SP3-FAIMS Chemoproteomics for High Coverage Profiling of the Human Cysteinome

Yan, Tianyang; Desai, Heta P.; Boatner, Lisa; Yen, S. P. S.; Cao, Jian; Palafox, Maria; Jami‐Alahmadi, Yasaman; Backus, Keriann M.

doi:10.26434/chemrxiv.13487364

Cited by 2 publications

(2 citation statements)

References 45 publications

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“…Additional strategies have proven to be promising for improving coverage including the use of multiple enzymes for protein digestion [82,83]. Moreover, advances in MS instrumentation will continue to provide an improved proteome coverage.…”

Section: Enhancing the Coverage Of The Redox Proteomementioning

confidence: 99%

“…For instance, the coupling of field asymmetric waveform ion mobility spectrometry (FAIMS), a gasphase separation technique, has resulted in higher proteome coverage in shotgun proteomics [84]. Yan et al recently also reported the optimization of the compensation voltages of FAIMS to achieve enhanced redox proteome coverage [83].…”

Section: Enhancing the Coverage Of The Redox Proteomementioning

confidence: 99%

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Thiol redox proteomics: Characterization of thiol‐based post‐translational modifications

Gluth

Zhang

et al. 2023

Proteomics

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Redox post-translational modifications on cysteine thiols (redox PTMs) have profound effects on protein structure and function, thus enabling regulation of various biological processes. Redox proteomics approaches aim to characterize the landscape of redox PTMs at the systems level. These approaches facilitate studies of condition-specific, dynamic processes implicating redox PTMs and have furthered our understanding of redox signaling and regulation. Mass spectrometry (MS) is a powerful tool for such analyses which has been demonstrated by significant advances in redox proteomics during the last decade. A group of well-established approaches involves the initial blocking of free thiols followed by selective reduction of oxidized PTMs and subsequent enrichment for downstream detection. Alternatively, novel chemoselective probe-based approaches have been developed for various redox PTMs. Direct detection of redox PTMs without any enrichment has also been demonstrated given the sensitivity of contemporary MS instruments. This review discusses the general principles behind different analytical strategies and covers recent advances in redox proteomics. Several applications of redox proteomics are also highlighted to illustrate how large-scale redox proteomics data can lead to novel biological insights.

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Section: Enhancing the Coverage Of The Redox Proteomementioning

confidence: 99%

Section: Enhancing the Coverage Of The Redox Proteomementioning

confidence: 99%

Thiol redox proteomics: Characterization of thiol‐based post‐translational modifications

Gluth

Zhang

et al. 2023

Proteomics

View full text Add to dashboard Cite

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Transforming chemical proteomics enrichment into high-throughput method using SP2E workflow

Becker

Wiest

Telek

et al. 2022

Preprint

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Protein post-translational modifications (PTMs) play a critical role in regulation of protein catalytic activity, localization and protein-protein interactions. An attachment of PTMs onto proteins significantly diversifies their structure and function resulting in so-called proteoforms. However, the sole identification of post-translationally modified proteins, which are often cell type and disease specific, is still a highly challenging task. Sub-stoichiometric amounts and modification of low abundant proteins necessitate purification or enrichment of the modified proteins. Although the introduction of the mass spectrometry-based chemical proteomic strategy has enabled to screen protein PTMs with increased throughput, sample preparation has remained highly time consuming and tedious. Here, we report an optimized workflow for enrichment of PTM proteins in 96-well plate format which can be possible extended to robotic automatization. This platform allows to significantly lower the input of total protein, which opens up the opportunity to screen specialized and difficult to culture cell lines in high-throughput manner. The presented SP2E protocol is robust, time- and cost-effective as well as suitable for large-scale screening of proteoforms. Application of the SP2E protocol will thus enable the characterization of proteoforms in various processes such as neurodevelopment, neurodegeneration and cancer and may contribute to an overall acceleration of the recently launched Human Proteoform Project.

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SP3-FAIMS Chemoproteomics for High Coverage Profiling of the Human Cysteinome

Cited by 2 publications

References 45 publications

Thiol redox proteomics: Characterization of thiol‐based post‐translational modifications

Thiol redox proteomics: Characterization of thiol‐based post‐translational modifications

Transforming chemical proteomics enrichment into high-throughput method using SP2E workflow

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