108 results match your criteria International journal of proteomics[Journal]


Miniaturized Digestion and Extraction of Surface Proteins from following Treatment with Histatin 5 for Mass Spectrometry Analysis.

Int J Proteomics 2016 1;2016:9812829. Epub 2016 Dec 1.

Department of Chemistry, Faculty of Science, University of Western Ontario, London, ON, Canada N6A 5B7; Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada N6A 5C1.

A common approach to isolate surface proteins from fungal and bacterial cells is to perform a proteolytic cleavage of proteins on the surface of intact cells suspended in solution. This paper describes miniaturization of this technique, in which cells are adhered on glass surfaces, and all sample treatments are conducted at L volumes. Specifically, cells were attached onto HSA-coated glass slides. Read More

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http://dx.doi.org/10.1155/2016/9812829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5156812PMC
December 2016
4 Reads

Comparative Proteomic Analysis of Differential Proteins in Response to Aqueous Extract of Quercus infectoria Gall in Methicillin-Resistant Staphylococcus aureus.

Int J Proteomics 2016 5;2016:4029172. Epub 2016 Sep 5.

School of Diagnostic & Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300 Kuala Lumpur, Malaysia.

The aim of this study is to analyze the differential proteins in MRSA ATCC 33591 treated with aqueous extract from Q. infectoria gall. Protein extracts were obtained from MRSA cells by sonication and were separated by 2D polyacrylamide gels. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5027293PMC
http://dx.doi.org/10.1155/2016/4029172DOI Listing
October 2016
12 Reads
1 Citation

Optimization of Urea Based Protein Extraction from Formalin-Fixed Paraffin-Embedded Tissue for Shotgun Proteomics.

Int J Proteomics 2016 31;2016:4324987. Epub 2016 Aug 31.

Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE 68198-5900, USA.

Urea based protein extraction of formalin-fixed paraffin-embedded (FFPE) tissue provides the most efficient workflow for proteomics due to its compatibility with liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). This study optimizes the use of urea for proteomic analysis of clinical FFPE tissue. A series of protein extraction conditions manipulating temperature and buffer composition were compared to reduce carbamylation introduced by urea and increase protein detection. Read More

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http://dx.doi.org/10.1155/2016/4324987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021876PMC
September 2016
3 Reads

S-Nitrosylation Proteome Profile of Peripheral Blood Mononuclear Cells in Human Heart Failure.

Int J Proteomics 2016 18;2016:1384523. Epub 2016 Aug 18.

Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA; Department of Microbiology and Immunology, UTMB, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, UTMB, Galveston, TX 77555, USA.

Nitric oxide (NO) protects the heart against ischemic injury; however, NO- and superoxide-dependent S-nitrosylation (S-NO) of cysteines can affect function of target proteins and play a role in disease outcome. We employed 2D-GE with thiol-labeling FL-maleimide dye and MALDI-TOF MS/MS to capture the quantitative changes in abundance and S-NO proteome of HF patients (versus healthy controls, n = 30/group). We identified 93 differentially abundant (59-increased/34-decreased) and 111 S-NO-modified (63-increased/48-decreased) protein spots, respectively, in HF subjects (versus controls, fold-change | ≥1. Read More

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http://dx.doi.org/10.1155/2016/1384523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007369PMC
September 2016
29 Reads

Label-Free Proteomic Analysis of Flavohemoglobin Deleted Strain of Saccharomyces cerevisiae.

Int J Proteomics 2016 11;2016:8302423. Epub 2016 Jan 11.

Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal 700 019, India.

Yeast flavohemoglobin, YHb, encoded by the nuclear gene YHB1, has been implicated in the nitrosative stress responses in Saccharomyces cerevisiae. It is still unclear how S. cerevisiae can withstand this NO level in the absence of flavohemoglobin. Read More

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http://dx.doi.org/10.1155/2016/8302423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737026PMC
February 2016
6 Reads

Molecular Integrity of Mitochondria Alters by Potassium Chloride.

Int J Proteomics 2015 10;2015:647408. Epub 2015 Dec 10.

Biochemistry and Molecular Biology Lab, Department of Zoology, Banaras Hindu University, Varanasi 221005, India.

Potassium chloride (KCl) has been commonly used in homogenization buffer and procedures of protein extraction. It is known to facilitate release of membrane-associated molecules but the higher concentration of KCl may affect the integrity of mitochondria by breaching the electrostatic force between the lipids and proteins. Therefore, it has been intended to explore the effect of KCl on mitochondrial proteome. Read More

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https://www.hindawi.com/archive/2015/647408/
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http://dx.doi.org/10.1155/2015/647408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689972PMC
January 2016
5 Reads

Human Urine Proteomics: Analytical Techniques and Clinical Applications in Renal Diseases.

