Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms.

abstract：:A proteoform family is a group of related molecular forms of a protein (proteoforms) derived from the same gene. We have previously described a strategy to identify proteoforms and elucidate proteoform families in complex mixtures of intact proteins. The strategy is based upon measurements of two properties for each p...

journal_title：Journal of proteome research

authors： Dai Y,Shortreed MR,Scalf M,Frey BL,Cesnik AJ,Solntsev S,Schaffer LV,Smith LM

更新日期：2017-11-03 00:00:00

abstract：:Broadly neutralizing antibodies (bNAbs) that target the trimeric HIV-1 envelope glycoprotein spike (Env) are tools that can guide the design of recombinant Env proteins intended to engage the predicted human germline precursors of bNAbs (gl-bNAbs). The protein components of gl-bNAb epitopes are often masked by glycans...

journal_title：Journal of proteome research

authors： Behrens AJ,Kumar A,Medina-Ramirez M,Cupo A,Marshall K,Cruz Portillo VM,Harvey DJ,Ozorowski G,Zitzmann N,Wilson IA,Ward AB,Struwe WB,Moore JP,Sanders RW,Crispin M

更新日期：2018-03-02 00:00:00

abstract：:The present study reports an in-depth proteome analysis of two Lactobacillus rhamnosus strains, the well-known probiotic strain GG and the dairy strain Lc705. We used GeLC-MS/MS, in which proteins are separated using 1-DE and identified using nanoLC-MS/MS, to generate high-quality protein catalogs. To maximize the num...

journal_title：Journal of proteome research

authors： Savijoki K,Lietzén N,Kankainen M,Alatossava T,Koskenniemi K,Varmanen P,Nyman TA

更新日期：2011-08-05 00:00:00

abstract：:Protein phosphorylation is essential for numerous cellular processes. Large-scale profiling of phosphoproteins continues to enhance the depth and speed at which we understand these processes. The development of effective phosphoprotein and peptide enrichment techniques and improvements to mass spectrometric instrument...

journal_title：Journal of proteome research

authors： Li X,Gerber SA,Rudner AD,Beausoleil SA,Haas W,Villén J,Elias JE,Gygi SP

更新日期：2007-03-01 00:00:00

abstract：:The production of virus-like particles (VLPs) has gained importance over the last few years owing to the benefits they provide compared to conventional vaccines. The biopharmaceutical industry is currently searching for safer candidates based on VLPs for new and existing vaccines and implementing new methods of manufa...

journal_title：Journal of proteome research

authors： Lavado-García J,Jorge I,Cervera L,Vázquez J,Gòdia F

更新日期：2020-03-06 00:00:00

abstract：:Diabetes mellitus is a complex polygenic disease caused by gene-environment interactions with multiple complications, and metabonomic analysis is crucial for pathogenesis, early diagnosis, and timely interventions. Here, we comprehensively analyzed the dynamic metabolic changes in rat urine and plasma, which were indu...

journal_title：Journal of proteome research

authors： Xu W,Wu J,An Y,Xiao C,Hao F,Liu H,Wang Y,Tang H

更新日期：2012-06-01 00:00:00

abstract：:Although some outer membrane (OM) proteins involved in antibiotic resistance have been previously reported, the OM proteins regulating chlortetracycline (CTC) resistance are largely unknown. In this study, we employed a subproteomics approach to identify altered OM proteins of Escherichia coli in response to CTC expos...

journal_title：Journal of proteome research

authors： Lin XM,Yang JN,Peng XX,Li H

更新日期：2010-11-05 00:00:00

abstract：:Automated sequencing of unknowns in bottom-up proteomics makes the data produced susceptible to process control errors, which can be propagated into mistakes in analyte identification. Inclusion of an unintrusive internal standard, such as lysozyme, allows monitoring all phases of the proteomics process including samp...

journal_title：Journal of proteome research

authors： Riter LS,Hodge BD,Gooding KM,Julian RK Jr

更新日期：2005-01-01 00:00:00

abstract：:Neutrophilic granulocytes play a major role in the initiation and resolution of the inflammatory response, and demonstrate significant transcriptional and translational activity. Although much was known about neutrophils prior to the introduction of proteomics, the use of MS-based methodologies has provided an unprece...

journal_title：Journal of proteome research

authors： Tomazella GG,daSilva I,Thomé CH,Greene LJ,Koehler CJ,Thiede B,Wiker HG,de Souza GA

更新日期：2010-04-05 00:00:00

abstract：:Affinity purification coupled to 1-D gel-free liquid chromatography mass spectrometry (LC-MS) is a well-established and widespread approach for the analyses of noncovalently interacting protein complexes. In this study, two proteins conjugated to a streptavidin-binding peptide and hemagglutinin double tag were express...

