The Clinical Proteomic Tumor Analysis Consortium (CPTAC) analyzes cancer biospecimens by mass spectrometry, characterizing and quantifying their constituent proteins, or proteome. Proteomic analysis for each CPTAC study is carried out independently by Proteomic Characterization Centers (PCCs) using a variety of protein fractionation techniques, instrumentation, and workflows. Mass spectrometry and...

This study showed that long interspersed element-1 (LINE-1) ORF2p expression is almost undetectable in human cancers. LINE-1 is the major driver of mobile DNA activity in humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. ORF2p expression is not well characterized in human tissues and cell lines. For the study,...

This dataset showed that mitovesicles, extracellular vesicles (EVs) of mitochondrial origin, are altered in Down syndrome (DS). Mitochondrial dysfunction is a distinctive feature of aging and neurodegenerative disorders, such as DS and Alzheimer’s disease. For this study, a high-resolution density gradient separation of EVs isolated from murine and human DS and diploid control brains was used. Using...

Adenovirus is a nuclear replicating DNA virus that relies on the host cell machinery for productive infection. Processing and metabolism of cellular RNAs are regulated by METTL3, which catalyzes the addition of N6-methyladenosine (m6A) to messenger RNAs. Although m6A-modified adenoviral RNAs have been detected previously, the location and function of m6A within the infectious cycle is unknown. For...

Fragile X syndrome (FXS) is caused by changes in FMR1 gene, which leads to transcriptional silencing and loss of its protein product fragile X mental retardation protein (FMRP). For this study, proteomic experiments were performed to investigate the de novo translational profile in FXS model mice is altered at steady state and in response to metabotropic glutamate receptor (mGluR) stimulation. Altered...

This dataset was collected to present a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics. For this study, they used SAMPEI for spectral alignment-based modified peptide identification. SAMPEI is an open-source algorithm that is designed for the discovery of functional protein and peptide signaling modifications. Human OCI-AML2...

Tau is one of the major microtubule-associated proteins in neurons. Its main role is to stabilize microtubules, supporting cytoskeletal organization, and axonal transport. Tau may undergo pathological modifications and become hyperphosphorylated. This causes the protein to accumulate into toxic assemblies that collectively lead to neurodegeneration. In Alzheimer's disease, tau proteins change shape...

This study investigated the pathways important for Mycobacterium tuberculosis, bacteria that cause tuberculosis, pathogenesis. They searched the Mycobacterium tuberculosis (M. tuberculosis) genome for open reading frames and identified an operon, Rv3679-Rv3680. This operon is predicted to encode proteins with ATPase activity. Using structure prediction modeling, they found that Rv3679 and Rv3680 have...

Tuberous sclerosis complex (TSC) and focal cortical dysplasia (FCD) are associated with dysfunctional mammalian target of rapamycin (mTOR) signaling, which results in increased cell growth and ribosomal S6 protein phosphorylation. TSC studies suggest mTOR inhibitors can reduce TSC tumor growth and seizure frequency, while FCD studies indicate seizure suppression. This study assessed safety of mTOR...

Neurological dysfunction associated with Down syndrome (DS) is the concomitant basal forebrain cholinergic neuron (BFCN) degeneration and onset of Alzheimer’s disease (AD) pathology. Previously, single population RNA sequencing analysis in the Ts65Dn (Ts) mouse model of DS revealed that the mitochondrial oxidative phosphorylation pathway was significantly impacted, where a large subset of genes within...