abstract：:InterMetalDB is a free-of-charge database and browser of intermolecular metal binding sites that are present on the interfaces of macromolecules forming larger assemblies based on structural information deposited in Protein Data Bank (PDB). It can be found and freely used at https://intermetaldb.biotech.uni.wroc.pl/. ...

journal_title：Journal of proteome research

authors： Tran JB,Krężel A

更新日期：2021-01-27 00:00:00

abstract：:Moving from macroscale preparative systems in proteomics to micro- and nanotechnologies offers researchers the ability to deeply profile smaller numbers of cells that are more likely to be encountered in clinical settings. Herein a recently developed microscale proteomic method, microdroplet processing in one pot for ...

journal_title：Journal of proteome research

authors： Weke K,Singh A,Uwugiaren N,Alfaro JA,Wang T,Hupp TR,O'Neill JR,Vojtesek B,Goodlett DR,Williams SM,Zhou M,Kelly RT,Zhu Y,Dapic I

更新日期：2021-01-25 00:00:00

abstract：:In this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a metaproteomics workflow within the Galaxy platform to detect cohabita...

journal_title：Journal of proteome research

authors： Thuy-Boun PS,Mehta S,Gruening B,McGowan T,Nguyen A,Rajczewski AT,Johnson JE,Griffin TJ,Wolan DW,Jagtap PD

更新日期：2021-01-04 00:00:00

abstract：:Rapid early triage and dose estimation is vital for limited medical resource allocation and treatment of a large number of the wounded after radiological accidents. Lipidomics has been utilized to delineate biofluid lipid signatures after irradiation. Here, high-coverage targeted lipidomics was employed to screen radi...

journal_title：Journal of proteome research

authors： Xi C,Zhao H,Lu X,Cai TJ,Li S,Liu KH,Tian M,Liu QJ

更新日期：2021-01-01 00:00:00

abstract：:Influenza viruses continue evolving and have the ability to cause a global pandemic, so it is very important to elucidate its pathogenesis and find new treatment methods. In recent years, proteomics has made important contributions to describing the dynamic interaction between influenza viruses and their hosts, especi...

journal_title：Journal of proteome research

authors： Zhang J,Peng Q,Zhao W,Sun W,Yang J,Liu N

更新日期：2021-01-01 00:00:00

abstract：:The current technique used for microbial identification in hospitals is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, it suffers from important limitations, in particular, for closely related species or when the database used for the identification lacks the appr...

journal_title：Journal of proteome research

authors： Dupré M,Duchateau M,Malosse C,Borges-Lima D,Calvaresi V,Podglajen I,Clermont D,Rey M,Chamot-Rooke J

更新日期：2021-01-01 00:00:00

abstract：:Metabolic phenotyping of tissues uses metabolomics and lipidomics to measure the relative polar and nonpolar (lipid) metabolite levels in biological samples. This approach aims to understand disease biochemistry and identify biochemical markers of disease. Sample preparation methods must be reproducible, sensitive (hi...

journal_title：Journal of proteome research

authors： Southam AD,Pursell H,Frigerio G,Jankevics A,Weber RJM,Dunn WB

更新日期：2021-01-01 00:00:00

abstract：:We investigated the effect of homogenization strategy and protein precipitation on downstream protein quantitation using multiple reaction monitoring mass spectrometry (MRM-MS). Our objective was to develop a workflow capable of processing disparate tissue types with high throughput, minimal variability, and maximum p...

journal_title：Journal of proteome research

authors： Michaud SA,Pětrošová H,Jackson AM,McGuire JC,Sinclair NJ,Ganguly M,Flenniken AM,Nutter LMJ,McKerlie C,Schibli D,Smith D,Borchers CH

更新日期：2021-01-01 00:00:00

abstract：:Catechol estrogens (CEs) are known to be toxic metabolites and the initiators of the oncogenesis of breast cancers via forming covalent adducts with DNAs. CEs shall also react with proteins, but their cellular protein targets remain unexplored. Here, we reported the identification of protein targets of CEs in the solu...

journal_title：Journal of proteome research

authors： Do QT,Huang TE,Liu YC,Tai JH,Chen SH

更新日期：2021-01-01 00:00:00

abstract：:Ricin is a type II ribosome-inactivating protein toxin consisting of A and B chains linked by one interchain disulfide bond. Because of its high toxicity depending on both chains together, confirming the presence of both A and B chains of intact ricin is required during the investigation of the illegal production and ...

