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...

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...

This study investigated the pathways important for Mycobacterium tuberculosis, bacteria that cause tuberculosis, pathogenesis. They searched the Mycobacterium 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 some structural...

This study identified biological targets in major depressive disorder (MDD). Acetyl-l-carnitine (LAC), which is critical for hippocampal function and several behavioral domains, has rapid and enduring antidepressant like effects in LAC deficient rodents. As a result, this study examined LAC levels in humans. Following an initial phone screen, potential participants were evaluated in person to determine...

Dinucleoside tetraphosphates have been shown to function in bacteria as precursors to nucleoside tetraphosphate (Np4) RNA caps. The removal of this cap is critical for initiating 5′ end-dependent degradation of those RNAs, which affects bacterial adaptability to stress. This study described that the RNA pyrophosphohydrolase (RppH) assumes a leading role in decapping those transcripts in Escherichia...

Leukocidins are crucial components of Staphylococcus aureus (S. aureus) and they are secreted toxins that directly target and lyse immune cells. One of the leukocidins, Leukocidin AB (LukAB), is associated with the bacterial cell envelope. This study examined how S. aureus regulates LukAB secretion as well as the role of bacteria-associated LukAB in host-pathogen interaction. They used tissue culture...

Periodontal disease (PD) is induced by a bacterial dysbiosis in the oral cavity that stimulates inflammation and bone loss. This study showed elevation of succinate in PD, which aggravates the disease through the succinate receptor (SUCNR1). Metabolomics assay compared the succinate level in the subgingival plaque of patients with PD. RNAscope and Immunofluorescence assays were conducted to validate...