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Article ; Online: Nontargeted Identification of D-Amino Acid-Containing Peptides Through Enzymatic Screening, Chiral Amino Acid Analysis, and LC-MS.

Okyem, Samuel / Romanova, Elena V / Tai, Hua-Chia / Checco, James W / Sweedler, Jonathan V

Methods in molecular biology (Clifton, N.J.)

2024 Volume 2758, Page(s) 227–240

Abstract: D-amino acid-containing peptides (DAACPs) in animals are a class of bioactive molecules formed via the posttranslational modification of peptides consisting of all-L-amino acid residues. Amino acid residue isomerization greatly impacts the function of ... ...

Abstract	D-amino acid-containing peptides (DAACPs) in animals are a class of bioactive molecules formed via the posttranslational modification of peptides consisting of all-L-amino acid residues. Amino acid residue isomerization greatly impacts the function of the resulting DAACP. However, because isomerization does not change the peptide's mass, this modification is difficult to detect by most mass spectrometry-based peptidomic approaches. Here we describe a method for the identification of DAACPs that can be used to systematically survey peptides extracted from a tissue sample in a nontargeted manner.
MeSH term(s)	Animals ; Amino Acids/chemistry ; Liquid Chromatography-Mass Spectrometry ; Chromatography, Liquid ; Tandem Mass Spectrometry/methods ; Peptides
Chemical Substances	Amino Acids ; Peptides
Language	English
Publishing date	2024-03-29
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3646-6_12
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Article ; Online: Bioinformatics for Prohormone and Neuropeptide Discovery.

Southey, Bruce R / Romanova, Elena V / Rodriguez-Zas, Sandra L / Sweedler, Jonathan V

Methods in molecular biology (Clifton, N.J.)

2024 Volume 2758, Page(s) 151–178

Abstract: Neuropeptides and peptide hormones are signaling molecules produced via complex posttranslational modifications of precursor proteins known as prohormones. Neuropeptides activate specific receptors and are associated with the regulation of physiological ... ...

Abstract	Neuropeptides and peptide hormones are signaling molecules produced via complex posttranslational modifications of precursor proteins known as prohormones. Neuropeptides activate specific receptors and are associated with the regulation of physiological systems and behaviors. The identification of prohormones-and the neuropeptides created by these prohormones-from genomic assemblies has become essential to support the annotation and use of the rapidly growing number of sequenced genomes. Here we describe a well-validated methodology for identifying the prohormone complement from genomic assemblies that employs widely available public toolsets and databases. The uncovered prohormone sequences can then be screened for putative neuropeptides to enable accurate proteomic discovery and validation.
MeSH term(s)	Proteomics ; Gene Expression Profiling ; Hormones/metabolism ; Computational Biology/methods ; Neuropeptides/genetics ; Neuropeptides/metabolism
Chemical Substances	Hormones ; Neuropeptides
Language	English
Publishing date	2024-03-08
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3646-6_8
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Article ; Online: Probe-based mass spectrometry approaches for single-cell and single-organelle measurements.

Castro, Daniel C / Chan-Andersen, Peter / Romanova, Elena V / Sweedler, Jonathan V

Mass spectrometry reviews

2023

Abstract: Exploring the chemical content of individual cells not only reveals underlying cell-to-cell chemical heterogeneity but is also a key component in understanding how cells combine to form emergent properties of cellular networks and tissues. Recent ... ...

Abstract	Exploring the chemical content of individual cells not only reveals underlying cell-to-cell chemical heterogeneity but is also a key component in understanding how cells combine to form emergent properties of cellular networks and tissues. Recent technological advances in many analytical techniques including mass spectrometry (MS) have improved instrumental limits of detection and laser/ion probe dimensions, allowing the analysis of micron and submicron sized areas. In the case of MS, these improvements combined with MS's broad analyte detection capabilities have enabled the rise of single-cell and single-organelle chemical characterization. As the chemical coverage and throughput of single-cell measurements increase, more advanced statistical and data analysis methods have aided in data visualization and interpretation. This review focuses on secondary ion MS and matrix-assisted laser desorption/ionization MS approaches for single-cell and single-organelle characterization, which is followed by advances in mass spectral data visualization and analysis.
Language	English
Publishing date	2023-04-03
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1491946-1
ISSN	1098-2787 ; 0277-7037
ISSN (online)	1098-2787
ISSN	0277-7037
DOI	10.1002/mas.21841
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Article ; Online: Animal Model Systems in Neuroscience.

