Verification of the biomarker candidates for non-small-cell lung cancer using a targeted proteomics approach.

abstract：:The two key steps for analyzing proteomic data generated by high-resolution MS are database searching and postprocessing. While the two steps are interrelated, studies on their combinatory effects and the optimization of these procedures have not been adequately conducted. Here, we investigated the performance of thre...

journal_title：Journal of proteome research

authors： Tu C,Sheng Q,Li J,Ma D,Shen X,Wang X,Shyr Y,Yi Z,Qu J

更新日期：2015-11-06 00:00:00

abstract：:Serum protein profiling by mass spectrometry is a promising method for early detection of cancer. We have implemented a combined strategy based on matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) and statistical data analysis for serum protein profiling and applied it in a well-described breast...

journal_title：Journal of proteome research

authors： Callesen AK,Vach W,Jørgensen PE,Cold S,Tan Q,Depont Christensen R,Mogensen O,Kruse TA,Jensen ON,Madsen JS

更新日期：2008-04-01 00:00:00

abstract：:Carcinoma, the most common type of cancer, arises from epithelial cells. The transition from adenoma to carcinoma is associated with the loss of E-cadherin and, in consequence, the disruption of cell-cell contacts. E-cadherin is a tumor suppressor, and it is down-regulated during epithelial-to-mesenchymal transition (...

journal_title：Journal of proteome research

authors： Díaz-Díaz A,Casas-Pais A,Calamia V,Castosa R,Martinez-Iglesias O,Roca-Lema D,Santamarina I,Valladares-Ayerbes M,Calvo L,Chantada V,Figueroa A

更新日期：2017-08-04 00:00:00

abstract：:The Biology/Disease-driven (B/D) working groups of the Human Proteome Project are alliances of research groups aimed at developing or improving proteomic tools to support specific biological or disease-related research areas. Here, we describe the activities and progress to date of the B/D working group focused on pro...

journal_title：Journal of proteome research

authors： Boersema PJ,Melnik A,Hazenberg BPC,Rezeli M,Marko-Varga G,Kamiie J,Portelius E,Blennow K,Zubarev RA,Polymenidou M,Picotti P

更新日期：2018-12-07 00:00:00

abstract：:Protein post-translational modification by ubiquitin-fold modifier 1, UFM1, regulates many biological processes such as response to endoplasmic reticulum stress and regulation of tumor progression. A recent study has indicated that the UFM1-binding and PCI domain-containing protein 1 (UFBP1) is required for the conjug...

journal_title：Journal of proteome research

authors： Zhu Y,Lei Q,Li D,Zhang Y,Jiang X,Hu Z,Xu G

更新日期：2018-04-06 00:00:00

abstract：:Dipetalogaster maxima is a blood-sucking Hemiptera that inhabits sylvatic areas in Mexico. It usually takes its blood meal from lizards, but following human population growth, it invaded suburban areas, feeding also on humans and domestic animals. Hematophagous insect salivary glands produce potent pharmacologic compo...

journal_title：Journal of proteome research

authors： Assumpção TC,Charneau S,Santiago PB,Francischetti IM,Meng Z,Araújo CN,Pham VM,Queiroz RM,de Castro CN,Ricart CA,Santana JM,Ribeiro JM

更新日期：2011-02-04 00:00:00

abstract：:Endometrial cancer (EC) is the most frequent gynecological cancer. Tumor dissemination affecting ∼20% of EC patients is characterized at the primary carcinoma by epithelial-to-mesenchymal transition (EMT) associated with myometrial infiltration. At distant sites, the interaction of circulating tumor cells (CTCs) with ...

journal_title：Journal of proteome research

authors： Mariscal J,Fernandez-Puente P,Calamia V,Abalo A,Santacana M,Matias-Guiu X,Lopez-Lopez R,Gil-Moreno A,Alonso-Alconada L,Abal M

更新日期：2019-03-01 00:00:00

abstract：:Triply and doubly charged iTRAQ ( isobaric tagging for relative and absolute quantitation) labeled peptide cations from a tryptic peptide mixture of bovine carbonic anhydrase II were subjected to electron transfer ion/ion reactions to investigate the effect of charge bearing modifications associated with iTRAQ on the ...

journal_title：Journal of proteome research

authors： Han H,Pappin DJ,Ross PL,McLuckey SA

更新日期：2008-09-01 00:00:00

abstract：:Interstitial cystitis/painful bladder syndrome (IC) is a chronic syndrome of unknown etiology that presents with bladder pain, urinary frequency, and urgency. The lack of specific biomarkers and a poor understanding of underlying molecular mechanisms present challenges for disease diagnosis and therapy. The goals of t...

journal_title：Journal of proteome research

authors： Wen H,Lee T,You S,Park SH,Song H,Eilber KS,Anger JT,Freeman MR,Park S,Kim J

