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Cancer Proteomics: The State of the Art

Now that the human genome has been determined, the field of proteomics is ramping up to tackle the vast protein networks that both control and are controlled by the information encoded by the genome ... Disease Markers 0278-0240 Cancer proteomics: The state of the art 0 Proteomics Unit, Division of Therapeutic Products, Center for Biologics Evaluation Research , FDA, Bldg. 29A Room 2B02, 8800

Global Strategies for Disease Detection and Treatment: Proteomics

Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute , Bethesda, MD 20892 , USA - The field of proteomics holds great promise for identifying nontargeted, global molecular ... profiles “signatures” of normal and diseased cells. While genomics offers a wide array of tools for identifying mutated or dysregulated genes, proteomics offers the ability to measure post-translational

Proteomics for blood biomarker exploration of severe mental illness: pitfalls of the past and potential for the future

psychiatric disorders, namely schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD), we queried PubMed. Here we delve into the findings from thirty studies, which used proteomics and ... between proteomic findings and genetic loci identified in genome-wide association studies (GWAS). The studies we appraised demonstrate that proteomics for psychiatric research has been heterogeneous in aims

Identification of PGAM1 as a putative therapeutic target for pancreatic ductal adenocarcinoma metastasis using quantitative proteomics

Identification of PGAM1 as a putative therapeutic target for pancreatic ductal adenocarcinoma metastasis using quantitative proteomics Xinlu Liu,1 Yejing Weng,2 Peng Liu,1 Zhigang Sui,2 Lei Zhou,1 ... analysis to perform the comparative proteomics of two homologous hamster pancreatic cancer cell lines that are different in metastatic ability: PC-1.0 (highly metastatic) and PC-1 (weakly metastatic

High throughput discovery of protein variants using proteomics informed by transcriptomics

Proteomics informed by transcriptomics (PIT), in which proteomic MS/MS spectra are searched against open reading frames derived from de novo assembled transcripts, can reveal previously unknown ... (proteomics informed by transcriptomics) methodology in which spectra acquired from liquid chromatography tandem mass spectrometry (LC–MS/MS) proteomics are searched against open reading frames (ORFs) derived

Proteomics Unravels the Regulatory Mechanisms in Human Tears Following Acute Renouncement of Contact Lens Use: A Comparison between Hard and Soft Lenses

mass spectrometry-based quantitative proteomics approach. The expression patterns of certain proteins clusters were specific to the use of a particular lens type and a large majority of these actively ... intricate molecular changes in the tear protein constituents employing the state-of-the-art mass spectrometry-based proteomics platform and bioinformatics tools. Importantly, this investigation has also

Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii

metabolism and storage occur in plastoglobuli. Functions of each of these compartments have been elucidated by proteomics; i.e. the use of mass spectrometry and bioinformatics to carry out large scale ... , photographed and then dried. 35S-labelled proteins were revealed by phosphorimaging. 5 / 20 Mass spectrometry Proteomics grade endoproteinases (Lys-C and Trypsin Gold) and ProteaseMax surfactant were purchased

Luteolin attenuates Wnt signaling via upregulation of FZD6 to suppress prostate cancer stemness revealed by comparative proteomics

quantitative proteomics study, we identified 208 differentially expressed proteins in luteolin-treated PC-3 cells. Subsequent mechanistic analysis revealed that luteolin inhibits Wnt signaling by transcriptional ... safety for clinical use. Thus, luteolin could be a good candidate for cancer therapy. Despite numerous studies, the mechanism of luteolin’s anti-prostate cancer activity is still elusive. Proteomics has

Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria

match the requirements of the rumen microbial population. Although challenging, the application of meta-proteomics has potential for a more complete understanding of the rumen ecosystem than sequencing ... rumen and thus the information from the rumen meta-proteome is much poorer than that generated from meta-genomic and meta-transcriptomic analyses. Meta-proteomics has been described as the entire protein

Salivary proteomics of healthy dogs: An in depth catalog

Wolfhound (1), Jack Russell Terrier (1), Mixed breed dog (1), Newfoundland (1), and Scottish Deerhound (1) (Fig 1). To try to investigate the potential effect of genetic lineage on the salivary proteomics ... protein data from the dog saliva was measured via protein spectral counts from the MS-based proteomics data. Normalized spectral counts were assigned to each 5 / 16 identified protein using the

