find out how the new Scheduled MRM™ Algorithm offered in the Analyst® software version 1.5, only monitors the MRM transitions of the targeted analytes around the expected retention time.

The purpose of this paper is to present an approach to assist the user in meeting 21 CFR Part 11 compliance with Analyst® LC/MS Software version 1.2 and above, including Analyst Software 1.4.1, when used in quantitative studies supporting Good Laboratory Practice (GLP) bioanalytical studies. In this paper, the joint responsibilities between a supplier and its customers to support users’ 21 CFR Part 11 compliance is outlined.

In this technical note, we describe a rapid and sensitive analysis of a comprehensive panel of forensic compounds in human urine using the ExionLCTM AC HPLC system and the QTRAP®/Triple Quad™ 4500 LC-MS/MS system (Figure 1). This forensic panel contains 93 compounds, and a total of 212 MRM transitions (including internal standards) are monitored.

This document outlines the 6 easy steps you can follow to import MS/MS spectral libraries into MasterView™ software and LibraryView™ software (3 easy steps) and to add new compounds to an existing library (3 easy steps). These MS/MS libraries can be used when analyzing samples using MRM-triggered MS/MS scans collected on a QTRAP® LC/MS/MS system and compare those results to MS/MS compound libraries to identify and confirm positive peaks in unknown samples.

This application note investigates the use of overlapping SWATH windows to improve the cycle time and reduce the SWATH window size. The ability to acquire all possible MS/MS fragments during each cycle of data acquisition has radically changed peptide quantitation capabilities. Since no prior information is required, data acquisition is greatly simplified. During data processing, the particulars of which peptides and proteins are studied can be changed at any time, without the need for reacquiring any data. This investigation demonstrated that overlapping windows enabled deconvolution to narrower windows without loss in duty cycle and that narrower windows improved MS/MS quality and quantitative properties.

More studies are using MRM and targeted proteomic strategies to quantify peptides/proteins of interest in biological samples. Scheduling the acquisition of MRM transitions of analytes in time greatly increases the number of peptides that can be monitored within a single assay. However, developing a robust time-scheduled assay for larger numbers of peptides can be time consuming. This poster demonstrates a range of techniques for improving the efficiency of assay development, allowing the optimizing of a large number of peptides at once.

This application note describes a procedure to update retention times and other parameters when transferring acquisition methods using the Scheduled MRM algorithm from one laboratory to another.