September 12, 2024 - Dr. Philip Remeš, a Senior Research Scientist at Thermo Fisher Scientific, presented an educational seminar on ion trap mass spectrometers. In addition to discussing how ion traps work fundamentally, Dr. Remeš covered the strengths and weaknesses of ion traps for proteomics, as well as how ion traps are likely to be used for proteomics in the near future. Approximately 50 participants were in attendance.
Ion traps have played a critical role in the birth of mass spectrometry-based proteomics. He began by tracing the historical development of ion traps, starting from their invention in the 1950s by Wolfgang Paul. Initially used in physics to manipulate ions, ion traps were later adapted for mass spectrometry, with significant improvements made by George Stafford and colleagues in the 1970s and 1980s that enhanced their efficiency and suitability for proteomics applications. From a historical perspective, Dr. Remeš highlighted the gradual increase of ion utility with ion traps relative to triple quadrupole mass spectrometers in commercial instruments. He discussed how linear ion traps have improved upon earlier 3D designs and how linear traps have changed throughout the last quarter century.
Dr. Remeš discussed the evolution of data acquisition technologies in proteomics, emphasizing the transition from qualitative analyses using data-dependent acquisition (DDA) to more quantitative approaches like data-independent acquisition (DIA) and parallel reaction monitoring (PRM). He explained that while DDA, often coupled with Tandem Mass Tags (TMT) for sample multiplexing, is effective for peptide identification, it faces quantitation challenges due to interference. DIA has emerged as a powerful method that enhances throughput and coverage by simultaneously acquiring data on all ions and generating extensive peptide lists. He then highlighted that advancements in ion trap technology have made PRM highly effective for quantitative proteomics. He pointed out that ion traps can now achieve quantitation performance comparable to, or even surpassing, that of Orbitraps and time-of-flight mass spectrometers, especially in targeted assays, thus broadening their applicability in modern proteomics workflows.
Several criticisms of ion trap usage in proteomics have been waged. In particular, ion traps have markedly lower mass resolution than Orbitraps or time-of-flight (ToF) mass spectrometers. Dr. Remeš emphasized that this lower mass accuracy is still generally sufficient for proteomics applications. Since peptides produce multiple fragment ions during mass spectrometry, a sufficient number of fragment ions generally remain interference-free even with low mass resolution. With technological advancements like automatic gain control (AGC) and the integration of deep learning tools that predict peptide fragmentation patterns, ion traps have become highly quantitative, even at low input levels. Therefore, despite their inherent limitations in mass accuracy, ion traps remain valuable and effective instruments in the field of proteomics due to their sensitivity, efficiency, and the sufficiency of their resolution for most proteomic analyses.
This session included an extended Q&A session with the audience, guided by Brian Searle (Ohio State University, USA). A full video recording of the session, including the Q&A session, is available on the HUPO Proteomics Webinars and Virtual Presentations website. If you haven’t had the chance yet, please check out the webinar. Share it with your colleagues, coworkers, or friends.
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