Romanova, Elena V / Sweedler, Jonathan V

ACS chemical neuroscience

2018 Volume 9, Issue 8, Page(s) 1869–1870

MeSH term(s)	Animals ; Models, Animal ; Nervous System Physiological Phenomena ; Neurosciences
Language	English
Publishing date	2018-08-11
Publishing country	United States
Document type	Editorial ; Introductory Journal Article
ISSN	1948-7193
ISSN (online)	1948-7193
DOI	10.1021/acschemneuro.8b00380
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Article ; Online: Bioinformatic tools for tRNA gene analyses in mitochondrial DNA sequence data.

Romanova, Elena V / Bukin, Yurij S / Sherbakov, Dmitry Yu

Data in brief

2020 Volume 29, Page(s) 105284

Abstract: The data presented here are related to the research article entitled "Hidden cases of tRNA genes duplication and remolding in mitochondrial genomes of amphipods" (Romanova et al., 2020) [1]. Correct tRNA gene sequence annotation in mitochondrial (mt) and ...

Abstract	The data presented here are related to the research article entitled "Hidden cases of tRNA genes duplication and remolding in mitochondrial genomes of amphipods" (Romanova et al., 2020) [1]. Correct tRNA gene sequence annotation in mitochondrial (mt) and nuclear genomes sometimes can be a challenging task because of the differential performances of tRNA annotation/prediction programmes. These programmes may cause false positive or false negative predictions. Moreover, additional difficulties with annotation may be caused by the presence of duplicated tRNA genes and those coding tRNAs with altered identities occurring as due to a mutation in their anticodon sequence (tRNA gene remolding/recruitment). We developed an R script automating the diagnosis of ancestor tRNA gene coding specificity regardless of anticodon sequence based on genetic distance comparison. Some of the predicted tRNA genes from the mt genomes of amphipods are presented. We also developed an R script for estimation of the best mode of sequence alignment, which was applied to determine the best alignment of tRNA genes in [1], but is also suitable for testing of any nucleotide alignment sets used in phylogenetic inferences.
Language	English
Publishing date	2020-02-22
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2020.105284
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Article ; Online: Analysis of Peptide Stereochemistry in Single Cells by Capillary Electrophoresis-Trapped Ion Mobility Spectrometry Mass Spectrometry.

Mast, David H / Liao, Hsiao-Wei / Romanova, Elena V / Sweedler, Jonathan V

Analytical chemistry

2021 Volume 93, Issue 15, Page(s) 6205–6213

Abstract: Single cell analysis strives to probe molecular heterogeneity in morphologically similar cell populations through quantitative or qualitative measurements of genetic, proteomic, or metabolic products. Here, we applied mass analysis of single neurons to ... ...

Abstract	Single cell analysis strives to probe molecular heterogeneity in morphologically similar cell populations through quantitative or qualitative measurements of genetic, proteomic, or metabolic products. Here, we applied mass analysis of single neurons to investigate cell-cell signaling peptides. The multiplicity of endogenous cell-cell signaling peptides is a common source of chemical diversity among cell populations. Certain peptides can undergo post-translational isomerization of select residues, which has important physiological consequences. The limited number of single cell analysis techniques that are sensitive to peptide stereochemistry make it challenging to study isomerization at the individual cell level. We performed capillary electrophoresis (CE) with mass spectrometry (MS) detection to characterize the peptide content of single cells. Using complementary trapped ion mobility spectrometry (TIMS) separations, we measured the stereochemical configurations of three neuropeptide gene products derived from the pleurin precursor in individual neurons (
MeSH term(s)	Electrophoresis, Capillary ; Ion Mobility Spectrometry ; Mass Spectrometry ; Peptides ; Proteomics
Chemical Substances	Peptides
Language	English
Publishing date	2021-04-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00445
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Article ; Online: Profiling 26,000 Aplysia californica neurons by single cell mass spectrometry reveals neuronal populations with distinct neuropeptide profiles.

