Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023

Lou, Ronghui; Shui, Wenqing

doi:10.1016/j.mcpro.2024.100712

Cited by 21 publications

(2 citation statements)

References 245 publications

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“…Furthermore, the AGC target was increased to 800% to fully use the 4 ms injection time. 41,42 , we wanted to explore how many glycoproteins could already be observed without glycopeptide enrichment. Therefore, we analyzed in parallel both plasma samples from which the glycopeptides had been enriched by cotton-HILIC, as well as what we term here "crude" plasma samples (Figure 1).…”

Section: Setting Up Narrow-window Nglycodiamentioning

confidence: 99%

Narrow window data-independent acquisition on the Orbitrap Astral Mass Spectrometer enables fast and deep coverage of the plasma glycoproteome

Jager,

Zeller,

Pashkova

et al. 2024

Preprint

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Recently, a conceptually new mass analyzer was introduced by pairing a quadrupole Orbitrap mass spectrometer with an asymmetric track lossless (Astral™) analyzer. This system provides >200-Hz MS/MS scanning speed, high resolving power and sensitivity, and low-ppm mass accuracy. This instrument allows a narrow-window data-independent (nDIA) strategy, improving sensitivity and reproducibility even when using very short LC gradients. Although this represents a new technical milestone in peptide-centric proteomics, this new system has not yet been evaluated for the analyses of very complex and clinically important proteomes, such as represented by the plasma glycoproteome. Here, we evaluated the Orbitrap Astral mass spectrometer for the analysis of the plasma glycoproteome, and pioneer a dedicated nDIA workflow, themed nGlycoDIA. With substantially adjusted parameters and varying collision energies, nGlycoDIA has clear benefits for plasma glycoproteomics. We tested our method both in glycopeptide enriched and crude plasma, leading to the identification of more than 3000 unique glycoPSMs from 181 glycoproteins, covering a dynamic range of 7 orders of magnitude in the enriched plasma sample in just 40 minutes. In addition, we detect for the first time several glycosylated cytokines that have a reported plasma concentration in the ng/L range. Furthermore, shortening the gradient to 10 min still allows the detection of almost 2500 unique glycoPSMs from enriched plasma, indicating that high-throughput indepth clinical plasma glycoproteomics may be within reach.

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Section: Setting Up Narrow-window Nglycodiamentioning

confidence: 99%

Narrow window data-independent acquisition on the Orbitrap Astral Mass Spectrometer enables fast and deep coverage of the plasma glycoproteome

Jager,

Zeller,

Pashkova

et al. 2024

Preprint

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show abstract

“…34 In contrast, DIA indiscriminately fragments all detectable precursor ions within a larger mass range. 35 Although DIA's methods, spectral libraries, and soware are better established in the proteomics eld, 36 DIA development and applications in metabolomics are starting to rise. [37][38][39] The classic DIA methods are based on alternation between low and high-energy channels, to acquire both MS 1 and MS 2 scans, respectively.…”

Section: Introductionmentioning

confidence: 99%

LC-MS/DIA-based strategy for comprehensive flavonoid profiling: an Ocotea spp. applicability case

Alves,

Katchborian-Neto,

Bueno

et al. 2024

RSC Adv.

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Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain

Flender,

Vilenne,

Adams

et al. 2024

Mass Spectrometry Reviews

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Immunopeptidomics is becoming an increasingly important field of study. The capability to identify immunopeptides with pivotal roles in the human immune system is essential to shift the current curative medicine towards personalized medicine. Throughout the years, the field has matured, giving insight into the current pitfalls. Nowadays, it is commonly accepted that generalizing shotgun proteomics workflows is malpractice because immunopeptidomics faces numerous challenges. While many of these difficulties have been addressed, the road towards the ideal workflow remains complicated. Although the presence of Posttranslational modifications (PTMs) in the immunopeptidome has been demonstrated, their identification remains highly challenging despite their significance for immunotherapies. The large number of unpredictable modifications in the immunopeptidome plays a pivotal role in the functionality and these challenges. This review provides a comprehensive overview of the current advancements in immunopeptidomics. We delve into the challenges associated with identifying PTMs within the immunopeptidome, aiming to address the current state of the field.

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Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023

Cited by 21 publications

References 245 publications

Narrow window data-independent acquisition on the Orbitrap Astral Mass Spectrometer enables fast and deep coverage of the plasma glycoproteome

Narrow window data-independent acquisition on the Orbitrap Astral Mass Spectrometer enables fast and deep coverage of the plasma glycoproteome

LC-MS/DIA-based strategy for comprehensive flavonoid profiling: an Ocotea spp. applicability case

Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain

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