Liberating Native Mass Spectrometry from Dependence on Volatile Salt Buffers by Use of Gábor Transform

Cleary, Sean P.; Prell, James S.

doi:10.1002/cphc.201900022

Cited by 24 publications

(31 citation statements)

References 43 publications

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“…The CRM is supported by the observation that the charge states of globular proteins are close to the Rayleigh charge of protein-sized water droplets . Also, the well-known tendency of protein ions to undergo nonspecific adduction to salts and other solutes under native ESI conditions , is consistent with solvent evaporation to dryness during the CRM. ,− …”

mentioning

confidence: 74%

Formation of Gaseous Proteins via the Ion Evaporation Model (IEM) in Electrospray Mass Spectrometry

Aliyari

Konermann

2020

Anal. Chem.

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The mechanisms whereby protein ions are released into the gas phase from charged droplets during electrospray ionization (ESI) continue to be controversial. Several pathways have been proposed. For native ESI the charged residue model (CRM) is favored; it entails the liberation of proteins via solvent evaporation to dryness. Unfolded proteins likely follow the chain ejection model (CEM), which involves the gradual expulsion of stretched-out chains from the droplet. According to the ion evaporation model (IEM) ions undergo electrostatically driven desorption from the droplet surface. The IEM is well supported for small precharged species such as Na+. However, it is unclear whether proteins can show IEM behavior as well. We examined this question using molecular dynamics (MD) simulations, mass spectrometry (MS), and ion mobility spectrometry (IMS) in positive ion mode. Ubiquitin was chosen as the model protein because of its structural stability which allows the protein charge in solution to be controlled via pH adjustment without changing the protein conformation. MD simulations on small ESI droplets (3 nm radius) showed CRM behavior regardless of the protein charge in solution. Surprisingly, many MD runs on larger droplets (5.5 nm radius) culminated in IEM ejection of ubiquitin, as long as the protein carried a sufficiently large positive solution charge. MD simulations predicted that nonspecific salt adducts are less prevalent for IEM-generated protein ions than for CRM products. This prediction was confirmed experimentally. Also, collision cross sections of MD structures were in good agreement with IMS data. Overall, this work reveals that the CRM, CEM, and IEM all represent viable pathways for generating gaseous protein ions during ESI. The IEM is favored for proteins that are tightly folded and highly charged in solution and for droplets in a suitable size regime.

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confidence: 74%

Formation of Gaseous Proteins via the Ion Evaporation Model (IEM) in Electrospray Mass Spectrometry

Aliyari

Konermann

2020

Anal. Chem.

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“…Multiple approaches to ESI deconvolution have been developed, − but there is no universal scoring scheme to judge the quality of the deconvolution. Early maximum entropy methods , remain common.…”

Section: Introductionmentioning

confidence: 99%

A Universal Score for Deconvolution of Intact Protein and Native Electrospray Mass Spectra

Marty

2020

Anal. Chem.

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The growing use of intact protein mass analysis, top-down proteomics, and native mass spectrometry have created a need for improved data analysis pipelines for deconvolution of electrospray (ESI) mass spectra containing multiple charge states and potentially without isotopic resolution. Although there are multiple deconvolution algorithms, there is no consensus for how to judge the quality of the deconvolution, and many scoring schemes are not published. Here, an intuitive universal score (UniScore) for ESI deconvolution is presented. The UniScore is the weighted average of deconvolution scores (DScores) for each peak multiplied by the R 2 of the fit to the data. Each DScore is composed of separate components to score (1) the uniqueness and fit of the deconvolution to the data, (2) the consistency of the peak shape across different charge states, (3) the smoothness of the charge state distribution, and (4) symmetry and separation of the peak. Example scores are provided for a range of experimental and simulated data. By providing a means of judging the quality of the overall deconvolution as well as individual mass peaks, the UniScore scheme provides a foundation for standardizing ESI data analysis of larger molecules and enabling the use of ESI deconvolution in automated data analysis pipelines.

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“…To overcome these challenges, multiple deconvolution software programs have been created to help assign charge states and deconvolve intact MS data. [15][16][17][18][19][20][21][22][23][24][25] A recent review has covered a wide variety of deconvolution software. [26] UniDec (Universal Deconvolution) software uses Bayesian deconvolution to quickly assign the charge states of m/z peaks and thus determine the mass.…”

Section: Introductionmentioning

confidence: 99%

Deconvolving Native and Intact Protein Mass Spectra with UniDec

Kostelic¹,

Marty

2020

Preprint

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Intact protein, top-down, and native mass spectrometry (MS) generally require the deconvolution of electrospray ionization (ESI) mass spectra to assign the mass of components from their charge state distribution. For small, well-resolved proteins, the charge can usually be assigned based on the isotope distribution. However, it can be challenging to determine charge states with larger proteins that lack isotopic resolution, in complex mass spectra with overlapping charge states, and in native spectra that show adduction. To overcome these challenges, UniDec uses Bayesian deconvolution to assign charge states and to create a zero-charge mass distribution. UniDec is fast, user-friendly, and includes a range of advanced tools to assist in intact protein, top-down, and native MS data analysis. This chapter provides a step-by-step protocol, an in-depth explanation of the UniDec algorithm, and highlights the parameters that affect the deconvolution. It also covers advanced data analysis tools, such as macromolecular mass defect analysis and tools for assigning potential PTMs and bound ligands. Overall, the chapter provides users with a deeper understanding of UniDec, which will enhance the quality of deconvolutions and allow for more intricate MS experiments.<br>

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Liberating Native Mass Spectrometry from Dependence on Volatile Salt Buffers by Use of Gábor Transform

Cited by 24 publications

References 43 publications

Formation of Gaseous Proteins via the Ion Evaporation Model (IEM) in Electrospray Mass Spectrometry

Formation of Gaseous Proteins via the Ion Evaporation Model (IEM) in Electrospray Mass Spectrometry

A Universal Score for Deconvolution of Intact Protein and Native Electrospray Mass Spectra

Deconvolving Native and Intact Protein Mass Spectra with UniDec

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