Characterization of the human primary visual cortex and cerebellum proteomes using shotgun mass spectrometry‐data‐independent analyses

Martins-de-Souza, Daniel; Guest, Paul C.; Guest, Francesca L.; Bauder, Corinna; Rahmoune, Hassan; Pietsch, Sandra; Roeber, Sigrum; Kretzschmar, Hans A.; Mann, David; Baborie, Atik; Bahn, Sabine

doi:10.1002/pmic.201100476

Cited by 15 publications

(10 citation statements)

References 25 publications

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“…Importantly, a portion of identified proteins are localized to neuronal-specific processes, including axons and synapses, and carry out vast biological functions from cell cycle regulation to RNA splicing and neuronal differentiation. In fact, the total number of identified proteins in our FFPE tissue subcompartments are comparable to previous regional fresh frozen proteomes of human brain (31)(32)(33) and the nonformalin fixed in vitro cultures presented here. Although the recent draft of the human protein reports much higher identification of 14,671 proteins in the human brain (2), this number reflects those identified following extensive peptide fractionations of bulk brains rather than single unfractionated brain subcompartments used in our study.…”

Section: Proteomic Profiles Of Developing Cerebral Compartments and Nsupporting

confidence: 83%

Spatiotemporal Proteomic Profiling of Human Cerebral Development

Djuric

Rodrigues

Batruch

et al. 2017

Molecular & Cellular Proteomics

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Mass spectrometry (MS) analysis of human post-mortem central nervous system (CNS) tissue and induced pluripotent stem cell (iPSC)-based directed differentiations offer complementary avenues to define protein signatures of neurodevelopment. Methodological improvements of formalin-fixed, paraffin-embedded (FFPE) protein isolation now enable widespread proteomic analysis of well-annotated archival tissue samples in the context of development and disease. Here, we utilize a shotgun label-free quantification (LFQ) MS method to profile magnetically enriched human cortical neurons and neural progenitor cells (NPCs) derived from iPSCs. We use these signatures to help define spatiotemporal protein dynamics of developing human FFPE cerebral regions. We show that the use of high resolution Q Exactive mass spectrometers now allow simultaneous quantification of >2700 proteins in a single LFQ experiment and provide sufficient coverage to define novel biomarkers and signatures of NPC maintenance and differentiation. Importantly, we show that this abbreviated strategy allows efficient recovery of novel cytoplasmic, membrane-specific and synaptic proteins that are shared between both and neuronal differentiation. This study highlights the discovery potential of non-comprehensive high-throughput proteomic profiling of unfractionated clinically well-annotated FFPE human tissue from a diverse array of development and diseased states.

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Section: Proteomic Profiles Of Developing Cerebral Compartments and Nsupporting

confidence: 83%

Spatiotemporal Proteomic Profiling of Human Cerebral Development

Djuric

Rodrigues

Batruch

et al. 2017

Molecular & Cellular Proteomics

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“…A total of 391 and 330 unique proteins were confidently identified in occipital lobe and cerebellum, respectively. Almost 300 proteins from those were found in common and some of them were previously associated to several neurodegenerative diseases . Analyzing the protein expression profiling of accurately dissected postmortem locus ceruleus, Van Dijk et al identified 2495 proteins by nanoLC‐FT‐MS/MS.…”

Section: Proteome‐wide Analysis Of Anatomical Regions From Human Brainmentioning

confidence: 99%

Toward defining the anatomo‐proteomic puzzle of the human brain: An integrative analysis

Fernández‐Irigoyen

Labarga

Zabaleta

et al. 2015

Proteomics Clinical Apps

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The human brain is exceedingly complex, constituted by billions of neurons and trillions of synaptic connections that, in turn, define ∼900 neuroanatomical subdivisions in the adult brain (Hawrylycz et al. An anatomically comprehensive atlas of the human brain transcriptome. Nature 2012, 489, 391-399). The human brain transcriptome has revealed specific regional transcriptional signatures that are regulated in a spatiotemporal manner, increasing the complexity of the structural and molecular organization of this organ (Kang et al. Spatio-temporal transcriptome of the human brain. Nature 2011, 478, 483-489). During the last decade, neuroproteomics has emerged as a powerful approach to profile neural proteomes using shotgun-based MS, providing complementary information about protein content and function at a global level. Here, we revise recent proteome profiling studies performed in human brain, with special emphasis on proteome mapping of anatomical macrostructures, specific subcellular compartments, and cerebrospinal fluid. Moreover, we have performed an integrative functional analysis of the protein compilation derived from these large-scale human brain proteomic studies in order to obtain a comprehensive view of human brain biology. Finally, we also discuss the potential contribution of our meta-analysis to the Chromosome-centric Human Proteome Project initiative.

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“…Mass spectrometry (MS)-based shotgun method is extremely powerful to analysize proteomes. Such a strategy relies heavily on the databases of complete proteomes [6,7]. In addition, 2D-PAGE approach has some its limitations: it can hardly separate very acidic, basic, small, large and hydrophobic proteins [8].…”

Section: Introductionmentioning

confidence: 99%