journal_title：Journal of proteome research

authors： Huber ML,Sacco R,Parapatics K,Skucha A,Khamina K,Müller AC,Rudashevskaya EL,Bennett KL

更新日期：2014-02-07 00:00:00

abstract：:During the development of cancer, changes in cellular glycosylation are observed, indicating that alterations of the glycome occur in extracellular fluids as well as in serum and could therefore serve as tumor biomarkers. In the case of epithelial ovarian cancer (EOC), common tumor markers such as CA125 are known to h...

journal_title：Journal of proteome research

authors： Biskup K,Braicu EI,Sehouli J,Fotopoulou C,Tauber R,Berger M,Blanchard V

更新日期：2013-09-06 00:00:00

abstract：:Proteomics by mass spectrometry (MS) allows the large-scale identification and quantitation of the cellular proteins in a given biological context. Systems biology studies from proteomics data are largely limited by the accuracy and coverage of quantitative proteomics along with missing values. Toward this end, statis...

journal_title：Journal of proteome research

authors： Aggarwal S,Talukdar NC,Yadav AK

更新日期：2019-06-07 00:00:00

abstract：:Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG repeat within the Huntingtin (HTT) gene, though the clinical presentation of disease and age-of-onset are strongly influenced by ill-defined environmental factors. We recently reported a gene-environment interaction wherein expressi...

journal_title：Journal of proteome research

authors： Wegrzynowicz M,Holt HK,Friedman DB,Bowman AB

更新日期：2012-02-03 00:00:00

abstract：:Plasma biomarkers of exposure to environmental contaminants play an important role in early detection of disease. The emerging field of proteomics presents an attractive opportunity for candidate biomarker discovery, as it simultaneously measures and analyzes a large number of proteins. This article presents a case st...

journal_title：Journal of proteome research

authors： Harezlak J,Wu MC,Wang M,Schwartzman A,Christiani DC,Lin X

更新日期：2008-01-01 00:00:00

abstract：:Proteogenomic searching is a useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual genome. The approach, however, can be laborious, as it often requires search segmentation and the use of several unintegrated tools. Furthermore, many proteogenomic efforts have be...

journal_title：Journal of proteome research

authors： Risk BA,Spitzer WJ,Giddings MC

更新日期：2013-06-07 00:00:00

abstract：:Human embryonic stem cells (hESCs) are promising in regenerative medicine (RM) due to their differentiation plasticity and proliferation potential. However, a major challenge in RM is the generation of a vascular system to support nutrient flow to newly synthesized tissues. Here we refined an existing method to genera...

journal_title：Journal of proteome research

authors： Tsolis KC,Bagli E,Kanaki K,Zografou S,Carpentier S,Bei ES,Christoforidis S,Zervakis M,Murphy C,Fotsis T,Economou A

更新日期：2016-06-03 00:00:00

abstract：:Acute stress may trigger systemic biochemical and physiological changes in living organisms, leading to a rapid loss of homeostasis, which can be gradually reinstated by self-regulatory mechanisms and/or drug intervention strategy. However, such a sophisticated metabolic regulatory process has so far been poorly under...

journal_title：Journal of proteome research

authors： Wang X,Su M,Qiu Y,Ni Y,Zhao T,Zhou M,Zhao A,Yang S,Zhao L,Jia W

更新日期：2007-09-01 00:00:00

abstract：:Target-decoy approach (TDA) is the dominant strategy for false discovery rate (FDR) estimation in mass-spectrometry-based proteomics. One of its main applications is direct FDR estimation based on counting of decoy matches above a certain score threshold. The corresponding equations are widely employed for filtering o...

journal_title：Journal of proteome research

authors： Levitsky LI,Ivanov MV,Lobas AA,Gorshkov MV

更新日期：2017-02-03 00:00:00

abstract：:Urine is an ideal material to study the cancer-related protein biomarkers in bladder, whereas exploration to these candidates is confronting technique challenges. Herein, we propose a comprehensive strategy of searching the urine proteins related with bladder cancer. The strategy consists of three core combinations, s...

journal_title：Journal of proteome research

authors： Guo J,Ren Y,Hou G,Wen B,Xian F,Chen Z,Cui P,Xie Y,Zi J,Lin L,Wu S,Li Z,Wu L,Lou X,Liu S

更新日期：2016-07-01 00:00:00

abstract：:Dendritic cells (DCs), the most potent and specialized antigen-presenting cells, play a key role in the regulation of the adaptive immunity. Immature DCs were generated by in vitro culturing of peripheral blood monocytes and functionally activated with the classical pathogen-associated molecular pattern lipopolysaccha...

