Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring

Abstract

New mass spectrometry (MS) methods, collectively known as data independent analysis and hyper reaction monitoring, have recently emerged. These methods hold promises to address the shortcomings of data-dependent analysis and selected reaction monitoring (SRM) employed in shotgun and targeted proteomics, respectively. They allow MS analyses of all species in a complex sample indiscriminately, or permit SRM-like experiments conducted with full high-resolution product ion spectra, potentially leading to higher sequence coverage or analytical selectivity. These methods include MS^E, all-ion fragmentation, Fourier transform-all reaction monitoring, SWATH Acquisition, multiplexed MS/MS, pseudo-SRM (pSRM) and parallel reaction monitoring (PRM). In this review, the strengths and pitfalls of these methods are discussed and illustrated with examples. In essence, the suitability of the use of each method is contingent on the biological questions posed. Although these methods do not fundamentally change the shape of proteomics, they are useful additional tools that should expedite biological discoveries.

Keywords::

• AIF
• DIA
• FT-ARM
• HRM
• MRM^HR
• MS^E
• MSX
• PRM
• pSRM
• SAWTH-MS

Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

No writing assistance was utilized in the production of this manuscript.

Key issues

• • Data dependent acquisition employed in shotgun proteomics and selected reaction monitoring (SRM) employed in targeted proteomics have a number of short-comings that limited researchers from examining complex biological systems in terms of depth and width.

• • Emerging mass spectrometry approaches, known as data independent analysis and hyper reaction monitoring, riding on the advantages of high speed and high-resolution hybrid mass spectrometers (e.g., Q-ToF and Orbitrap), could address the short-comings of DDA and SRM.

• • One such approach eliminates the ion selection stage and produces alternating scan of precursor ions and fragments of all the precursors. The resulting product ion spectra are highly convoluted, but an algorithm capable of correlating the products with the precursors based on the retention time, chromatographic peak shapes, charge state, etc., for the ions is available. Enhancements can be brought by the use of ultra-performance liquid chromatography and ion-mobility gas-phase separation.

• • An alternative approach sequentially fragments all the ions in a relative wide isolation window, typically from 10–100 Th. The resulting product ion spectra are convoluted but can be searched against theoretical reference spectra or be mined with SRM-like targeted data extraction.

• • There are also novel targeted methods that sequence the precursor ions in a relative narrow precursor isolation window in a way similar to SRM. However, these methods do not measure the SRM transitions but to record the whole product ion spectra. The spectra can either be searched against conventional database or extracted with SRM-like ion chromatograph.

• • There is also a strategy, in which multiple but separated narrow precursor isolation windows are analyzed simultaneously. The multiplexed spectra are demultiplexed and extracted to SRM ion chromatographs. Such approach enjoys the sampling rate of the methods using wide isolation windows but has the selectivity of the methods using relative narrow precursor isolation windows.

• • These new approaches are not faultless themselves and are not substitution to data dependent acquisition or SRM. However, they are useful additional tools or new opportunity for biomedical and bimolecular investigations and may produce an impact to the field in the next few years.

Notes

MRM: Multiple reaction monitoring; SRM: Selected reaction monitoring.