Proteomics and transcriptomics analyses of ataxia telangiectasia cells treated with Dexamethasone

staining protocols for high sensitivity protein identification using matrix-assisted laser desorption/ionization-time of flight analysis . Proteomics 1 : 1359 ± 1363 . https://doi.org/10.1002/ 1615 - 9861 ... 77 : 1137 ± 1142 . https://doi.org/10.1292/jvms.14-0651 PMID: 25947323 54. Cheema AK , Varghese RS , Timofeeva O , Zhang L , Kirilyuk A , Zandkarimi F , et al. ( 2013 ) Functional proteomics analysis

Tetrazine ligation for chemical proteomics

Determining small molecule—target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding

A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics

‑ values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal ... available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html. Peptide identification; Protein identification; Proteomics; Tandem mass spectrometry Introduction RAId is a

An Innovative Approach for The Integration of Proteomics and Metabolomics Data In Severe Septic Shock Patients Stratified for Mortality

untargeted proteomics allowed us to quantify absolute metabolites concentration and relative proteins abundance. We computed the ratio D7/D1 to take into account their variation from day 1 (D1) to day 7 (D7 ... on metabolites and proteins and one to integrate metabolomics and proteomics data with clinical parameters. Linear discriminant analysis and Partial least squares Discriminant Analysis were also

Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases

) of 9-12 months. Understanding mechanisms of resistance and identifying effective therapeutic alternatives is one of the most important scientific challenges in melanoma. Using proteomics, we want to ... might serve as treatment targets or as predictive markers for these kinds of metastasis. BRAF mutation; Cerebral melanoma metastases; Drug resistance; Melanoma; MAP kinase inhibitor; Proteomics

Identification of blood biomarkers in glioblastoma by SWATH mass spectrometry and quantitative targeted absolute proteomics

targeted absolute proteomics analysis. As a result, we identified eight biomarker candidates for GBM (leucine-rich alpha-2-glycoprotein (LRG1), complement component C9 (C9), C-reactive protein (CRP), alpha-1 ... fragment ion data sets [ 19 ]. SWATH-MS analysis offers several advantages, including high reproducibility and reliability of quantitative information, in discovery proteomics [ 20,21 ]. However, it has

Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

DTR protocol as a viable and straightforward alternative to the FASP protocol for proteomicsbased clinical research. Mass spectrometry; Proteomics; Label-free quantitation; FFPE; Archival tissue; FASP ... mass spectrometry based shot-gun proteomics [ 6–14 ]. This represents a significant leap forward in clinical proteomics. For a long time the highly crosslinked FFPE tissue specimens were considered to

Label free quantitative proteomics reveals the role of miR-200b in androgen-independent prostate cancer cells

studies indicated that miR‑ 200b inhibits the growth of androgen‑ independent prostate cancer (AIPC) cells. In this study, we employed quantitative proteomics techniques to unravel the role of miR‑ 200b in ... were analyzed by label‑ free proteomics. PANTHER was applied to analyze biological processes, molecular functions and pathways of proteins regulated by miR‑ 200b. miRBase was used to evaluate target

Editorial and Review: 29th ASMS Sanibel Conference on Mass Spectrometry—Peptidomics: Bridging the Gap between Proteomics and Metabolomics by MS

Hotel in Clearwater Beach, FL. The topic of the conference was BPeptidomics: Bridging the Gap between Proteomics and Metabolomics by Mass Spectrometry^. Peptidomics is the characterization and study of ... MS confirmation. The final presentation in this session was given by Marshall Bern (Protein Metrics) on BBacterial Peptidoglycan Analysis using a Proteomics Search Engine^. He presented the use of

Proteomics analysis identified peroxiredoxin 2 involved in early-phase left ventricular impairment in hamsters with cardiomyopathy

myocardial proteins involved in early-phase cardiac impairment, using proteomics analysis. Using the two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) combined with MALDI-TOF/TOF tandem ... hamsters that might be involved in compensatory cardiac hypertrophy or cardiac dysfunction [ 9 ]. The field of proteomics provides a systematic approach for quantitative and qualitative mapping of the