Direct Ionization of Large Proteins and Protein Complexes by Desorption Electrospray Ionization-Mass Spectrometry

Ferguson, Carly N.; Benchaar, Sabrina A.; Miao, Zhixin; Loo, Joseph A.; Chen, Hao

doi:10.1021/ac201390w

Cited by 97 publications

(102 citation statements)

References 49 publications

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“…In fact, there are many reported examples where buffer optimization was a critical step in enabling the characterization of the interaction. A variety of strategies have been proposed for ESI-MS analysis of solutions containing physiological buffers at relevant concentrations, including the use of high ammonium acetate concentrations [76,77], carrying out ESI in the presence of high velocity air (gas) [78], and decoupling the sample solution from the ESI process through the use of desorption electrospray ionization (DESI) [79]. However, for the direct ESI-MS binding assay to become a truly universal binding assay, significant technological/methodological advances in this area are still needed.…”

Section: Other Challengesmentioning

confidence: 99%

Reliable Determinations of Protein–Ligand Interactions by Direct ESI-MS Measurements. Are We There Yet?

Kitova

El-Hawiet

Schnier

et al. 2012

J. Am. Soc. Mass Spectrom.

217

321

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The association-dissociation of noncovalent interactions between protein and ligands, such as other proteins, carbohydrates, lipids, DNA, or small molecules, are critical events in many biological processes. The discovery and characterization of these interactions is essential to a complete understanding of biochemical reactions and pathways and to the design of novel therapeutic agents that may be used to treat a variety of diseases and infections. Over the last 20 y, electrospray ionization mass spectrometry (ESI-MS) has emerged as a versatile tool for the identification and quantification of protein-ligand interactions in vitro. Here, we describe the implementation of the direct ESI-MS assay for the determination of protein-ligand binding stoichiometry and affinity. Additionally, we outline common sources of error encountered with these measurements and various strategies to overcome them. Finally, we comment on some of the outstanding challenges associated with the implementation of the assay and highlight new areas where direct ESI-MS measurements are expected to make significant contributions in the future.

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Section: Other Challengesmentioning

confidence: 99%

Reliable Determinations of Protein–Ligand Interactions by Direct ESI-MS Measurements. Are We There Yet?

Kitova

El-Hawiet

Schnier

et al. 2012

J. Am. Soc. Mass Spectrom.

217

321

View full text Add to dashboard Cite

show abstract

“…Third, the last decade has seen very significant advances in MS with respect to ion sources and the sensitivity of the instruments themselves (20)(21)(22)(23)(24)(25)(26)(27). Ambient ionization methods combined with significant improvements in sensitivity and mass accuracy of MS instrumentation now enable the detection of intact molecules directly from surfaces (7,(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40). Using the ambient method nanoDESI, the molecular characterization of microbial colonies directly from agar surfaces without any prior sample preparation has become possible (7).…”

