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.

Online Peptide Fractionation Using a Multiphasic Microfluidic Liquid Chromatography Chip Improves Reproducibility and Detection Limits for Quantitation in Discovery and Targeted Proteomics*

“…Data independent MS acquisition experiments are highly topical in modern proteomics (3,(45)(46)(47)(48). For in-depth sample characterization and quantitation it is currently a necessity to use reference spectral libraries from peptides that have been identified in previous data dependent LC-MS/MS analyses.…”

“…Nonetheless, a key requirement yet to be realized is to ensure that quantitative proteomics can be carried out in a timely manner while satisfying the aforementioned challenges associated with reproducibility. This is especially important for recent developments using data independent MS quantitation and multiple reaction monitoring on high-resolution MS (MRM-HR) 1 as they are both highly dependent on LC peptide retention time reproducibility and precursor detectability, while attempting to maximize proteome coverage (3). Strategies usually employed to increase the depth of proteome coverage utilize various sample fractionation methods including gelbased separation, affinity enrichment or depletion, protein or peptide chemical modification-based enrichment, and various peptide chromatography methods, particularly ion exchange chromatography (4 -10).…”

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

“…Since the introduction of its concept in 2004, several DIA strategies have been described and were reviewed in detail (66,(105)(106)(107). In essence, this acquisition mode converts all peptides in a physical sample into a permanent digital map composed of multiplexed MS2 spectra derived from the fragmentation of all precursor ions.…”

Label-Free Protein Quantification for Plant Golgi Protein Localization and Abundance

“…Several groups have suggested data-independent acquisition, in which individual peptide ions are not selected for fragmentation but rather, groups of peptides of similar m/z are fragmented together. The exact number of cofragmented precursors depends on the speed and sensitivity of instrument configuration (for review, see Law and Lim, 2013). The simplest approach involves alternating between low-energy and high-energy scans of equal duration; low-energy scans record precursor peptide ions, whereas in high-energy scans, all precursors entering the mass spectrometer are cofragmented, and their fragments are recorded simultaneously.…”