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Article ; Online: Structural Insights into Linkage-Specific Ubiquitin Chains Using Ion Mobility Mass Spectrometry.

Jung, Ji Eun / Ewing, Michael A / Valentine, Stephen J / Clemmer, David E

Journal of the American Society for Mass Spectrometry

2024

Abstract: The structural characterization and differentiation of four types of oligoubiquitin conjugates [linear (Met1)-, Lys11-, Lys48-, Lys63-linked di-, tri-, and tetraubiquitin chains] using ion mobility mass spectrometry are reported. A comparison of ... ...

Abstract	The structural characterization and differentiation of four types of oligoubiquitin conjugates [linear (Met1)-, Lys11-, Lys48-, Lys63-linked di-, tri-, and tetraubiquitin chains] using ion mobility mass spectrometry are reported. A comparison of collision cross sections for the same linkage of di-, tri-, and tetraubiquitin chains shows differences in conformational elongation for higher charge states due to the interplay of linkage-derived structure and Coulombic repulsion. For di- and triubiquitin chains, this elongation results in a single narrow feature representing an elongated conformation type for multiple higher charge state species. In contrast, higher charge state tetraubiquitin species do not form a single conformer type as readily. A comparison of different linkages in tetraubiquitin chains reveals greater similarity in conformation type at lower charge states; with increasing charge state, the four linkage types diverge in the relative proportions of elongated conformer types with Met1- ≥ Lys11- > Lys63- > Lys48-linkage. These differences in conformational trends could be discussed with respect to biological functions of linkage-specific polyubiquitinated proteins.
Language	English
Publishing date	2024-04-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.4c00019
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Zs.MO 241: Show issues

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Article ; Online: Resolving Hidden Solution Conformations of Hemoglobin Using IMS-IMS on a Cyclic Instrument.

Sharon, Edie M / Henderson, Lucas W / Clemmer, David E

Journal of the American Society for Mass Spectrometry

2023 Volume 34, Issue 8, Page(s) 1559–1568

Abstract: Ion mobility spectrometry-mass spectrometry (IMS-MS) experiments on a cyclic IMS instrument were used to examine heterogeneous distributions of structures found in the 15+ to 18+ charge states of the hemoglobin tetramer (Hb). The resolving power of IMS ... ...

Abstract	Ion mobility spectrometry-mass spectrometry (IMS-MS) experiments on a cyclic IMS instrument were used to examine heterogeneous distributions of structures found in the 15+ to 18+ charge states of the hemoglobin tetramer (Hb). The resolving power of IMS measurements is known to increase with increasing drift-region length. This effect is not significant for Hb charge states as peaks were shown to broaden with increasing drift-region length. This observation suggests that multiple structures with similar cross sections may be present. To examine this hypothesis, selections of drift time distributions were isolated and subsequently reinjected into the mobility region for additional separation. These IMS-IMS experiments demonstrate that selected regions separate further upon additional passes around the drift cell, consistent with the idea that initial resolving power was limited due to the presence of many closely related conformations. Additional variable temperature electrospray ionization (vT-ESI) experiments were conducted to study how changing the solution temperature affects solution conformations. Some features in these IMS-IMS studies were observed to change similarly with solution temperature compared to features in the single IMS distribution. Other features changed differently in the selected mobility data, indicating that solution structures that were obscured upon IMS analysis because of the complex heterogeneity of the original distribution are discernible after reducing the number of conformers that are analyzed by further IMS analysis. These results illustrate that the combination of vT-ESI with IMS-IMS is useful for resolving and exploring conformer distributions and stabilities in systems that exhibit a large degree of structural heterogeneity.
MeSH term(s)	Mass Spectrometry/methods ; Molecular Conformation ; Ion Mobility Spectrometry ; Temperature ; Hemoglobins
Chemical Substances	Hemoglobins
Language	English
Publishing date	2023-07-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.3c00032
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Zs.A 4618: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 241: Show issues

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Article ; Online: Editorial: Focus on Ionization Technologies Used in MS: Fundamentals and Applications, Honoring Dr. Sarah Trimpin, Recipient of the 2019 ASMS Biemann Medal.

Russell, David H / Clemmer, David E

Journal of the American Society for Mass Spectrometry

2021 Volume 32, Issue 3, Page(s) 616–617

Language	English
Publishing date	2021-06-23
Publishing country	United States
Document type	Editorial
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.1c00030
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Zs.MO 241: Show issues

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Article ; Online: Human Cerebellum Gangliosides: A Comprehensive Analysis by Ion Mobility Tandem Mass Spectrometry.