journal_title：Journal of proteome research

authors： Liu CC,Liang LH,Yang Y,Yu HL,Yan L,Li XS,Chen B,Liu SL,Xi HL

更新日期：2021-01-01 00:00:00

abstract：:The localization of proteins at a tissue- or cell-type-specific level is tightly linked to the protein function. To better understand each protein's role in cellular systems, spatial information constitutes an important complement to quantitative data. The standard methods for determining the spatial distribution of p...

journal_title：Journal of proteome research

authors： Sivertsson Å,Lindström E,Oksvold P,Katona B,Hikmet F,Vuu J,Gustavsson J,Sjöstedt E,von Feilitzen K,Kampf C,Schwenk JM,Uhlén M,Lindskog C

更新日期：2020-12-04 00:00:00

abstract：:We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (meta...

journal_title：Journal of proteome research

authors： Saunders JK,Gaylord DA,Held NA,Symmonds N,Dupont CL,Shepherd A,Kinkade DB,Saito MA

更新日期：2020-11-06 00:00:00

abstract：:The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world, and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions a...

journal_title：Journal of proteome research

authors： Barros RO,Junior FLCC,Pereira WS,Oliveira NMN,Ramos RM

更新日期：2020-11-06 00:00:00

abstract：:The development of computational strategies for the quantitative characterization of the functional mechanisms of SARS-CoV-2 spike proteins is of paramount importance in efforts to accelerate the discovery of novel therapeutic agents and vaccines combating the COVID-19 pandemic. Structural and biophysical studies have...

journal_title：Journal of proteome research

authors： Verkhivker GM

更新日期：2020-11-06 00:00:00

abstract：:The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has impacted a large portion of the world population. From a virus genetic perspective, a recent study described what genomic data revealed about the origin and emergence of SARS-CoV-2, proposing stronger a...

journal_title：Journal of proteome research

authors： Zhang YM,Wang L,Liu XZ,Zhang H

更新日期：2020-11-06 00:00:00

abstract：:Method development is one of the objectives of the astrophysical community for characterizing the organic matter in objects of the solar system. In this context, we report on the development of an enzyme-catalyzed stereoselective hydrolysis, inspired by the proteomics discipline, which has enabled the indirect detecti...

journal_title：Journal of proteome research

authors： Lange J,Djago F,Eddhif B,Remaury QB,Ruf A,Leitner NKV,Hendecourt LLS,Danger G,Rodier CG,Papot S,Poinot P

更新日期：2020-10-20 00:00:00

abstract：:Mutagenesis through fast neutron (FN) radiation of soybean resulted in a mutant with a 15% increase in seed protein content. A comparative genomic hybridization analysis confirmed that the mutant is lacking 24 genes located at chromosomes 5 and 10. A tandem mass tag-based proteomic profiling of the wild type and the F...

journal_title：Journal of proteome research

authors： Islam N,Krishnan HB,Natarajan S

更新日期：2020-10-02 00:00:00

abstract：:Proteoforms containing post-translational modifications (PTMs) represent a degree of functional diversity only harnessed through analytically precise simultaneous quantification of multiple PTMs. Here we present a method to accurately differentiate an unmodified peptide from its PTM-containing counterpart through data...

journal_title：Journal of proteome research

authors： Robinson AE,Binek A,Venkatraman V,Searle BC,Holewinski RJ,Rosenberger G,Parker SJ,Basisty N,Xie X,Lund PJ,Saxena G,Mato JM,Garcia BA,Schilling B,Lu SC,Van Eyk JE

更新日期：2020-10-02 00:00:00

abstract：:Coronary artery disease is one of the most frequent causes of morbidity and mortality worldwide. It is even more prevalent in patients with type 2 diabetes mellitus who suffer from obesity and increased accumulation of epicardial fat with a possible contributing role in the development of coronary artery disease. We p...

journal_title：Journal of proteome research

authors： Tomášová P,Čermáková M,Pelantová H,Vecka M,Kratochvílová H,Lipš M,Lindner J,Ivák P,Netuka I,Šedivá B,Haluzík M,Kuzma M

更新日期：2020-10-02 00:00:00

abstract：:Proteins are continuously exposed to diverse chemical stresses, and the resulting chemical modifications can provide significant information on biological events. Keratins are the main constituent of human skin and are the major target proteins of various chemical modifications. We have previously developed a mass spe...

