One-step sample concentration, purification, and albumin depletion method for urinary proteomics.

Abstract:

:Workflows in urinary proteomics studies are often complex and require many steps to enrich, purify, deplete, and separate the complex mixture. Many of these methods are laborious, are time-consuming, and have the potential for error. Although individual steps of these methods have been previously studied, their downstream compatibilities with fractionation technologies such as off-gel electrophoresis have not been investigated. We developed a one-step sample preparation workflow that simultaneously (i) concentrates proteins, (ii) purifies by removing salts and other low molecular weight compounds, and (iii) depletes (albumin) from urine samples. This simple and robust workflow can be multiplexed and is compatible with a diverse range of downstream multidimensional separation technologies. Additionally, because of its high reproducibility and flexibility in processing samples with different volumes and concentrations, it has the potential to be used for standardization of urinary proteomics studies, as well as for studying other body fluids of similar complexity.

journal_name

J Proteome Res

authors

Vaezzadeh AR,Briscoe AC,Steen H,Lee RS

doi

10.1021/pr100924s

subject

Has Abstract

pub_date

2010-11-05 00:00:00

pages

6082-9

issue

11

eissn

1535-3893

issn

1535-3907

journal_volume

9

pub_type

杂志文章
  • Top-down targeted proteomics for deep sequencing of tropomyosin isoforms.

    abstract::Tropomyosins (Tm) constitute a family of ubiquitous and highly conserved actin-binding proteins, playing essential roles in a variety of biological processes. Tm isoforms produced by multiple Tm encoding genes and alternatively expressed exons along with post-translational modifications (PTMs) regulate Tm function. Th...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr301054n

    authors: Peng Y,Chen X,Zhang H,Xu Q,Hacker TA,Ge Y

    更新日期:2013-01-04 00:00:00

  • Comparative Glycoproteomic Profiling of Human Body Fluid between Healthy Controls and Patients with Papillary Thyroid Carcinoma.

    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

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00672

    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

  • Direct protein detection from biological media through electrospray-assisted laser desorption ionization/mass spectrometry.

    abstract::We report here using a novel technology-electrospray-assisted laser desorption ionization (ELDI)/mass spectrometry-for the rapid and sensitive detection of the major proteins that exist in dried biological fluids (e.g., blood, tears, saliva, serum), bacterial cultures, and tissues (e.g., porcine liver and heart) under...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050442f

    authors: Huang MZ,Hsu HJ,Lee JY,Jeng J,Shiea J

    更新日期:2006-05-01 00:00:00

  • Processing of data generated by 2-dimensional gel electrophoresis for statistical analysis: missing data, normalization, and statistics.

    abstract::Several high-throughput statistical methods were evaluated for processing data generated by two-dimensional polyacrylamide gel electrophoresis, including how to handle missing data, normalization, and statistical analysis of data obtained from 2-D gels. Quantile normalization combined with a nonparametric permutation ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr049886m

    authors: Chang J,Van Remmen H,Ward WF,Regnier FE,Richardson A,Cornell J

    更新日期:2004-11-01 00:00:00

  • Prediction of Protein Lysine Acylation by Integrating Primary Sequence Information with Multiple Functional Features.

    abstract::Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic methods have been widely used to identify lysine acylation proteins. However, these experimental approaches often fail to detect proteins that are in low abundance or absent in specific biological samples. To circumvent these problems, we develo...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00240

    authors: Du Y,Zhai Z,Li Y,Lu M,Cai T,Zhou B,Huang L,Wei T,Li T

    更新日期:2016-12-02 00:00:00

  • Identification of Alzheimer's Disease Autoantibodies and Their Target Biomarkers by Phage Microarrays.

    abstract::The characterization of the humoral response in Alzheimer's disease (AD) patients might aid in detecting the disease at early stages. We have combined phage display and protein microarrays to identify AD autoantibodies and their target biomarkers. After enrichment of the T7 phage display libraries from AD and healthy ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00258

    authors: San Segundo-Acosta P,Montero-Calle A,Fuentes M,Rábano A,Villalba M,Barderas R

    更新日期:2019-07-05 00:00:00

  • Metabolic regulatory network alterations in response to acute cold stress and ginsenoside intervention.