Section: Significancementioning

confidence: 99%

MS/MS networking guided analysis of molecule and gene cluster families

Nguyen

Moree

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

235

238

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The ability to correlate the production of specialized metabolites to the genetic capacity of the organism that produces such molecules has become an invaluable tool in aiding the discovery of biotechnologically applicable molecules. Here, we accomplish this task by matching molecular families with gene cluster families, making these correlations to 60 microbes at one time instead of connecting one molecule to one organism at a time, such as how it is traditionally done. We can correlate these families through the use of nanospray desorption electrospray ionization MS/MS, an ambient pressure MS technique, in conjunction with MS/MS networking and peptidogenomics. We matched the molecular families of peptide natural products produced by 42 bacilli and 18 pseudomonads through the generation of amino acid sequence tags from MS/MS data of specific clusters found in the MS/MS network. These sequence tags were then linked to biosynthetic gene clusters in publicly accessible genomes, providing us with the ability to link particular molecules with the genes that produced them. As an example of its use, this approach was applied to two unsequenced Pseudoalteromonas species, leading to the discovery of the gene cluster for a molecular family, the bromoalterochromides, in the previously sequenced strain P. piscicida JCM 20779 T . The approach itself is not limited to 60 related strains, because spectral networking can be readily adopted to look at molecular family-gene cluster families of hundreds or more diverse organisms in one single MS/MS network.MS/MS molecular networking | mass spectrometry | microbial ecology T ens of thousands of sequenced microbial genomes or rough drafts of genomes are available at this time, and this number is predicted to grow into the millions over the next decades. This wealth of sequence data has the potential to be used for the discovery of small bioactive molecules through genome mining (1-6). Genome mining is a process in which small molecules are discovered by predicting what compound will be genetically encoded based on the sequences of biosynthetic gene clusters. However, the process of mining genetically encoded small molecules is not keeping pace with the rate by which genome sequences are being obtained. In general, genome mining is still done one gene cluster at a time and requires many person-years of effort to annotate a single molecule. The time and significant expertise that current genome mining requires also make genome mining very expensive. In light of this extensive effort and cost, alternative approaches to genome mining and annotating specialized metabolites must be developed that not only take advantage of the sequenced resources available and make it efficient to perform genome mining on a more global scale but also enable the molecular analysis of unsequenced organisms. Such methods will then significantly reduce the cost of genome mining by increasing the speed with which molecules are connected to candidate genes and using resources already available. Here, we put fo...

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“…Finally, the ability of desorption electrospray ionization (DESI) mass spectrometry to detect large proteins and protein complexes directly from solutions [56]-so-called "liquid sample DESI" [57]-has recently been demonstrated. While for the most part, the examples provided are soluble proteins (e.g., superoxide dismutase and hemoglobin), the authors point out that this configuration has added flexibility in that solvent systems can be separately tailored for both the analyte and the ionizing spray [56].…”

Section: Mass Spectrometry For Direct Interrogation Of Lipid-protein mentioning

confidence: 99%

“…While for the most part, the examples provided are soluble proteins (e.g., superoxide dismutase and hemoglobin), the authors point out that this configuration has added flexibility in that solvent systems can be separately tailored for both the analyte and the ionizing spray [56]. Such a configuration may surmount some of the challenges in ESI, where the solvent system often Figure 5.…”

Section: Mass Spectrometry For Direct Interrogation Of Lipid-protein mentioning

confidence: 99%

Time to Face the Fats: What Can Mass Spectrometry Reveal about the Structure of Lipids and Their Interactions with Proteins?

Brown

Mitchell

Oakley

et al. 2012

J. Am. Soc. Mass Spectrom.

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Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.Key words: Lipid-protein interactions, Structural biology, Structural lipidomics, Protein mass spectrometry Lipid-Protein Interactions P roteins and lipids, both integral for the function of all biological systems, are chemically distinct. A protein's three-dimensional structure and ultimately its function are defined by peptide-bonded amino acids and subsequent posttranslational modifications. In contrast, lipids are smaller molecules than proteins, but have a larger array of building blocks and linkage chemistries. Because of these inherent chemical differences, the optimal tools for de novo structural characterization differ between proteins and lipids.Lipid-protein interactions are critical for maintaining biological function in the membrane bilayer, the cytosol, and extracellular space. In the membrane, the chemical structures of lipid solvent molecules are important for the correct folding, insertion, structure, and function of membrane proteins. The interactions between enzymes and their respective lipid substrates are critical for correct substrate recognition and catalysis (e.g., lipoxygenase [1]). Additionally, lipid-protein interactions are increasingly being realized as important in maintaining cellular structure (e.g., cytoskeletal anchoring [2]), scaffolding and localization of multi-subunit protein complexes (e.g., associated kinase anchoring protein complexes [3]), and as second messengers in signal transduction (e.g., protein kinase C [4]).

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Direct Ionization of Large Proteins and Protein Complexes by Desorption Electrospray Ionization-Mass Spectrometry

Cited by 97 publications

References 49 publications

Reliable Determinations of Protein–Ligand Interactions by Direct ESI-MS Measurements. Are We There Yet?

Reliable Determinations of Protein–Ligand Interactions by Direct ESI-MS Measurements. Are We There Yet?

MS/MS networking guided analysis of molecule and gene cluster families

Time to Face the Fats: What Can Mass Spectrometry Reveal about the Structure of Lipids and Their Interactions with Proteins?

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