Oligos 301 – Higher Level Mass Spec Detection

What is a Q-TOF and Why is it Useful?

High-resolution mass spectrometry is used for a vast array of applications due to its wide mass range, fast acquisition speed, high sensitivity, high-quality resolution, and accurate molecular weight. With the increased resolution and mass accuracy, quadrupole time-of-flight (Q-TOF) instrumentation can distinguish co-eluting compounds by resolving peaks that are of the same nominal. The accurate monoisotopic mass measurements and high-resolution MS/MS spectra for target confirmation allow the Q-TOF systems to be used for the identification of unknown compounds and much more.

Presenter: Rebecca Glaskin, PhD (LC/MS Application Scientist, Agilent Technologies, Inc.)

Rebecca Glaskin is an LC/MS Application Scientist at Agilent with a focus on BioPharma applications supporting the LC-Q/TOF and IM-QTOF platforms. Prior to joining Agilent, Rebecca received her Ph.D. in analytical chemistry from Indiana University in the lab of Professor David Clemmer. While there she designed and constructed home-built instruments, pushing the limits of the mobility resolution that can be obtained with a circular drift tube for the separation of biomolecules (peptides, proteins, carbohydrates, and metabolites). While there, she also studied hydrogen/deuterium exchange of proteins in the gas-phase as a function of time and pressure. Rebecca then went to Boston University as a Postdoctoral Associate in the lab of Professor Catherine Costello to develop a database containing collision cross section values for glycans, peptides, and glycopeptides utilizing Agilent Technologies 6560 IM-QTOF. This database can be used to determine how the collision cross section is altered with the addition of individual saccharide units. The trendlines obtained from this database will be used to predict collision cross sections for glycopeptides based on the conformation and structure of the specific glycoform.

The Analysis of Oligonucleotides using OligoSearch, a Purpose Built Software for Confirming Full Length Product and Annotating Impurities

The analysis of oligonucleotides can be difficult because the synthesis and degradation of the intended products can also generate impurities. These impurities add to the complexity of oligonucleotide sample analysis and consequently, the annotation of these impurity species ( a critical step for R&D, process improvement, and reliability) can be very time-consuming. OligoSearch software simplifies this process by

• (1) accepting the oligonucleotide sequence for the product in a common format (.txt,.csv, or .xls)
• (2) provides sample-specific processing methods with FLP and impurity information, and
• (3) creates a single-click process for the acquisition and data analysis of large sample sets.

The result of this automated analysis is searched against a software-generated impurities database, annotated, and reported. This seminar will cover the Oligo Search software, LC/TOF and LCQTOF acquisition considerations for optimum oligonucleotide performance, and MassHunter data processing techniques.

Presenter: Jim Lau, PhD (HRAMS LC/MS Application Engineer, Agilent Technologies, Inc.)

Jim Lau received his Ph.D. From the University of Colorado. There he worked in the laboratories of Peter Albersheim and Robert Shapiro. This work involved the structure elucidation of plant natural products and, in particular, elucidating the structures of oligosaccharides derived from plant cell wall polysaccharides. This work was done in the early days of LCMS and made use of DLI-LCMS and (at the time) recently invented Thermospray-LCMS.

After the completion of his Ph.D., Jim joined Hewlett-Packard to work on LCMS ionization techniques with Paul Goodley during the early days of Electrospray-LCMS. He then moved to work on field applications and collaborations with Hewlett-Packard’s LCMS customers. More than 30 years later, Jim continues to work with Agilent’s customers in High Resolution Accurate Mass applications of LCMS. While involved in many areas of HRAMS LCMS, his recent work has focused on the area of Screening/Qual&Quant of small molecules and on the high throughput confirmation of oligonucleotidesynthesis.

High-Throughput Oligo Analysis Using RapidFire (Q)TOF Mass Spectrometry

The RapidFire (Q)TOF MS system is well suited for high-throughput oligo analyses because it replaces chromatography with a quick in-line desalt, enabling a sample-to-sample cycle time of just 15 seconds. In addition to the speed capabilities of data acquisition, analysis, and review, this presentation will cover the reproducibility and versatility of the system, showing data on a wide range of oligos using both ion-pairing reverse-phase and HILIC-based methods.

Presenter: Peter Rye, PhD (LC/MS Applications Scientist, Agilent Technologies, Inc.)

Peter is a pre-sales Application Engineer with Agilent Technologies. He has been with Agilent for 10 years developing LC, RapidFire, and mass spec methods on a wide range of molecules. Prior to Agilent, Peter worked in analytical development groups for BioTove and BIOCIUS, the original companies that developed the RapidFire platform. In his spare time, you can find Peter relaxing with his wife and kids in Beverly Massachusetts, trying to fix the many problems with his home, or staying active outdoors.