    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

    pub_type: 杂志文章

    doi:10.1021/pr070051w

    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

  • Biological pathways contributing to organ-specific phenotype of brain metastatic cells.

    abstract::Secondary to the increased survival following chemotherapy, brain metastases have recently become a significant clinical problem for breast cancer patients. The aim of this study was to characterize those functional phenotypes that might enhance brain metastasis in breast cancer cells. We first analyzed by two-dimensi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070426d

    authors: Martín B,Aragüés R,Sanz R,Oliva B,Boluda S,Martínez A,Sierra A

    更新日期:2008-03-01 00:00:00

  • Metabolomic Analysis of Liver Tissues for Characterization of Hepatocellular Carcinoma.

    abstract::Hepatocellular carcinoma (HCC) causes more than half a million annual deaths worldwide. Understanding the mechanisms contributing to HCC development is highly desirable for improved surveillance, diagnosis, and treatment. Liver tissue metabolomics has the potential to reflect the physiological changes behind HCC devel...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00185

    authors: Ferrarini A,Di Poto C,He S,Tu C,Varghese RS,Kara Balla A,Jayatilake M,Li Z,Ghaffari K,Fan Z,Sherif ZA,Kumar D,Kroemer A,Tadesse MG,Ressom HW

    更新日期:2019-08-02 00:00:00

  • Identification of Api88 Binding Partners in Escherichia coli Using a Photoaffinity-Cross-Link Strategy and Label-Free Quantification.

    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

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00283

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

    更新日期:2015-08-07 00:00:00

  • Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation.

    abstract::Tandem mass spectrometry (MS/MS) combined with bioinformatics tools have enabled fast and systematic protein identification based on peptide-to-spectrum matches. However, it remains challenging to obtain accurate identification of endogenous peptides, such as neuropeptides, peptide hormones, peptide pheromones, venom ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr400446z

    authors: Hayakawa E,Menschaert G,De Bock PJ,Luyten W,Gevaert K,Baggerman G,Schoofs L

    更新日期:2013-12-06 00:00:00

  • Comparative proteomic analysis of primary schwann cells and a spontaneously immortalized schwann cell line RSC 96: a comprehensive overview with a focus on cell adhesion and migration related proteins.

    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

    pub_type: 杂志文章

    doi:10.1021/pr201221u

    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

  • Differential N-Glycosylation Patterns in Lung Adenocarcinoma Tissue.

    abstract::To decrease the mortality of lung cancer, better screening and diagnostic tools as well as treatment options are needed. Protein glycosylation is one of the major post-translational modifications that is altered in cancer, but it is not exactly clear which glycan structures are affected. A better understanding of the ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00255

    authors: Ruhaak LR,Taylor SL,Stroble C,Nguyen UT,Parker EA,Song T,Lebrilla CB,Rom WN,Pass H,Kim K,Kelly K,Miyamoto S

    更新日期:2015-11-06 00:00:00

  • NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine.

    abstract::A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragm...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00184

    authors: Bingol K,Brüschweiler R

    更新日期:2015-06-05 00:00:00

  • Rapid alteration of the phosphoproteome in the moss Physcomitrella patens after cytokinin treatment.

    abstract::Cytokinin hormones are crucial regulators of a large number of processes in plant development. Recently, significant progress has been made toward the elucidation of the molecular details of cytokinin that has led to a model for signal transduction involving a phosphorylation cascade. However, the current knowledge of...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr060152e

    authors: Heintz D,Erxleben A,High AA,Wurtz V,Reski R,Van Dorsselaer A,Sarnighausen E

    更新日期:2006-09-01 00:00:00

  • Radioactive Chernobyl environment has produced high-oil flax seeds that show proteome alterations related to carbon metabolism during seed development.

    abstract::Starting in 2007, we have grown soybean (Glycine max [L.] Merr. variety Soniachna) and flax (Linum usitatissimum, L. variety Kyivskyi) in the radio-contaminated Chernobyl area and analyzed the seed proteomes. In the second-generation flax seeds, we detected a 12% increase in oil content. To characterize the bases for ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr400528m

    authors: Klubicová K,Danchenko M,Skultety L,Berezhna VV,Rashydov NM,Hajduch M

    更新日期:2013-11-01 00:00:00

  • Optimizing performance of glycopeptide capture for plasma proteomics.

    abstract::Selective capture of glycopolypeptides followed by release and analysis of the former glycosylation-site peptides has been shown to have promise for reducing the complexity of body fluids such as blood for biomarker discovery. In this work, a protocol based on capture of polypeptides containing a N-linked carbohydrate...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr900845m

    authors: Berven FS,Ahmad R,Clauser KR,Carr SA

    更新日期:2010-04-05 00:00:00

  • Phospho-iTRAQ: assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry.

    abstract::The ability to distinguish between phosphopeptides of high and low stoichiometry is essential to discover the true extent of protein phosphorylation. We here extend the strategy whereby a peptide sample is briefly split in two identical parts and differentially labeled preceding the phosphatase treatment of one part. ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500889v

    authors: Glibert P,Meert P,Van Steendam K,Van Nieuwerburgh F,De Coninck D,Martens L,Dhaenens M,Deforce D

    更新日期:2015-02-06 00:00:00

  • Heterogeneous nuclear ribonucleoprotein A1 is identified as a potential biomarker for colorectal cancer based on differential proteomics technology.