更新日期：2015-01-02 00:00:00

abstract：:Protein phosphorylation is a major mechanism of signal transduction in bacteria. Here, we analyzed the proteome and phosphoproteome of a wild-type strain of the food-borne pathogen Listeria monocytogenes that was grown in either chemically defined medium or rich medium containing glucose. We then compared these result...

journal_title：Journal of proteome research

authors： Misra SK,Moussan Désirée Aké F,Wu Z,Milohanic E,Cao TN,Cossart P,Deutscher J,Monnet V,Archambaud C,Henry C

更新日期：2014-12-05 00:00:00

abstract：:Multiple reaction monitoring (MRM) is emerging as a promising technique for the detection and quantification of protein biomarkers in complex biological samples. Compared to Western blotting or enzyme assays, its high sensitivity, specificity, accuracy, assay speed, and sample throughput represent a clear advantage fo...

journal_title：Journal of proteome research

authors： Martínez-Márquez A,Morante-Carriel J,Sellés-Marchart S,Martínez-Esteso MJ,Pineda-Lucas JL,Luque I,Bru-Martínez R

更新日期：2013-12-06 00:00:00

abstract：:Schwann cells (SCs) are the principal glial cells of the peripheral nervous system (PNS). As a result of tissue heterogeneity and difficulties in the isolation and culture of primary SCs, a considerable understanding of SC biology is obtained from SC lines. However, the differences between the primary SCs and SC lines...

journal_title：Journal of proteome research

authors： Ji Y,Shen M,Wang X,Zhang S,Yu S,Chen G,Gu X,Ding F

更新日期：2012-06-01 00:00:00

abstract：:Gene-encoded antimicrobial peptides (AMPs) kill bacteria very efficiently by either lytic mechanisms or inhibition of specific bacterial targets. Proline-rich AMPs (PrAMPs), for example, produced in insects and mammals rely on the second mechanism. They bind to the 70 kDa bacterial heat shock protein DnaK and the 60 k...

journal_title：Journal of proteome research

authors： Volke D,Krizsan A,Berthold N,Knappe D,Hoffmann R

更新日期：2015-08-07 00:00:00

abstract：:Hepatocellular carcinoma (HCC) is a major liver malignancy possessing a high mortality rate and is particularly prevalent in China and Asia. While surgery is the most effective treatment for liver tumor, about 80% of HCC patients are inoperable at presentation and die early due to late diagnosis. For early cancer dete...

journal_title：Journal of proteome research

authors： Sun S,Xu MZ,Poon RT,Day PJ,Luk JM

更新日期：2010-01-01 00:00:00

abstract：:Various mammalian cells including tumor cells secrete extracellular vesicles (EVs), otherwise known as exosomes and microvesicles. EVs are nanosized bilayered proteolipids and play multiple roles in intercellular communication. Although many vesicular proteins have been identified, their functional interrelationships ...

journal_title：Journal of proteome research

authors： Choi DS,Yang JS,Choi EJ,Jang SC,Park S,Kim OY,Hwang D,Kim KP,Kim YK,Kim S,Gho YS

更新日期：2012-02-03 00:00:00

abstract：:Protein-protein interactions play a major role in the molecular machinery of life, and various techniques such as AP-MS are dedicated to their identification. However, those techniques return lists of proteins devoid of organizational structure, not detailing which proteins interact with which others. Proposing a hier...

journal_title：Journal of proteome research

authors： Postic G,Marcoux J,Reys V,Andreani J,Vandenbrouck Y,Bousquet MP,Mouton-Barbosa E,Cianférani S,Burlet-Schiltz O,Guerois R,Labesse G,Tufféry P

更新日期：2020-07-02 00:00:00

abstract：:Fast (120 s) and high-throughput (more than six samples at once) in-gel trypsin digestion of proteins using sonoreactor technology has been achieved. Successful protein identification was done by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, MALDI-TOF-MS. Specific identification of the ...

journal_title：Journal of proteome research

authors： Rial-Otero R,Carreira RJ,Cordeiro FM,Moro AJ,Fernandes L,Moura I,Capelo JL

更新日期：2007-02-01 00:00:00

abstract：:Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and ...

journal_title：Journal of proteome research

authors： Shah AD,Inder KL,Shah AK,Cristino AS,McKie AB,Gabra H,Davis MJ,Hill MM

更新日期：2016-10-07 00:00:00

abstract：:Frontotemporal lobar degeneration (FTLD) is an umbrella term for a heterogeneous group of young-onset dementias of uncertain prevalence and incidence worldwide. Atypical cases of FTLD with fused in sarcoma inclusions (aFTLD-U) have been described recently, but their molecular characterization is still due. Using shotg...

journal_title：Journal of proteome research

authors： Martins-de-Souza D,Guest PC,Mann DM,Roeber S,Rahmoune H,Bauder C,Kretzschmar H,Volk B,Baborie A,Bahn S

更新日期：2012-04-06 00:00:00

abstract：:Ovarian cancer remains a deadly threat to women as the disease is often diagnosed in the late stages when the chance of survival is low. There are no good biomarkers available for early detection and only a few markers have shown clinical utility for prognosis, response to therapy and disease recurrence. We mined cond...