journal_title：Journal of proteome research

authors： Gundacker NC,Haudek VJ,Wimmer H,Slany A,Griss J,Bochkov V,Zielinski C,Wagner O,Stöckl J,Gerner C

更新日期：2009-06-01 00:00:00

abstract：:A new fast method for identification and characterization of proteolytic digests of proteins by monolithic liquid chromatography coupled with mass spectrometry has been developed. The advantages of the monolithic columns are a high-pressure stability and low back pressure resulting in higher flow rates for capillary o...

journal_title：Journal of proteome research

authors： Marcus K,Schäfer H,Klaus S,Bunse C,Swart R,Meyer HE

更新日期：2007-02-01 00:00:00

abstract：:A glycomic approach is developed to identify oligosaccharide markers for ovarian cancer by rapidly profiling globally released oligosaccharides. Glycoproteins shed by cancer cells are found in the supernatant (or conditioned media) of cultured cells. In this approach, shed glycoproteins are profiled for their oligosac...

journal_title：Journal of proteome research

authors： An HJ,Miyamoto S,Lancaster KS,Kirmiz C,Li B,Lam KS,Leiserowitz GS,Lebrilla CB

更新日期：2006-07-01 00:00:00

abstract：:Somatic embryo development (SED) in upland cotton shows low frequencies of embryo maturation and plantlet regeneration. Progress in increasing the regeneration rate has been limited. Here a global analysis of proteome dynamics between globular and cotyledonary embryos was performed using isobaric tags for relative and...

journal_title：Journal of proteome research

authors： Ge X,Zhang C,Wang Q,Yang Z,Wang Y,Zhang X,Wu Z,Hou Y,Wu J,Li F

更新日期：2015-01-02 00:00:00

abstract：:The effects of increased intake of dietary fiber as either whole grain rye or as resistant starch compared to a typical low dietary fiber Western-style diet on the metabolomics responses were studied in gastrointestinal content and tissue, peripheral plasma, and urine using a multicompartmental nontargeted liquid chro...

journal_title：Journal of proteome research

authors： Ingerslev AK,Karaman I,Bağcıoğlu M,Kohler A,Theil PK,Bach Knudsen KE,Hedemann MS

更新日期：2015-08-07 00:00:00

abstract：:Assessing metabolomic alterations in age-related macular degeneration (AMD) can provide insights into its pathogenesis. We compared the metabolomic profiles of the aqueous humor between wet AMD patients (n = 26) and age- and sex-matched patients undergoing cataract surgery without AMD as controls (n = 20). A global un...

journal_title：Journal of proteome research

authors： Han G,Wei P,He M,Teng H,Chu Y

更新日期：2020-06-05 00:00:00

abstract：:Glycosylation is one of the most common post-translational modifications in proteins, existing in ~50% of mammalian proteins. Several research groups have demonstrated that mass spectrometry is an efficient technique for glycopeptide identification; however, this problem is still challenging because of the enormous di...

journal_title：Journal of proteome research

authors： Zhang Y,Yu CY,Song E,Li SC,Mechref Y,Tang H,Liu X

更新日期：2015-12-04 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：:Microorganisms release effector molecules that modulate the host machinery enabling survival, replication, and dissemination of a pathogen. Here we characterized the extracellular proteome of Paracoccidioides brasiliensis at its pathogenic yeast phase. Cell-free culture supernatants from the Pb18 isolate, cultivated i...

journal_title：Journal of proteome research

authors： Vallejo MC,Nakayasu ES,Matsuo AL,Sobreira TJ,Longo LV,Ganiko L,Almeida IC,Puccia R

更新日期：2012-03-02 00:00:00

abstract：:Nutrient starvation is an important survival challenge for bacteria during industrial production of functional foods. As next-generation sequencing technology has greatly advanced, we performed proteomic and genomic analysis to investigate the response of Lactobacillus casei Zhang to a glucose-restricted environment. ...

journal_title：Journal of proteome research

authors： Yu J,Hui W,Cao C,Pan L,Zhang H,Zhang W

更新日期：2018-03-02 00:00:00

abstract：:Proteolysis of autoantigens can alter normal MHC class II antigen processing and has been implicated in the induction of autoimmune diseases. Many autoantigens are substrates for the protease granzyme B (GrB), but the mechanistic significance of this association is unknown. Peptidylarginine deiminase 4 (PAD4) is a fre...

journal_title：Journal of proteome research

authors： Darrah E,Kim A,Zhang X,Boronina T,Cole RN,Fava A,Giles JT,Bingham III CO,Chalmers MJ,Griffin PR,Sadegh-Nasseri S,Rosen A

更新日期：2017-01-06 00:00:00