Chan-Andersen, Peter C / Romanova, Elena V / Rubakhin, Stanislav S / Sweedler, Jonathan V

The Journal of biological chemistry

2022 Volume 298, Issue 8, Page(s) 102254

Abstract: Neuropeptides are a chemically diverse class of cell-to-cell signaling molecules that are widely expressed throughout the central nervous system, often in a cell-specific manner. While cell-to-cell differences in neuropeptides is expected, it is often ... ...

Abstract	Neuropeptides are a chemically diverse class of cell-to-cell signaling molecules that are widely expressed throughout the central nervous system, often in a cell-specific manner. While cell-to-cell differences in neuropeptides is expected, it is often unclear how exactly neuropeptide expression varies among neurons. Here we created a microscopy-guided, high-throughput single cell matrix-assisted laser desorption/ionization mass spectrometry approach to investigate the neuropeptide heterogeneity of individual neurons in the central nervous system of the neurobiological model Aplysia californica, the California sea hare. In all, we analyzed more than 26,000 neurons from 18 animals and assigned 866 peptides from 66 prohormones by mass matching against an in silico peptide library generated from known Aplysia prohormones retrieved from the UniProt database. Louvain-Jaccard (LJ) clustering of mass spectra from individual neurons revealed 40 unique neuronal populations, or LJ clusters, each with a distinct neuropeptide profile. Prohormones and their related peptides were generally found in single cells from ganglia consistent with the prohormones' previously known ganglion localizations. Several LJ clusters also revealed the cellular colocalization of behaviorally related prohormones, such as an LJ cluster exhibiting achatin and neuropeptide Y, which are involved in feeding, and another cluster characterized by urotensin II, small cardiac peptide, sensorin A, and FRFa, which have shown activity in the feeding network or are present in the feeding musculature. This mass spectrometry-based approach enables the robust categorization of large cell populations based on single cell neuropeptide content and is readily adaptable to the study of a range of animals and tissue types.
MeSH term(s)	Animals ; Aplysia/physiology ; Central Nervous System/metabolism ; Neurons/chemistry ; Neurons/metabolism ; Neuropeptides/chemistry ; Neuropeptides/metabolism ; Single-Cell Analysis ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Chemical Substances	Neuropeptides
Language	English
Publishing date	2022-07-11
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.102254
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Uc I Zs.108: Show issues

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Article ; Online: Mass Spectrometry Approaches Empowering Neuropeptide Discovery and Therapeutics.

Anapindi, Krishna D B / Romanova, Elena V / Checco, James W / Sweedler, Jonathan V

Pharmacological reviews

2022 Volume 74, Issue 3, Page(s) 662–679

Abstract: The discovery of insulin in the early 1900s ushered in the era of research related to peptides acting as hormones and neuromodulators, among other regulatory roles. These essential gene products are found in all organisms, from the most primitive to the ... ...

