Spiked human substantia nigra proteome data set for use as a spectral library for protein modelling and protein mapping

We investigated the anatomical and functional organization of the human substantia nigra (SN) using diffusion and functional MRI data from the Human Connectome Project. We identified a tripartite connectivity-based parcellation of SN with a limbic, cognitive, motor arrangement. The medial SN connects with limbic striatal and cortical regions and encodes value (greater response to monetary wins than losses during fMRI), while the ventral SN connects with associative regions of cortex and striatum and encodes salience (equal response to wins and losses). The lateral SN connects with somatomotor regions of striatum and cortex and also encodes salience. Behavioral measures from delay discounting and flanker tasks supported a role for the value-coding medial SN network in decisional impulsivity, while the salience-coding ventral SN network was associated with motor impulsivity. In sum, there is anatomical and functional heterogeneity of human SN, which underpins value versus salience coding, and impulsive choice versus impulsive action.

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Nucleolin in Neurons of the Human Substantia Nigra

Biochemistry (Moscow) Supplement Series A Membrane and Cell Biology ◽

10.1134/s1990747818020137 ◽

2018 ◽

Vol 12 (2) ◽

pp. 205-208

Author(s):

D. A. Sufieva ◽

V. V. Guselnikova ◽

D. E. Korzhevskii

Keyword(s):

Substantia Nigra ◽

Human Substantia Nigra

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N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search

BioMed Research International ◽

10.1155/2018/1564136 ◽

2018 ◽

Vol 2018 ◽

pp. 1-11 ◽

Cited By ~ 2

Author(s):

Zhiwu An ◽

Qingbo Shu ◽

Hao Lv ◽

Lian Shu ◽

Jifeng Wang ◽

...

Keyword(s):

Mass Spectrometry ◽

Human Cancer ◽

Cancer Cell Line ◽

Peptide Identification ◽

High Energy ◽

Mass Spectral Library ◽

Spectral Library ◽

Data Set ◽

Library Search ◽

Mass Spectral

Confident characterization of intact glycopeptides is a challenging task in mass spectrometry-based glycoproteomics due to microheterogeneity of glycosylation, complexity of glycans, and insufficient fragmentation of peptide bones. Open mass spectral library search is a promising computational approach to peptide identification, but its potential in the identification of glycopeptides has not been fully explored. Here we present pMatchGlyco, a new spectral library search tool for intact N-linked glycopeptide identification using high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS) data. In pMatchGlyco, (1) MS/MS spectra of deglycopeptides are used to create spectral library, (2) MS/MS spectra of glycopeptides are matched to the spectra in library in an open (precursor tolerant) manner and the glycans are inferred, and (3) a false discovery rate is estimated for top-scored matches above a threshold. The efficiency and reliability of pMatchGlyco were demonstrated on a data set of mixture sample of six standard glycoproteins and a complex glycoprotein data set generated from human cancer cell line OVCAR3.

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The Hubble PanCET program: Transit and Eclipse Spectroscopy of the Hot-Jupiter WASP-74b

The Astronomical Journal ◽

10.3847/1538-3881/ac3008 ◽

2021 ◽

Vol 162 (6) ◽

pp. 271

Author(s):

Guangwei Fu ◽

Drake Deming ◽

Erin May ◽

Kevin Stevenson ◽

David K. Sing ◽

...

Keyword(s):

Rayleigh Scattering ◽

Hubble Space Telescope ◽

Absorption Feature ◽

Spectral Library ◽

Data Set ◽

Space Telescope ◽

Methane Absorption ◽

James Webb Space Telescope ◽

Hot Jupiter

Abstract Planets are like children with each one being unique and special. A better understanding of their collective properties requires a deeper understanding of each planet. Here we add the transit and eclipse spectra of hot-Jupiter WASP-74b into the ever growing data set of exoplanet atmosphere spectral library. With six transits and three eclipses using the Hubble Space Telescope and Spitzer Space Telescope (Spitzer), we present the most complete and precise atmospheric spectra of WASP-74b. We found no evidence for TiO/VO nor super-Rayleigh scattering reported in previous studies. The transit shows a muted water feature with strong Rayleigh scattering extending into the infrared. The eclipse shows a featureless blackbody-like WFC3/G141 spectrum and a weak methane absorption feature in the Spitzer 3.6 μm band. Future James Webb Space Telescope follow-up observations are needed to confirm these results.

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Distribution of [3H]SCH 23390 Binding Sites in the Human Substantia Nigra

Presynaptic Receptors and Neuronal Transporters ◽

10.1016/b978-0-08-041165-1.50034-x ◽

1991 ◽

pp. 93-94

Author(s):

F. Thibaut ◽

E.C. Hirsch ◽

R. Raisman ◽

F. Javoy-Agid ◽

Y. Agid

Keyword(s):

Substantia Nigra ◽

Binding Sites ◽

Sch 23390 ◽

Human Substantia Nigra

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Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue

Molecular & Cellular Proteomics ◽

10.1074/mcp.ra119.001889 ◽

2020 ◽

Vol 19 (5) ◽

pp. 839-851 ◽

Cited By ~ 3

Author(s):

Eva Griesser ◽

Hannah Wyatt ◽

Sara Ten Have ◽

Birgit Stierstorfer ◽

Martin Lenter ◽

...

Keyword(s):

Substantia Nigra ◽

Solid Phase ◽

Neuronal Cell ◽

Alpha Synuclein ◽

Ffpe Tissue ◽

Specific Gene ◽

Tissue Specimens ◽

Laser Capture ◽

Go Terms ◽

Human Substantia Nigra

Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. We first optimized the protocol for efficient LCM analysis of FFPE tissue specimens. The use of SDS containing extraction buffer in combination with the single-pot solid-phase-enhanced sample preparation (SP3) digest method gave the best results regarding protein yield and protein/peptide identifications. Microdissected FFPE human substantia nigra tissue samples (∼3,000 cells) were then analyzed, using tandem mass tag (TMT) labeling and LC-MS/MS, resulting in the quantification of >5,600 protein groups. Nigral proteins were classified and analyzed by abundance, showing an enrichment of extracellular exosome and neuron-specific gene ontology (GO) terms among the higher abundance proteins. Comparison of microdissected samples with intact tissue sections, using a label-free shotgun approach, revealed an enrichment of neuronal cell type markers, such as tyrosine hydroxylase and alpha-synuclein, as well as proteins annotated with neuron-specific GO terms. Overall, this study provides a detailed protocol for laser-capture proteomics using FFPE tissue and demonstrates the efficiency of LCM analysis of distinct cell subpopulations for proteomic analysis using low sample amounts.

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