journal_title：Journal of proteome research

authors： Lee SH,Kawase J,Hiroshima Y,Oe T

更新日期：2020-09-04 00:00:00

abstract：:Quantifying peptides based on unique peptide fragment ions avoids the issue of ratio distortion that is commonly observed for reporter ion-based quantification approaches. Herein, we present a collision-induced dissociation-cleavable, isobaric acetyl-isoleucine-proline-glycine (Ac-IPG) tag, which conserves the merits ...

journal_title：Journal of proteome research

authors： Tian X,de Vries MP,Permentier HP,Bischoff R

更新日期：2020-09-04 00:00:00

abstract：:Yeast two-hybridization (Y2H) is a classical method to study protein-protein interactions in organisms, and the top limitation of Y2H is the high ratio of false negatives and false positives. The most efficient way to reduce this error is to improve the quality of the library. The traditional library quality evaluatio...

journal_title：Journal of proteome research

authors： Yu Q,Hu Y,Su J,Li P,Zhang L,Fu X,Chen F,Song A

更新日期：2020-08-07 00:00:00

abstract：:Methotrexate (MTX) is a chemotherapeutic agent that can cause a range of toxic side effects including gastrointestinal damage, hepatotoxicity, myelosuppression, and nephrotoxicity and has potentially complex interactions with the gut microbiome. Following untargeted UPLC-qtof-MS analysis of urine and fecal samples fro...

journal_title：Journal of proteome research

authors： Letertre MPM,Munjoma N,Wolfer K,Pechlivanis A,McDonald JAK,Hardwick RN,Cherrington NJ,Coen M,Nicholson JK,Hoyles L,Swann JR,Wilson ID

更新日期：2020-08-07 00:00:00

abstract：:Due to their ease of use and high binding affinity, streptavidin-based purification tools have become widely used for isolating biotinylated compounds from complex mixtures. We and others routinely use streptavidin-sepharose matrices to isolate biotinylated polypeptides generated in proximity-dependent biotinylation a...

journal_title：Journal of proteome research

authors： St-Germain JR,Samavarchi Tehrani P,Wong C,Larsen B,Gingras AC,Raught B

更新日期：2020-08-07 00:00:00

abstract：:TGFBR2 serves as an initial regulator of the TGF-β signaling pathway, and loss or reduction of its expression can lead to uncontrolled cell growth. This study was conducted to further explore the mechanism of TGFBR2/SMAD4 on the migration and proliferation of CC cells. Here, TGFBR2 and SMAD4 expressions in CC cells an...

journal_title：Journal of proteome research

authors： Yuan J,Yi K,Yang L

更新日期：2020-08-07 00:00:00

abstract：:To cope with sudden changes in the external environment, the budding yeast Saccharomyces cerevisiae orchestrates a multifaceted response that spans many levels of physiology. Several studies have interrogated the transcriptome response to endoplasmic reticulum (ER) stress and the role of regulators such as the Ire1 ki...

journal_title：Journal of proteome research

authors： MacGilvray ME,Shishkova E,Place M,Wagner ER,Coon JJ,Gasch AP

更新日期：2020-08-07 00:00:00

abstract：:Gas chromatography-mass spectrometry (GC-MS) platforms are typically run in electron ionization (EI) mode for mass spectral matching and metabolite annotation. With the advent of high resolution mass spectrometry (HRMS), soft ionization techniques such as chemical ionization (CI) may provide additional coverage for co...

journal_title：Journal of proteome research

authors： Misra BB,Olivier M

更新日期：2020-07-02 00:00:00

abstract：:Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer among women worldwide. It is confirmed mainly by fine-needle aspiration biopsy (FNAB), an invasive diagnostic method. The key proteins responsible for thyroid hormone biosynthesis are glycosylated. Hence, changes in site-specific glycosylation...

journal_title：Journal of proteome research

authors： Zhang Y,Zhao W,Zhao Y,Mao Y,Su T,Zhong Y,Wang S,Zhai R,Cheng J,Fang X,Zhu J,Yang H

更新日期：2020-07-02 00:00:00

abstract：:Coronary artery disease remains a leading cause of death in industrialized nations, and early detection of disease is a critical intervention target to effectively treat patients and manage risk. Proteomic analysis of mixed tissue homogenates may obscure subtle protein changes that occur uniquely in underlying tissue ...

journal_title：Journal of proteome research

authors： Parker SJ,Chen L,Spivia W,Saylor G,Mao C,Venkatraman V,Holewinski RJ,Mastali M,Pandey R,Athas G,Yu G,Fu Q,Troxlair D,Vander Heide R,Herrington D,Van Eyk JE,Wang Y