journal_title：Journal of proteome research

authors： Gunawardana CG,Kuk C,Smith CR,Batruch I,Soosaipillai A,Diamandis EP

更新日期：2009-10-01 00:00:00

abstract：:Detergents are indispensable solubilizing agents in the purification and analysis of membrane proteins. For mass spectrometric identification of proteins, it is essential that detergents are removed prior to analysis, necessitating an in-gel digestion step. Here, we report a procedure that allows use of detergents and...

journal_title：Journal of proteome research

authors： Nagaraj N,Lu A,Mann M,Wiśniewski JR

更新日期：2008-11-01 00:00:00

abstract：:A proteome of a model organism, Caenorhabditis elegans, was analyzed by an integrated liquid chromatography (LC)-based protein identification system, which was constructed by microscale two-dimensional liquid chromatography (2DLC) coupled with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) on a high-re...

journal_title：Journal of proteome research

authors： Mawuenyega KG,Kaji H,Yamuchi Y,Shinkawa T,Saito H,Taoka M,Takahashi N,Isobe T

更新日期：2003-01-01 00:00:00

abstract：:Arctic ground squirrels provide a unique model to investigate metabolic responses to hibernation in mammals. During winter months these rodents are exposed to severe hypothermia, prolonged fasting, and hypoxemia. In the light of their role in oxygen transport/off-loading and owing to the absence of nuclei and organell...

journal_title：Journal of proteome research

authors： Gehrke S,Rice S,Stefanoni D,Wilkerson RB,Nemkov T,Reisz JA,Hansen KC,Lucas A,Cabrales P,Drew K,D'Alessandro A

更新日期：2019-04-05 00:00:00

abstract：:Phencyclidine (PCP), a noncompetitive N-methyl-D-aspartate receptor antagonist, induces psychotomimetic effects in humans and animals. Administration of PCP to rodents is used as a preclinical model for schizophrenia; however, the molecular mechanisms underlying the symptoms remain largely unknown. Acute PCP treatment...

journal_title：Journal of proteome research

authors： Palmowski P,Rogowska-Wrzesinska A,Williamson J,Beck HC,Mikkelsen JD,Hansen HH,Jensen ON

更新日期：2014-03-07 00:00:00

abstract：:Membrane proteins play a critical role in the process of neural stem cell self-renewal and differentiation. Here, we apply the SILAC (stable isotope labeling by amino acids in cell culture) approach to quantitatively compare the membrane proteome of the self-renewing and the astroglial differentiating cells. High-reso...

journal_title：Journal of proteome research

authors： Cao R,Chen K,Song Q,Zang Y,Li J,Wang X,Chen P,Liang S

更新日期：2012-02-03 00:00:00

abstract：:Novel biomarker verification assays are urgently required to improve the efficiency of biomarker development. Benefitting from lower development costs, multiple reaction monitoring (MRM) has been used for biomarker verification as an alternative to immunoassay. However, in general MRM analysis, only one sample can be ...

journal_title：Journal of proteome research

authors： Yin HR,Zhang L,Xie LQ,Huang LY,Xu Y,Cai SJ,Yang PY,Lu HJ

更新日期：2013-09-06 00:00:00

abstract：:Workflows for large-scale (MS)-based shotgun proteomics can potentially lead to costly errors in the form of incorrect peptide-spectrum matches (PSMs). To improve the robustness of these workflows, we have investigated the use of the precursor mass discrepancy (PMD) to detect and filter potentially false PSMs that hav...

journal_title：Journal of proteome research

authors： Hubler SL,Kumar P,Mehta S,Easterly C,Johnson JE,Jagtap PD,Griffin TJ

更新日期：2020-01-03 00:00:00

abstract：:Today's highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most wide...

journal_title：Journal of proteome research

authors： Dorfer V,Pichler P,Stranzl T,Stadlmann J,Taus T,Winkler S,Mechtler K

更新日期：2014-08-01 00:00:00

abstract：:The use of combinatorial peptide ligand libraries, containing hexapeptides terminating with a primary amine, or modified with a terminal carboxyl group, allowed discovering and identifying a large number of previously unreported proteins in cow's whey. Whereas comprehensive whey protein lists progressively increased i...

journal_title：Journal of proteome research

authors： D'Amato A,Bachi A,Fasoli E,Boschetti E,Peltre G,Sénéchal H,Righetti PG

更新日期：2009-08-01 00:00:00

abstract：:Almond, as a part of the nut family, is an important source of biological compounds, and specifically, almond skins have been considered an important source of polyphenols, including flavan-3-ols and flavonols. Polyphenol metabolism may produce several classes of metabolites that could often be more biologically activ...

journal_title：Journal of proteome research

authors： Llorach R,Garrido I,Monagas M,Urpi-Sarda M,Tulipani S,Bartolome B,Andres-Lacueva C

更新日期：2010-11-05 00:00:00