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Baldur: Bayesian hierarchical modeling for label-free proteomics exploiting gamma dependent mean-variance trends
Mol Cell Proteomics. 2023 Oct 6:100654. doi: 10.1016/j.mcpro.2023.100658. Online ahead of print.ABSTRACTLabel-free proteomics is a fast-growing methodology to infer abundances in mass spectrometry proteomics. Extensive research has focused on spectral quantification and peptide identification. However, research towards modeling and understanding quantitative proteomics data is scarce. We propose here a Bayesian hierarchical decision model (Baldur) to test for differences in means between conditions for proteins, peptides, and post-translation modifications. We develop a Bayesian regression model to characterize local mean-...
Source: Molecular and Cellular Proteomics : MCP - October 8, 2023 Category: Molecular Biology Authors: Philip Berg George Popescu Source Type: research

Experience-induced remodeling of the hippocampal post-synaptic proteome and phosphoproteome
Mol Cell Proteomics. 2023 Oct 6:100661. doi: 10.1016/j.mcpro.2023.100661. Online ahead of print.ABSTRACTThe postsynaptic density (PSD) of excitatory synapses contains a highly organized protein network with thousands of proteins and is key node in the regulation of synaptic plasticity. To gain new mechanistic insight into experience-induced changes in the PSD, we examined the global dynamics of the hippocampal PSD proteome and phosphoproteome in mice following 4 different types of experience. Mice were trained using an inhibitory avoidance (IA) task and hippocampal PSD fractions were isolated from individual mice to invest...
Source: Molecular and Cellular Proteomics : MCP - October 8, 2023 Category: Molecular Biology Authors: Seok Heo Taewook Kang Alexei M Bygrave Martin R Larsen Richard L Huganir Source Type: research

Higher-order structural organization of the mitochondrial proteome charted by in situ cross-linking mass spectrometry
We describe some of the most recent technological advances in XL-MS that may benefit the in situ characterization of PPIs even further, especially when combined with electron microscopy and structural modelling.PMID:37805037 | DOI:10.1016/j.mcpro.2023.100657 (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - October 7, 2023 Category: Molecular Biology Authors: Johannes F Hevler Albert J R Heck Source Type: research

Proteomics and β-hydroxybutyrylation Modification Characterization in the Hearts of Naturally Senescent Mice
Mol Cell Proteomics. 2023 Oct 5:100659. doi: 10.1016/j.mcpro.2023.100659. Online ahead of print.ABSTRACTAging is widely accepted as an independent risk factor for cardiovascular disease (CVD), which contributes to increasing morbidity and mortality in the elderly population. Lysine β-hydroxybutyrylation (Kbhb) is a novel post-translational protein modification wherein β-hydroxybutyrate is covalently attached to lysine ε-amino groups. Recent studies have revealed that histone Kbhb contributes to tumor progression, diabetic cardiomyopathy progression, and postnatal heart development. However, no studies have yet reported ...
Source: Molecular and Cellular Proteomics : MCP - October 7, 2023 Category: Molecular Biology Authors: Xuechun Yang Xuehui Li Na Yu Rong Yan Yan Sun Congmin Tang Wenjing Ding Mingying Ling Yiping Song Haiqing Gao Wenjuan Gao Junchao Feng Shaopeng Wang Zhen Zhang Yanqiu Xing Source Type: research

The role of serine/threonine-specific protein kinases in cyanobacteria - SpkB is involved in acclimation to fluctuating conditions in Synechocystis sp. PCC 6803
Mol Cell Proteomics. 2023 Oct 3:100656. doi: 10.1016/j.mcpro.2023.100656. Online ahead of print.ABSTRACTProtein phosphorylation via serine/threonine protein kinases (Spk) is a widespread mechanism to adjust cellular processes toward changing environmental conditions. To study their role(s) in cyanobacteria, we investigated a collection of 11 completely segregated spk mutants among the 12 annotated Spk's in the model cyanobacterium Synechocystis sp. PCC 6803. Screening of the mutant collection revealed that especially the mutant defective in SpkB encoded by slr1697 showed clear deviations regarding carbon metabolism, i.e., ...
Source: Molecular and Cellular Proteomics : MCP - October 5, 2023 Category: Molecular Biology Authors: Thomas Barske Philipp Sp ät Hendrik Schubert Peter Walke Boris Ma ček Martin Hagemann Source Type: research

Impact of Bmal1 rescue and time-restricted feeding on liver and muscle proteomes during the active phase in mice
CONCLUSIONS: In liver and muscle, BMAL1 is a more potent regulator of dark phase proteomes than daily feeding cycles, highlighting the need to assess protein levels in addition to mRNA when investigating clock mechanisms. The proteome is more extensively regulated by BMAL1 in liver than in muscle and many metabolic pathways in peripheral tissues are reliant on the function of the clock system as a whole.PMID:37793502 | DOI:10.1016/j.mcpro.2023.100655 (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - October 4, 2023 Category: Molecular Biology Authors: Jacob G Smith Jeffrey Molendijk Ronnie Blazev Wan Hsi Chen Qing Zhang Christopher Litwin Valentina M Zinna Patrick-Simon Welz Salvador Aznar Benitah Carolina M Greco Paolo Sassone-Corsi Pura Mu ñoz-Cánoves Benjamin L Parker Kevin B Koronowski Source Type: research

Early proteomic characteristics and changes in the optic nerve head, optic nerve, and retina in a rat model of ocular hypertension
This study aimed to identify the early proteomic alterations in the retina, optic nerve head (ONH), and optic nerve (ON). After establishing a rat model of OHT, we harvested the tissues from control and glaucomatous eyes, and analyzed the changes in protein expression using a multiplexed quantitative proteomics approach (TMT-MS3). Our study identified 6403 proteins after 1-day OHT and 4399 proteins after 7-day OHT in the retina, 5493 proteins after 1-day OHT and 4544 proteins after 7-day OHT in ONH, and 5455 proteins after 1-day OHT and 3835 proteins after 7-day OHT in the ON. Of these, 560 and 489 differential proteins we...
Source: Molecular and Cellular Proteomics : MCP - October 4, 2023 Category: Molecular Biology Authors: Danting Lin Shen Wu Ying Cheng Xuejing Yan Qian Liu Tianmin Ren Jingxue Zhang Ningli Wang Source Type: research

MCP's New Editorial Posture Moving Forward
Mol Cell Proteomics. 2023 Sep 27;22(10):100646. doi: 10.1016/j.mcpro.2023.100646. Online ahead of print.NO ABSTRACTPMID:37774463 | DOI:10.1016/j.mcpro.2023.100646 (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - September 29, 2023 Category: Molecular Biology Authors: Al Burlingame Source Type: research