更新日期：2020-07-02 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：:Protein microarrays consist of known proteins spotted onto solid substrates and are used to perform highly multivariate assessments of protein-binding interactions. Human protein arrays are routinely applied to pathogen detection, immune response biomarker profiling, and antibody specificity profiling. Here, we descri...

journal_title：Journal of proteome research

authors： Feng F,Ataca ST,Ran M,Wang Y,Breen M,Kepler TB

更新日期：2020-07-02 00:00:00

abstract：:Comparative phosphoproteomics of Mycobacterium tuberculosis (Mtb)- and Mycobacterium bovis BCG (BCG)-infected macrophages could be instrumental in understanding the characteristic post-translational modifications of host proteins and their subsequent involvement in determining Mtb pathogenesis. To identify proteins ac...

journal_title：Journal of proteome research

authors： Choudhary E,Bullen CK,Goel R,Singh AK,Praharaj M,Thakur P,Dhiman R,Bishai WR,Agarwal N

更新日期：2020-06-05 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：:Severe acute pancreatitis (SAP) is caused by complicated biological factors, and revealing its complex pathogenesis by single-target analysis is difficult. Systematic studies have developed slowly because extraction of degradable pancreatic proteins exposed to multiple proteases is challenging. We present integrated w...

journal_title：Journal of proteome research

authors： Wang C,Zhang Y,Tan J,Chen B,Sun L

更新日期：2020-06-05 00:00:00

abstract：:Increased throughput as well as increased multiplexing of liquid chromatography coupled to selected reaction monitoring mass spectrometry (LC-SRM-MS) assays for protein quantification challenges routine data analysis. Despite the measurement of multiple transitions from multiple peptides, for clinical applications a s...

journal_title：Journal of proteome research

authors： van den Broek I,Mastali M,Mouapi K,Bystrom C,Bairey Merz CN,Van Eyk JE

更新日期：2020-06-05 00:00:00

abstract：:The mechanisms whereby Mycobacterium tuberculosis (Mtb) rewires the host metabolism in vivo are surprisingly unexplored. Here, we used three high-resolution mass spectrometry platforms to track altered lung metabolic changes associated with Mtb infection of mice. The multiplatform data sets were merged using consensus...

journal_title：Journal of proteome research

authors： Fernández-García M,Rey-Stolle F,Boccard J,Reddy VP,García A,Cumming BM,Steyn AJC,Rudaz S,Barbas C

更新日期：2020-05-01 00:00:00

abstract：:Francisella tularensis is a Gram-negative bacterium that causes the zoonotic disease tularemia. The historical development of tularemia as a biological weapon has led to it being characterized by the CDC as a category A biothreat agent. Neither posttranslational modification (PTM) of proteins, in particular lysine ace...

journal_title：Journal of proteome research

authors： Marakasova E,Ii A,Nelson KT,van Hoek ML

更新日期：2020-04-03 00:00:00

abstract：:Transferrin purification from mice serum samples by immunoaffinity chromatography (IAC) was optimized in order to study the possible modifications occurring in its glycans in collagen-induced arthritis (CIA) samples. SDS-PAGE and nanoLC-MS/MS were used to monitor the IAC purification performance. Afterward, a relative...

journal_title：Journal of proteome research

authors： Mancera-Arteu M,Giménez E,Sancho J,Sanz-Nebot V

更新日期：2020-04-03 00:00:00

abstract：:Herein, we report on the venom proteome of Vipera anatolica senliki, a recently discovered and hitherto unexplored subspecies of the critically endangered Anatolian meadow viper endemic to the Antalya Province of Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and...

journal_title：Journal of proteome research

authors： Hempel BF,Damm M,Mrinalini,Göçmen B,Karış M,Nalbantsoy A,Kini RM,Süssmuth RD

更新日期：2020-04-03 00:00:00

abstract：:Using an integrated transcriptomic and proteomic approach, we characterized the venom peptidome of the European red ant, Manica rubida. We identified 13 "myrmicitoxins" that share sequence similarities with previously identified ant venom peptides, one of them being identified as an EGF-like toxin likely resulting fro...

journal_title：Journal of proteome research

authors： Touchard A,Aili SR,Téné N,Barassé V,Klopp C,Dejean A,Kini RM,Mrinalini,Coquet L,Jouenne T,Lefranc B,Leprince J,Escoubas P,Nicholson GM,Treilhou M,Bonnafé E

更新日期：2020-04-03 00:00:00