LC-MS FOR OLIGONUCLEOTIDES - FRAGMENTATION AND SEQUENCING TRAINING COURSE
Understanding oligonucleotide fragmentation is essential for confirming sequence, detecting modifications, and troubleshooting complex spectra. This advanced course provides a clear, practical pathway to interpreting MS/MS data and building confident oligo sequence assignments.
This course is ideal for analytical scientists, mass spectrometrists, and lab personnel involved in oligonucleotide R&D, bioanalysis, or QC - particularly those who are expanding into large molecule analysis, or needing to characterize or sequence oligo-based materials. This course moves step-by-step from fragmentation fundamentals to full sequence reconstruction.
LC-MS FOR OLIGONUCLEOTIDES - FRAGMENTATION AND SEQUENCING COURSE DETAILS
- Fundamentals of Fragmentation: Learn how ionisation sites, ion stability, and common oligo cleavage positions influence the fragmentation landscape
- Charge State Influence: Understand how parent ion charge affects the formation and abundance of product ions
- Q2 Energy Optimisation: Optimise collision energy to improve fragmentation quality and diagnostic output
- Working with m/z Signals: Gain confidence interpreting product-ion m/z values and connecting them to specific nucleotide losses or fragments
- Neutral Fragment Calculations: Calculate neutral losses and link them directly to nucleotide identification for sequence building
- w-Series & y-Series Fragmentation: Explore the key fragmentation pathways used for oligo sequencing and learn to interpret spectra containing w and y ions
- Incomplete Fragmentation Series: Work with partial w and y series to extract maximum information, even from non-ideal spectra
- a-Series & a-B Fragmentation: Understand additional mechanistic pathways and how these ions complement w/y data in structural elucidation
- Complex Spectra Interpretation: Learn to read spectra containing combinations of w, y, a, and a-B ions, including multiply charged and overlapping fragments
- Internal, Internal-B, and d-Hâ‚‚O Fragments: Identify and interpret common secondary and internal fragments that support or complicate sequence assignment
- Building a Sequence from Fragmentation Data: Use a combination of incomplete series and multiple fragment types to confidently piece together an oligonucleotide sequence
- Deconvolution Software Approaches: Get an overview of tools and strategies used in software-assisted oligo MS/MS interpretation
- Workshops: Learn to apply all the taught techniques in carefully designed graded workshops that allow you to practice as you learn
We offer flexible delivery options for this instructor-led course:
- On-site: One full-day session at your laboratory or any location of your choice.
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Online: Two half-day interactive sessions.
View our online training calendar for upcoming dates.
Experienced in small molecule LC-MS.
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Introduction to fragmentation – ionisation sites, ion stability, common cleavage sites within oligonucleotides
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Effect of parent charge state on product ion fragments
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How we work with m/z signals in product ion scan
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Calculation of neutral fragments and how they relate to nucleotide identification / sequencing
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w-series fragmentation
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y-series fragmentation
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Interpreting combined w and y series spectra
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Incomplete series – examples working with w and y for clarity / simplicity
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a series fragmentation
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a-B fragmention
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Interpreting spectra containing w, y, a, a-B, with incomplete series and multiple charged m/z fragments
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Internal fragments
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Internal-B fragments
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d-H2O fragments
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Building an oligonucleotide sequence from combination of incomplete fragmentation series
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Overview of some of the approaches used by deconvolution software