    abstract::Colorectal cancer (CRC) is the third most common cancer worldwide and has poor prognosis. To identify the proteins involved in colorectal carcinogenesis, we employed 2-DE and MALDI-TOF/TOF-based proteomics approach to study the differentially expressed proteins in tumor and adjacent nontumor tissue samples. Samples fr...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr900365e

    authors: Ma YL,Peng JY,Zhang P,Huang L,Liu WJ,Shen TY,Chen HQ,Zhou YK,Zhang M,Chu ZX,Qin HL

    更新日期:2009-10-01 00:00:00

  • Occurrence and detection of phosphopeptide isomers in large-scale phosphoproteomics experiments.

    abstract::The past decade has been marked by the emergence of selective affinity media and sensitive mass spectrometry instrumentation that facilitated large-scale phosphoproteome analyses and expanded the repertoire of protein phosphorylation. Despite these remarkable advances, the precise location of the phosphorylation site ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr300229m

    authors: Courcelles M,Bridon G,Lemieux S,Thibault P

    更新日期:2012-07-06 00:00:00

  • Proteome Wide Profiling of N-ε-Lysine Acetylation Reveals a Novel Mechanism of Regulation of the Chitinase Activity in Francisella novicida.

    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

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00512

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

    更新日期:2020-04-03 00:00:00

  • Antibiotic Exposure Disturbs the Gut Microbiota and Its Metabolic Phenotype Differently in Rats with Advanced-Stage Type 1 Diabetes and Age-Matched Controls.

    abstract::Antibiotic-induced microbial perturbations alter host metabolism and affect host physiology. In this study, we aimed to investigate the effects of vancomycin (Vanc) and ciprofloxacin/metronidazole (CiMe) exposures on the gut microbiome and metabolome in the colonic content and tissue samples from advanced-stage type 1...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00402

    authors: Zheng H,Fan K,Ji H,Jiang Q,Ning J,Xu P,Li C,Gao H

    更新日期:2019-11-01 00:00:00

  • Venom Peptide Repertoire of the European Myrmicine Ant Manica rubida: Identification of Insecticidal Toxins.

    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

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00048

    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

  • Peppy: proteogenomic search software.

    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

    pub_type: 杂志文章

    doi:10.1021/pr400208w

    authors: Risk BA,Spitzer WJ,Giddings MC

    更新日期:2013-06-07 00:00:00

  • Identification of novel protein biomarkers of preterm birth in human cervical-vaginal fluid.

    abstract::Spontaneous preterm birth (SPTB) is a major contributor to perinatal morbidity and mortality. However, the diagnosis of preterm labor (PTL) that leads to preterm birth is difficult, and there is a pressing need for improved diagnosis. We utilized multidimensional liquid chromatography-tandem mass spectrometry (LC/LC-M...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0605421

    authors: Pereira L,Reddy AP,Jacob T,Thomas A,Schneider KA,Dasari S,Lapidus JA,Lu X,Rodland M,Roberts CT Jr,Gravett MG,Nagalla SR

    更新日期:2007-04-01 00:00:00

  • The protein interaction network of extracellular vesicles derived from human colorectal cancer cells.

    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

    pub_type: 杂志文章

    doi:10.1021/pr200842h

    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

  • 2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample.

    abstract::For the 2018 YPIC Challenge, contestants were invited to try to decipher two unknown English questions encoded by a synthetic protein expressed in Escherichia coli. In addition to deciphering the sentence, contestants were asked to determine the three-dimensional structure and detect any post-translation modifications...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00384

    authors: Pino L,Lin A,Bittremieux W

    更新日期:2019-11-01 00:00:00

  • Network-Based Analysis on Orthogonal Separation of Human Plasma Uncovers Distinct High Density Lipoprotein Complexes.

    abstract::High density lipoprotein (HDL) particles are blood-borne complexes whose plasma levels have been associated with protection from cardiovascular disease (CVD). Recent studies have demonstrated the existence of distinct HDL subspecies; however, these have been difficult to isolate and characterize biochemically. Here, w...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00419

    authors: Li H,Gordon SM,Zhu X,Deng J,Swertfeger DK,Davidson WS,Lu LJ

    更新日期:2015-08-07 00:00:00

  • Proteome analysis of a hepatocyte-specific BIRC5 (survivin)-knockout mouse model during liver regeneration.

    abstract::The Baculoviral IAP repeat-containing protein 5 (BIRC5), also known as inhibitor of apoptosis protein survivin, is a member of the chromosomal passenger complex and a key player in mitosis. To investigate the function of BIRC5 in liver regeneration, we analyzed a hepatocyte-specific BIRC5-knockout mouse model using a ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr401188r

    authors: Bracht T,Hagemann S,Loscha M,Megger DA,Padden J,Eisenacher M,Kuhlmann K,Meyer HE,Baba HA,Sitek B

    更新日期:2014-06-06 00:00:00

  • In-depth exploration of cow's whey proteome via combinatorial peptide ligand libraries.

    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

    pub_type: 杂志文章

    doi:10.1021/pr900221x

    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