Abstract	The discovery of insulin in the early 1900s ushered in the era of research related to peptides acting as hormones and neuromodulators, among other regulatory roles. These essential gene products are found in all organisms, from the most primitive to the most evolved, and carry important biologic information that coordinates complex physiology and behavior; their misregulation has been implicated in a variety of diseases. The evolutionary origins of at least 30 neuropeptide signaling systems have been traced to the common ancestor of protostomes and deuterostomes. With the use of relevant animal models and modern technologies, we can gain mechanistic insight into orthologous and paralogous endogenous peptides and translate that knowledge into medically relevant insights and new treatments. Groundbreaking advances in medicine and basic science influence how signaling peptides are defined today. The precise mechanistic pathways for over 100 endogenous peptides in mammals are now known and have laid the foundation for multiple drug development pipelines. Peptide biologics have become valuable drugs due to their unique specificity and biologic activity, lack of toxic metabolites, and minimal undesirable interactions. This review outlines modern technologies that enable neuropeptide discovery and characterization, and highlights lessons from nature made possible by neuropeptide research in relevant animal models that is being adopted by the pharmaceutical industry. We conclude with a brief overview of approaches/strategies for effective development of peptides as drugs. SIGNIFICANCE STATEMENT: Neuropeptides, an important class of cell-cell signaling molecules, are involved in maintaining a range of physiological functions. Since the discovery of insulin's activity, over 100 bioactive peptides and peptide analogs have been used as therapeutics. Because these are complex molecules not easily predicted from a genome and their activity can change with subtle chemical modifications, mass spectrometry (MS) has significantly empowered peptide discovery and characterization. This review highlights contributions of MS-based research towards the development of therapeutic peptides.
MeSH term(s)	Animals ; Humans ; Insulins ; Mammals/metabolism ; Mass Spectrometry/methods ; Neuropeptides/analysis ; Neuropeptides/genetics ; Neuropeptides/metabolism ; Peptides ; Power, Psychological
Chemical Substances	Insulins ; Neuropeptides ; Peptides
Language	English
Publishing date	2022-06-16
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	209898-2
ISSN	1521-0081 ; 0031-6997
ISSN (online)	1521-0081
ISSN	0031-6997
DOI	10.1124/pharmrev.121.000423
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Uf I Zs.148: Show issues

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Article ; Online: Mass Spectrometry Measurements of Neuropeptides: From Identification to Quantitation.

De La Toba, Eduardo A / Bell, Sara E / Romanova, Elena V / Sweedler, Jonathan V

Annual review of analytical chemistry (Palo Alto, Calif.)

2022 Volume 15, Issue 1, Page(s) 83–106

Abstract: Neuropeptides (NPs), a unique class of neuronal signaling molecules, participate in a variety of physiological processes and diseases. Quantitative measurements of NPs provide valuable information regarding how these molecules are differentially ... ...

Abstract	Neuropeptides (NPs), a unique class of neuronal signaling molecules, participate in a variety of physiological processes and diseases. Quantitative measurements of NPs provide valuable information regarding how these molecules are differentially regulated in a multitude of neurological, metabolic, and mental disorders. Mass spectrometry (MS) has evolved to become a powerful technique for measuring trace levels of NPs in complex biological tissues and individual cells using both targeted and exploratory approaches. There are inherent challenges to measuring NPs, including their wide endogenous concentration range, transport and postmortem degradation, complex sample matrices, and statistical processing of MS data required for accurate NP quantitation. This review highlights techniques developed to address these challenges and presents an overview of quantitative MS-based measurement approaches for NPs, including the incorporation of separation methods for high-throughput analysis, MS imaging for spatial measurements, and methods for NP quantitation in single neurons.
MeSH term(s)	Humans ; Mass Spectrometry/methods ; Neuropeptides/analysis ; Neuropeptides/metabolism
Chemical Substances	Neuropeptides
Language	English
Publishing date	2022-03-24
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2398707-8
ISSN	1936-1335 ; 1936-1327
ISSN (online)	1936-1335
ISSN	1936-1327
DOI	10.1146/annurev-anchem-061020-022048
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Article ; Online: Peptidomics.

Hellinger, Roland / Sigurdsson, Arnar / Wu, Wenxin / Romanova, Elena V / Li, Lingjun / Sweedler, Jonathan V / Süssmuth, Roderich D / Gruber, Christian W

Nature reviews. Methods primers

2023 Volume 3

Abstract: Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, ... ...

Abstract	Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.
Language	English
Publishing date	2023-05-30
Publishing country	England
Document type	Journal Article
ISSN	2662-8449
ISSN (online)	2662-8449
DOI	10.1038/s43586-023-00205-2
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