Biricioiu, Maria Roxana / Sarbu, Mirela / Ica, Raluca / Vukelić, Željka / Clemmer, David E / Zamfir, Alina D

Journal of the American Society for Mass Spectrometry

2024 Volume 35, Issue 4, Page(s) 683–695

Abstract: The human cerebellum is an ultraspecialized region of the brain responsible for cognitive functions and movement coordination. The fine mechanisms through which the process of aging impacts such functions are not well understood; therefore, a rigorous ... ...

Abstract	The human cerebellum is an ultraspecialized region of the brain responsible for cognitive functions and movement coordination. The fine mechanisms through which the process of aging impacts such functions are not well understood; therefore, a rigorous exploration of this brain region at the molecular level is deemed necessary. Gangliosides, sialylated glycosphingolipids, highly and specifically expressed in the human central nervous system, represent possible molecular markers of cerebellum development and aging. In this context, for a comprehensive determination of development- and age-specific components, we have conducted here a comparative profiling and structural determination of the gangliosides expressed in fetal cerebellum in two intrauterine developmental stages and aged cerebellum by ion mobility separation (IMS) mass spectrometry (MS) and tandem MS (MS/MS). Due to the high sensitivity and efficiency of separation provided by IMS MS, no less than 551 chemically distinct species were identified, which represents 4.5 times more gangliosides than ever discovered in this brain region. The detailed assessment of fetal vs aged cerebellum gangliosidome showed marked discrepancies not only in the general number of the species expressed, but also in their sialylation patterns, the modifications of the glycan core, and the composition of the ceramides. All of these characteristics are potential markers of cerebellum development and aging. The structural analysis by collision-induced dissociation (CID) documented the occurrence of GD1b (d18:1/18:0) isomer in the fetal cerebellum in the second gestational trimester, with all probability of GQ1b (t18:1/18:0) in the near-term fetus and of GQ1b (d18:1/18:0) in aged cerebellum.
MeSH term(s)	Humans ; Aged ; Tandem Mass Spectrometry ; Spectrometry, Mass, Electrospray Ionization/methods ; Gangliosides/analysis ; Brain ; Cerebellum
Chemical Substances	Gangliosides
Language	English
Publishing date	2024-03-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.3c00360
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Zs.MO 241: Show issues

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Article ; Online: Influence of N Terminus Amino Acid on Peptide Cleavage in Solution through Diketopiperazine Formation.

Zhang, Zhi-Chao / Hales, David A / Clemmer, David E

Journal of the American Society for Mass Spectrometry

2022 Volume 33, Issue 8, Page(s) 1368–1376

Abstract: Diketopiperazine (DKP) formation is an important degradation pathway for peptides and proteins. It can occur during synthesis and storage in either solution or the solid state. The kinetics of peptide cleavage through DKP formation have been analyzed for ...

Abstract	Diketopiperazine (DKP) formation is an important degradation pathway for peptides and proteins. It can occur during synthesis and storage in either solution or the solid state. The kinetics of peptide cleavage through DKP formation have been analyzed for the model peptides Xaa
MeSH term(s)	Amino Acid Sequence ; Amino Acids ; Carbon ; Diketopiperazines ; Peptides/chemistry ; Proline/chemistry
Chemical Substances	Amino Acids ; Diketopiperazines ; Peptides ; Carbon (7440-44-0) ; Proline (9DLQ4CIU6V)
Language	English
Publishing date	2022-05-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.2c00037
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Zs.A 4618: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 241: Show issues

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Article ; Online: Glycomics by ion mobility tandem mass spectrometry of chondroitin sulfate disaccharide domain in biglycan

Sarbu, Mirela / Ica, Raluca / Sharon, Edie / Clemmer, David E. / Zamfir, Alina D.

Journal of Mass Spectrometry. 2023 Mar., v. 58, no. 3 p.e4908-

2023

Abstract: Biglycan (BGN), a small leucine‐rich repeat proteoglycan, is involved in a variety of pathological processes including malignant transformation, for which the upregulation of BGN was found related to cancer cell invasiveness. Because the functions of BGN ...

Abstract	Biglycan (BGN), a small leucine‐rich repeat proteoglycan, is involved in a variety of pathological processes including malignant transformation, for which the upregulation of BGN was found related to cancer cell invasiveness. Because the functions of BGN are mediated by its chondroitin/dermatan sulfate (CS/DS) chains through the sulfates, the determination of CS/DS structure and sulfation pattern is of major importance. In this study, we have implemented an advanced glycomics method based on ion mobility separation (IMS) mass spectrometry (MS) and tandem MS (MS/MS) to characterize the CS disaccharide domains in BGN. The high separation efficiency and sensitivity of this technique allowed the discrimination of five distinct CS disaccharide motifs, of which four irregulated in their sulfation pattern. For the first time, trisulfated unsaturated and bisulfated saturated disaccharides were found in BGN, the latter species documenting the non‐reducing end of the chains. The structural investigation by IMS MS/MS disclosed that in one or both of the CS/DS chains, the non‐reducing end is 3‐O‐sulfated GlcA in a rather rare bisulfated motif having the structure 3‐O‐sulfated GlcA‐4‐O‐sulfated GalNAc. Considering the role played by BGN in cancer cell spreading, the influence on this process of the newly identified sequences will be investigated in the future.
Keywords	chondroitin sulfate ; dermatan sulfate ; glycomics ; neoplasm cells ; proteoglycans ; tandem mass spectrometry
Language	English
Dates of publication	2023-03
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	1221763-3
ISSN	1096-9888 ; 1076-5174
ISSN (online)	1096-9888
ISSN	1076-5174
DOI	10.1002/jms.4908
Database	NAL-Catalogue (AGRICOLA)

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Zs.A 4254: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 220: Show issues

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Article ; Online: Variable-Temperature Native Mass Spectrometry for Studies of Protein Folding, Stabilities, Assembly, and Molecular Interactions.

Laganowsky, Arthur / Clemmer, David E / Russell, David H

Annual review of biophysics

2021 Volume 51, Page(s) 63–77

Abstract: The structures and conformational dynamics of proteins, protein complexes, and their noncovalent interactions with other molecules are controlled specifically by the Gibbs free energy (entropy and enthalpy) of the system. For some organisms, temperature ... ...

Abstract	The structures and conformational dynamics of proteins, protein complexes, and their noncovalent interactions with other molecules are controlled specifically by the Gibbs free energy (entropy and enthalpy) of the system. For some organisms, temperature is highly regulated, but the majority of biophysical studies are carried out at room, nonphysiological temperature. In this review, we describe variable-temperature electrospray ionization (vT-ESI) mass spectrometry (MS)-based studies with unparalleled sensitivity, dynamic range, and selectivity for studies of both cold- and heat-induced chemical processes. Such studies provide direct determinations of stabilities, reactivities, and thermodynamic measurements for native and non-native structures of proteins and protein complexes and for protein-ligand interactions. Highlighted in this review are vT-ESI-MS studies that reveal 40 different conformers of chymotrypsin inhibitor 2, a classic two-state (native → unfolded) unfolder, and thermochemistry for a model membrane protein system binding lipid and its regulatory protein.
MeSH term(s)	Ligands ; Protein Folding ; Spectrometry, Mass, Electrospray Ionization/methods ; Temperature ; Thermodynamics
Chemical Substances	Ligands
Language	English
Publishing date	2021-12-21
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	2434725-5
ISSN	1936-1238 ; 1936-122X
ISSN (online)	1936-1238
ISSN	1936-122X
DOI	10.1146/annurev-biophys-102221-101121
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Article ; Online: Tautomerization of H

Beckett, Daniel / El-Baba, Tarick J / Zhang, Zhichao / Clemmer, David E / Raghavachari, Krishnan

The journal of physical chemistry. A

2023 Volume 127, Issue 30, Page(s) 6282–6291

Abstract: Ion mobility spectrometry-mass spectrometry and quantum chemical calculations are used to determine the structures and stabilities of the singly protonated peptide ... ...

Abstract	Ion mobility spectrometry-mass spectrometry and quantum chemical calculations are used to determine the structures and stabilities of the singly protonated peptide H
MeSH term(s)	Hydrogen Bonding ; Peptides/chemistry ; Hydrogen/chemistry ; Models, Molecular ; Protein Structure, Tertiary ; Entropy ; Methylation
Chemical Substances	Peptides ; Hydrogen (7YNJ3PO35Z)
Language	English
Publishing date	2023-07-25
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.3c03744
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Article ; Online: Glycomics by ion mobility tandem mass spectrometry of chondroitin sulfate disaccharide domain in biglycan.

Sarbu, Mirela / Ica, Raluca / Sharon, Edie / Clemmer, David E / Zamfir, Alina D

Journal of mass spectrometry : JMS

2023 Volume 58, Issue 3, Page(s) e4908

Abstract: Biglycan (BGN), a small leucine-rich repeat proteoglycan, is involved in a variety of pathological processes including malignant transformation, for which the upregulation of BGN was found related to cancer cell invasiveness. Because the functions of BGN ...

Abstract	Biglycan (BGN), a small leucine-rich repeat proteoglycan, is involved in a variety of pathological processes including malignant transformation, for which the upregulation of BGN was found related to cancer cell invasiveness. Because the functions of BGN are mediated by its chondroitin/dermatan sulfate (CS/DS) chains through the sulfates, the determination of CS/DS structure and sulfation pattern is of major importance. In this study, we have implemented an advanced glycomics method based on ion mobility separation (IMS) mass spectrometry (MS) and tandem MS (MS/MS) to characterize the CS disaccharide domains in BGN. The high separation efficiency and sensitivity of this technique allowed the discrimination of five distinct CS disaccharide motifs, of which four irregulated in their sulfation pattern. For the first time, trisulfated unsaturated and bisulfated saturated disaccharides were found in BGN, the latter species documenting the non-reducing end of the chains. The structural investigation by IMS MS/MS disclosed that in one or both of the CS/DS chains, the non-reducing end is 3-O-sulfated GlcA in a rather rare bisulfated motif having the structure 3-O-sulfated GlcA-4-O-sulfated GalNAc. Considering the role played by BGN in cancer cell spreading, the influence on this process of the newly identified sequences will be investigated in the future.
MeSH term(s)	Chondroitin Sulfates/chemistry ; Biglycan ; Tandem Mass Spectrometry ; Disaccharides/chemistry ; Dermatan Sulfate/analysis ; Dermatan Sulfate/chemistry ; Glycomics
Chemical Substances	Chondroitin Sulfates (9007-28-7) ; Biglycan ; Disaccharides ; Dermatan Sulfate (24967-94-0)
Language	English
Publishing date	2023-02-17
Publishing country	England
Document type	Journal Article
ZDB-ID	1221763-3
ISSN	1096-9888 ; 1076-5174
ISSN (online)	1096-9888
ISSN	1076-5174
DOI	10.1002/jms.4908
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Zs.MO 220: Show issues

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Article ; Online: Ion mobility mass spectrometry of human melanoma gangliosides.

Sarbu, Mirela / Clemmer, David E / Zamfir, Alina D

Biochimie

2020 Volume 177, Page(s) 226–237

Abstract: Malignant melanoma is an aggressive type of skin cancer, rarely detected in the early stages. Various sets of methods and techniques, including dermatoscopical inspection of the "ABCDE" signs of the lesion, imaging techniques or microscopical, ... ...

Abstract	Malignant melanoma is an aggressive type of skin cancer, rarely detected in the early stages. Various sets of methods and techniques, including dermatoscopical inspection of the "ABCDE" signs of the lesion, imaging techniques or microscopical, immunohistochemical and serological biomarkers are available and used nowadays to diagnose malignant melanoma. To date, different biomarkers were proposed for melanoma, but only a few, including circulating proteins, such as lactate dehydrogenase, molecular and metabolite biomarkers, have reached clinical applications. Gangliosides represent an emerging class, being used as tumor markers and targets of antibody therapy in melanomas, based on their elevated abundance in melanoma, especially of GM3 and GD3, when compared with the corresponding normal tissues. The conjunction of mass spectrometry (MS) with ion mobility separation (IMS) demonstrated an elevated potential in detection and identification of low abundant components, with biomarker role, in extremely complex biological mixtures. Therefore, here, a native ganglioside extract originating from human melanoma was investigated for the first time by IMS MS to provide the first profiling of gangliosides in this type of cancer. The present approach revealed the high incidence of species belonging to GD3 and GM3 classes, as well as of de-N-acetyl GM3 (d-GM3) and de-N-acetyl GD3 (d-GD3), characteristic for human melanoma. Additionally, the structure of two molecules characterized by shorter glycan chains associated to melanoma, were investigated in detail. The present approach brings valuable data related to this type of cancer, completing the existing inventory of melanoma-associated biomarkers and opens new directions for further research in this field.
MeSH term(s)	Adult ; Biomarkers, Tumor/analysis ; Biomarkers, Tumor/chemistry ; Gangliosides/analysis ; Gangliosides/chemistry ; Humans ; Ion Mobility Spectrometry/methods ; Male ; Mass Spectrometry/methods ; Melanoma/diagnosis ; Melanoma/metabolism ; Polysaccharides/analysis ; Skin Neoplasms/diagnosis ; Skin Neoplasms/metabolism
Chemical Substances	Biomarkers, Tumor ; Gangliosides ; Polysaccharides
Language	English
Publishing date	2020-08-25
Publishing country	France
Document type	Journal Article
ZDB-ID	120345-9
ISSN	1638-6183 ; 0300-9084
ISSN (online)	1638-6183
ISSN	0300-9084
DOI	10.1016/j.biochi.2020.08.011
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