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...

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...

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...

The data from this study displays the complexity of the varicella-zoster virus (VZV) transcriptome architecture. VZV causes varicella and reactivates later in life to cause herpes zoster. The VZV genome is known to produce multitudes of overlapping transcripts and distinct open reading frames (ORFs) have been studied as well. However, the architecture of the VZV transcriptome remains unknown. This...

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...

Long interspersed element-1 (LINE-1) is an autonomous retroelement that utilizes copy and paste mechanism to propagate themselves throughout the genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p and ORF2. While LINE-1 transcription is usually repressed in most healthy somatic cells, ORF1p expression has been observed in tumors, including prostate...

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...

This study used proteomic analysis, respirometry, and electron microscopy to examine the development of condensed mitochondria. The dataset contains proteomic and imaging data. The data indicate that condensed mitochondria formed from orthodox mitochondria during meiosis in order to support the formation of the acrosomal matrix. Condensed mitochondria also respired more actively and contained more...