Int J Proteomics 2015 29;2015:782798. Epub 2015 Nov 29.

Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Urine has been in the center of attention among scientists of clinical proteomics in the past decade, because it is valuable source of proteins and peptides with a relative stable composition and easy to collect in large and repeated quantities with a noninvasive procedure. In this review, we discuss technical aspects of urinary proteomics in detail, including sample preparation, proteomic technologies, and their advantage and disadvantages. Several recent experiments are presented which applied urinary proteome for biomarker discovery in renal diseases including diabetic nephropathy, immunoglobulin A (IgA) nephropathy, focal segmental glomerulosclerosis, lupus nephritis, membranous nephropathy, and acute kidney injury. Read More

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http://dx.doi.org/10.1155/2015/782798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4677025PMC
December 2015
5 Reads
9 Citations

A Multicenter Trial Defining a Serum Protein Signature Associated with Pancreatic Ductal Adenocarcinoma.

Int J Proteomics 2015 26;2015:587250. Epub 2015 Oct 26.

Department of Immunotechnology and CREATE Health, Lund University, Medicon Village 406, 223 81 Lund, Sweden.

Background. Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with rapid tumor progression and poor prognosis. This study was motivated by the lack of sensitive and specific PDAC biomarkers and aimed to identify a diagnostic, serum protein signature for PDAC. Read More

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http://dx.doi.org/10.1155/2015/587250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4637476PMC
November 2015
27 Reads

Hypoxia Strongly Affects Mitochondrial Ribosomal Proteins and Translocases, as Shown by Quantitative Proteomics of HeLa Cells.

Int J Proteomics 2015 2;2015:678527. Epub 2015 Sep 2.

The Biotechnology Centre of Oslo, University of Oslo, P.O. Box 1125 Blindern, 0317 Oslo, Norway ; Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway.

Hypoxia is an important and common characteristic of many human tumors. It is a challenge clinically due to the correlation with poor prognosis and resistance to radiation and chemotherapy. Understanding the biochemical response to hypoxia would facilitate the development of novel therapeutics for cancer treatment. Read More

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http://downloads.hindawi.com/journals/ijpro/2015/678527.pdf
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http://www.hindawi.com/journals/ijpro/2015/678527/
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http://dx.doi.org/10.1155/2015/678527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4572459PMC
September 2015
8 Reads

A Proteomic Characterization of Bordetella pertussis Clinical Isolates Associated with a California State Pertussis Outbreak.

Int J Proteomics 2015 24;2015:536537. Epub 2015 May 24.

Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, GA 30341, USA.

Bordetella pertussis (Bp) is the etiologic agent of pertussis (whooping cough), a highly communicable infection. Although pertussis is vaccine preventable, in recent years there has been increased incidence, despite high vaccine coverage. Possible reasons for the rise in cases include the following: Bp strain adaptation, waning vaccine immunity, increased surveillance, and improved clinical diagnostics. Read More

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http://dx.doi.org/10.1155/2015/536537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458276PMC
June 2015
25 Reads

SILAC-Based Quantitative Proteomic Analysis of Diffuse Large B-Cell Lymphoma Patients.

Int J Proteomics 2015 28;2015:841769. Epub 2015 Apr 28.

Sahlgrenska Academy, University of Gothenburg, 413 45 Göteborg, Sweden ; Unit of Hematology, Department of Medicine, Södra Älvsborg Hospital, 504 55 Borås, Sweden.

Diffuse large B-cell lymphoma (DLBCL), the most common lymphoma, is a heterogeneous disease where the outcome for patients with early relapse or refractory disease is very poor, even in the era of immunochemotherapy. In order to describe possible differences in global protein expression and network patterns, we performed a SILAC-based shotgun (LC-MS/MS) quantitative proteomic analysis in fresh-frozen tumor tissue from two groups of DLBCL patients with totally different clinical outcome: (i) early relapsed or refractory and (ii) long-term progression-free patients. We could identify over 3,500 proteins; more than 1,300 were quantified in all patients and 87 were significantly differentially expressed. Read More

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http://dx.doi.org/10.1155/2015/841769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427854PMC
June 2015
6 Reads

Quantitative Proteomics and Lipidomics Analysis of Endoplasmic Reticulum of Macrophage Infected with Mycobacterium tuberculosis.

Int J Proteomics 2015 16;2015:270438. Epub 2015 Feb 16.

Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India ; Drug Discovery Research Centre, Translational Health Science & Technology Institute, