Mass profiling-directed isolation and identification of a stage-specific serologic protein biomarker of advanced prostate cancer.

Abstract:

:Carcinoma of the prostate (CaP) is the second leading cause of cancer-related mortality among American men. While high cure rates are associated with localized CaP, no cure exists for advanced recurrent disease. At present there are no known serologic biomarkers specific to this stage of the disease. Several groups have used mass spectrometry (MS) based mass profiling (MP) combined with multivariate analysis to identify diagnostically predictive protein peaks for CaP in serum and tissues. Nevertheless, an appreciable level of skepticism exists for MP attributed primarily to a lack of definitive protein characterization. To address this problem, we have applied an approach that combines MP with a whole-protein based top-down separation strategy for the identification of a stage-specific marker in a group comprising 16 patients with CaP (metastatic and localized disease) and 15 healthy individuals. MP, combined with multivariate analysis, yielded 17 serum proteins specific to metastatic disease. A single protein detected at m/z 7771 was found to be significantly decreased in the sera of all the metastatic CaP patients but not in localized CaP or healthy individuals. This protein was therefore chosen as the primary candidate for further analysis. The complex nature of the serologic proteome necessitated an isolation strategy that included a C18 prefractionation, followed by multidimensional liquid chromatography and, finally, two-dimensional gel electrophoresis. The separation process was monitored by UV-Vis and matrix-assisted laser desorption/ionization-time of flight MS analysis. This strategy was found to greatly facilitate subsequent MS characterization of the unknown protein, which was identified as platelet factor 4, a chemokine with prothrombolytic and antiangiogenic activities. Confirmation was achieved using both Western blot analysis and enzyme-linked immunosorbent assay. With the growing interest in using MP for patient classification and diagnosis, our approach and its variations should be powerful in the separation and characterization of proteins following MP.

journal_name

Proteomics

journal_title

Proteomics

authors

Lam YW,Mobley JA,Evans JE,Carmody JF,Ho SM

doi

10.1002/pmic.200401165

subject

Has Abstract

pub_date

2005-07-01 00:00:00

pages

2927-38

issue

11

eissn

1615-9853

issn

1615-9861

journal_volume

5

pub_type

杂志文章
  • An interaction proteomics survey of transcription factor binding at recurrent TERT promoter mutations.

    abstract::Aberrant telomerase reactivation in differentiated cells represents a major event in oncogenic transformation. Recurrent somatic mutations in the human telomerase reverse transcriptase (TERT) promoter region, predominantly localized to two nucleotide positions, are highly prevalent in many cancer types. Both mutations...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201500327

    authors: Makowski MM,Willems E,Fang J,Choi J,Zhang T,Jansen PW,Brown KM,Vermeulen M

    更新日期:2016-02-01 00:00:00

  • Protein profile in neuroblastoma cells incubated with S- and R-enantiomers of ibuprofen by iTRAQ-coupled 2-D LC-MS/MS analysis: possible action of induced proteins on Alzheimer's disease.

    abstract::Ibuprofen is a member of the proprionic acid group of nonsteroidal anti-inflammatory drugs (NSAID), with the S-enantiomer being more active than the R-enantiomer. It has been shown to display protective effects against neuroinflammation, which is linked to the pathogenesis of several neurodegenerative disorders, inclu...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200700556

    authors: Zhang J,Sui J,Ching CB,Chen WN

    更新日期:2008-04-01 00:00:00

  • Dynamic proteomic analysis reveals diurnal homeostasis of key pathways in rice leaves.

    abstract::Diurnal physiological acclimation regulated by a circadian system is an advantage for plant fitness. The circadian system is composed of a signal input, the clock and output pathways. Understanding the regulation mechanism of the output pathways remains a major challenge. Diurnal proteomic change reflects the state of...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201000065

    authors: Wang Z,Wang T

    更新日期:2011-01-01 00:00:00

  • Phosphorylation of the SSBP2 and ABL proteins by the ZNF198-FGFR1 fusion kinase seen in atypical myeloproliferative disorders as revealed by phosphopeptide-specific MS.

    abstract::The ZNF198-fibroblast growth factor receptor-1 (FGFR1) fusion kinase is a constitutively activated tyrosine kinase associated with a specific atypical myeloproliferative disease. The chimeric protein localizes to the cytoplasm, unlike the wild type FGFR1 receptor kinase, and presumably inappropriately phosphorylates s...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200800852

    authors: Kasyapa C,Gu TL,Nagarajan L,Polakiewicz R,Cowell JK

    更新日期:2009-08-01 00:00:00

  • Contribution of the antibodies response induced by a low virulent Candida albicans strain in protection against systemic candidiasis.

    abstract::A low virulent Candida albicans mutant, CNC13, deleted in the Mitogen Activated Protein (MAP) kynase HOG1 was used to immunize BALB/c mice. Hog1p is essential for the oxidative stress and hyperosmolarity responses. Several doses and immunization procedures were employed. The protection capacity of the different sera g...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200300678

    authors: Fernández-Arenas E,Molero G,Nombela C,Diez-Orejas R,Gil C

    更新日期:2004-04-01 00:00:00

  • Characterization of the human urine proteome by preparative electrophoresis in combination with 2-DE.

    abstract::The protein components of urine are useful indicators of renal function and human health in general. Urine samples are easily attainable making them ideal substrates for biomarker research. Analysis of the urine proteome however, has been hindered by the great variability of the urine specimens, and the presence of va...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200500671

    authors: Zerefos PG,Vougas K,Dimitraki P,Kossida S,Petrolekas A,Stravodimos K,Giannopoulos A,Fountoulakis M,Vlahou A

    更新日期:2006-08-01 00:00:00

  • Identification of phosphopeptides with unknown cleavage specificity by a de novo sequencing assisted database search strategy.

    abstract::In theory, proteases with broad cleavage specificity could be applied to digest protein samples to improve the phosphoproteomic analysis coverage. However, in practice this approach is seldom employed. This is because the identification of phosphopeptides without enzyme specificity by conventional database search stra...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201400268

    authors: Dong M,Ye M,Cheng K,Dong J,Zhu J,Qin H,Bian Y,Zou H

    更新日期:2014-11-01 00:00:00

  • ICPLQuant - A software for non-isobaric isotopic labeling proteomics.

    abstract::The main goal of many proteomics experiments is an accurate and rapid quantification and identification of regulated proteins in complex biological samples. The bottleneck in quantitative proteomics remains the availability of efficient software to evaluate and quantify the tremendous amount of mass spectral data acqu...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200900174

    authors: Brunner A,Keidel EM,Dosch D,Kellermann J,Lottspeich F

    更新日期:2010-01-01 00:00:00

  • NetPhosBac - a predictor for Ser/Thr phosphorylation sites in bacterial proteins.

    abstract::There is ample evidence for the involvement of protein phosphorylation on serine/threonine/tyrosine in bacterial signaling and regulation, but very few exact phosphorylation sites have been experimentally determined. Recently, gel-free high accuracy MS studies reported over 150 phosphorylation sites in two bacterial m...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200800285

    authors: Miller ML,Soufi B,Jers C,Blom N,Macek B,Mijakovic I

    更新日期:2009-01-01 00:00:00

  • Analysis of the tryptic search space in UniProt databases.

    abstract::In this article, we provide a comprehensive study of the content of the Universal Protein Resource (UniProt) protein data sets for human and mouse. The tryptic search spaces of the UniProtKB (UniProt knowledgebase) complete proteome sets were compared with other data sets from UniProtKB and with the corresponding Inte...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201400227

    authors: Alpi E,Griss J,da Silva AW,Bely B,Antunes R,Zellner H,Ríos D,O'Donovan C,Vizcaíno JA,Martin MJ

    更新日期:2015-01-01 00:00:00

  • Proteome analysis of hepatocellular carcinoma cell strains, MHCC97-H and MHCC97-L, with different metastasis potentials.

    abstract::To better understand the mechanism underlying hepatocellular carcinoma (HCC) metastasis and to search for potential markers for HCC prognosis, differential proteome analysis on two HCC cell strains with high and low metastatic potentials, MHCC97-H and MHCC97-L, was conducted using two-dimensional (2-D) gel electrophor...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200300653

    authors: Ding SJ,Li Y,Shao XX,Zhou H,Zeng R,Tang ZY,Xia QC

    更新日期:2004-04-01 00:00:00

  • Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm.

    abstract::LTQ Orbitrap data analyzed with ProteinPilot can be further improved by MaxQuant raw data processing, which utilizes precursor-level high mass accuracy data for peak processing and MGF creation. In particular, ProteinPilot results from MaxQuant-processed peaklists for Orbitrap data sets resulted in improved spectral u...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201100097

    authors: Jagtap P,Bandhakavi S,Higgins L,McGowan T,Sa R,Stone MD,Chilton J,Arriaga EA,Seymour SL,Griffin TJ

    更新日期:2012-06-01 00:00:00

  • Proteomic analysis in human breast cancer: identification of a characteristic protein expression profile of malignant breast epithelium.

    abstract::Gene expression analysis has become a promising tool in predicting the clinical course of malignant disease and the response to antineoplastic therapy. Surprisingly, only little is known about the protein expression pattern of human tumors. Recent advances in proteomic analysis allow proteins of interest to be identif...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200500129

    authors: Hudelist G,Singer CF,Pischinger KI,Kaserer K,Manavi M,Kubista E,Czerwenka KF

    更新日期:2006-03-01 00:00:00

  • Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae and H. sapiens.

    abstract::Large-scale interaction studies contribute the largest fraction of protein interactions information in databases. However, co-purification of non-specific or indirect ligands, often results in data sets that are affected by a considerable number of false positives. For the fraction of interactions mediated by short li...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201000030

    authors: Panni S,Montecchi-Palazzi L,Kiemer L,Cabibbo A,Paoluzi S,Santonico E,Landgraf C,Volkmer-Engert R,Bachi A,Castagnoli L,Cesareni G

    更新日期:2011-01-01 00:00:00

  • Proteome-wide analysis of the amino terminal status of Escherichia coli proteins at the steady-state and upon deformylation inhibition.

    abstract::A proteome wide analysis was performed in Escherichia coli to identify the impact on protein N-termini of actinonin, an antibiotic specifically inhibiting peptide deformylase (PDF). A strategy and tool suite (SILProNaQ) was employed to provide large-scale quantitation of N-terminal modifications. In control conditions...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201500027

    authors: Bienvenut WV,Giglione C,Meinnel T

    更新日期:2015-07-01 00:00:00

  • Proteomic signatures in antibiotic research.

    abstract::Antibiotics disturb the physiological homeostasis of bacterial cells by interfering with essential cellular functions or structures. The bacterial proteome adjusts quickly in response to antibiotic challenge. This physiological response is specifically tailored to overcome the inflicted damage and, thus, closely linke...

    journal_title:Proteomics

    pub_type: 杂志文章,评审

    doi:10.1002/pmic.201100046

    authors: Wenzel M,Bandow JE

    更新日期:2011-08-01 00:00:00

  • Mapping the Spatial Proteome of Metastatic Cells in Colorectal Cancer.

    abstract::Colorectal cancer (CRC) is the second deadliest cancer worldwide. Here, we aimed to study metastasis mechanisms using spatial proteomics in the KM12 cell model. Cells were SILAC-labeled and fractionated into five subcellular fractions corresponding to: cytoplasm, plasma, mitochondria and ER/golgi membranes, nuclear, c...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201700094

    authors: Mendes M,Peláez-García A,López-Lucendo M,Bartolomé RA,Calviño E,Barderas R,Casal JI

    更新日期:2017-10-01 00:00:00

  • Subcellular pH and predicted pH-dependent features of proteins.

    abstract::A characteristic of two-dimensional proteomics gels is a general bimodal distribution of isoelectric (pI) values. Discussion of this feature has focussed on the balance of acidic and basic ionisable residues, and potential relationships between pI distributions and organism classification or protein subcellular locati...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200500534

    authors: Chan P,Lovrić J,Warwicker J

    更新日期:2006-06-01 00:00:00

  • RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database.

    abstract::RADARS, a rapid, automated, data archiving and retrieval software system for high-throughput proteomic mass spectral data processing and storage, is described. The majority of mass spectrometer data files are compatible with RADARS, for consistent processing. The system automatically takes unprocessed data files, iden...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:

    authors: Field HI,Fenyö D,Beavis RC

    更新日期:2002-01-01 00:00:00

  • A proteomic approach to the bilirubin-induced toxicity in neuronal cells reveals a protective function of DJ-1 protein.

    abstract::Unconjugated bilirubin (UCB) is a powerful antioxidant and a modulator of cell growth through the interaction with several signal transduction pathways. Although newborns develop a physiological jaundice, in case of severe hyperbilirubinemia UCB may become neurotoxic causing severe long-term neuronal damages, also kno...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200900579

    authors: Deganuto M,Cesaratto L,Bellarosa C,Calligaris R,Vilotti S,Renzone G,Foti R,Scaloni A,Gustincich S,Quadrifoglio F,Tiribelli C,Tell G

    更新日期:2010-04-01 00:00:00

  • Quantitative proteome analysis of age-related changes in mouse gastrocnemius muscle using mTRAQ.

    abstract::Aging is associated with a progressive loss of skeletal muscular function that often leads to progressive disability and loss of independence. Although muscle aging is well documented, the molecular mechanisms of this condition still remain unclear. To gain greater insight into the changes associated with aging of ske...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201200497

    authors: Hwang CY,Kim K,Choi JY,Bahn YJ,Lee SM,Kim YK,Lee C,Kwon KS

    更新日期:2014-01-01 00:00:00

  • Analysis of PNGase F-Resistant N-Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities.

    abstract::SugarQb (www.imba.oeaw.ac.at/sugarqb) is a freely available collection of computational tools for the automated identification of intact glycopeptides from high-resolution HCD MS/MS datasets in the Proteome Discoverer environment. We report the migration of SugarQb to the latest and free version of Proteome Discoverer...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201700436

    authors: Stadlmann J,Hoi DM,Taubenschmid J,Mechtler K,Penninger JM

    更新日期:2018-07-01 00:00:00

  • A proteomic approach to cisplatin resistance in the cervix squamous cell carcinoma cell line A431.

    abstract::Since drug resistance is a complex and multifactorial event involving activation/repression of multiple biochemical pathways, we used a proteomic approach to study cisplatin resistance and drug response in human tumor cell lines. The cervix squamous cell carcinoma cell line A431 and its cisplatin-resistant subline, A4...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200400835

    authors: Castagna A,Antonioli P,Astner H,Hamdan M,Righetti SC,Perego P,Zunino F,Righetti PG

    更新日期:2004-10-01 00:00:00

  • Serum biomarker discovery in renal cancer using 2-DE and prefractionation by immunodepletion and isoelectric focusing; increasing coverage or more of the same?

    abstract::As an initial screen for novel markers of renal cancer and to minimise background heterogeneity, we have compared the within-patient profiles of serum samples from seven patients pre- and post-nephrectomy. Samples were depleted of six of the most abundant proteins using Agilent's multiple affinity removal system (MARS...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200800497

    authors: Vasudev NS,Ferguson RE,Cairns DA,Stanley AJ,Selby PJ,Banks RE

    更新日期:2008-12-01 00:00:00

  • Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome.

    abstract::In order to discover novel protein markers indicative of disease processes or drug effects, the proteomics technology platform most commonly used consists of high resolution protein separation by two-dimensional electrophoresis (2-DE), mass spectrometric identification of proteins from stained gel spots and a bioinfor...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200390057

    authors: Pieper R,Su Q,Gatlin CL,Huang ST,Anderson NL,Steiner S

    更新日期:2003-04-01 00:00:00

  • Proteins unique to intraphagosomally grown Mycobacterium tuberculosis.

    abstract::Pathogenic mycobacteria persist and replicate within phagosomes of host phagocytes by inhibiting phagosome maturation at an early endosome stage. The molecular basis for this behavior is not understood. To identify proteins of Mycobacterium tuberculosis unique to the intraphagosomal phase, mycobacteria were purified f...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200500547

    authors: Mattow J,Siejak F,Hagens K,Becher D,Albrecht D,Krah A,Schmidt F,Jungblut PR,Kaufmann SH,Schaible UE

    更新日期:2006-04-01 00:00:00

  • Microparticles released from Mycobacterium tuberculosis-infected human macrophages contain increased levels of the type I interferon inducible proteins including ISG15.

    abstract::Microparticles (MPs) are small membranous particles (100-1000 nm) released under normal steady-state conditions and are thought to provide a communication network between host cells. Previous studies demonstrated that Mycobacterium tuberculosis (M. tb) infection of macrophages increased the release of MPs, and these M...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201400610

    authors: Hare NJ,Chan B,Chan E,Kaufman KL,Britton WJ,Saunders BM

    更新日期:2015-09-01 00:00:00

  • Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics.

    abstract::Selected reaction monitoring (SRM) - also known as multiple reaction monitoring (MRM) - has emerged as a promising high-throughput targeted protein quantification technology for candidate biomarker verification and systems biology applications. A major bottleneck for current SRM technology, however, is insufficient se...

    journal_title:Proteomics

    pub_type: 杂志文章,评审

    doi:10.1002/pmic.201100436

    authors: Shi T,Su D,Liu T,Tang K,Camp DG 2nd,Qian WJ,Smith RD

    更新日期:2012-04-01 00:00:00

  • Identification of Arabidopsis salt and osmotic stress responsive proteins using two-dimensional difference gel electrophoresis and mass spectrometry.

    abstract::Arabidopsis thaliana cell suspension cultures have been used to investigate the effects of salinity and hyperosmotic stress on plant cellular proteins. We show that 200 mM NaCl and 400 mM sorbitol treatments induce extracellular medium acidification in Arabidopsis cell cultures, a typical response of plant cells to sa...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200401282

    authors: Ndimba BK,Chivasa S,Simon WJ,Slabas AR

    更新日期:2005-11-01 00:00:00

  • Arrestin-Domain Containing Protein 1 (Arrdc1) Regulates the Protein Cargo and Release of Extracellular Vesicles.

    abstract::Extracellular vesicles (EVs) are lipid-bilayered vesicles that are released by multiple cell types and contain nucleic acids and proteins. Very little is known about how the cargo is packaged into EVs. Ubiquitination of proteins is a key posttranslational modification that regulates protein stability and trafficking t...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201800266

    authors: Anand S,Foot N,Ang CS,Gembus KM,Keerthikumar S,Adda CG,Mathivanan S,Kumar S

    更新日期:2018-09-01 00:00:00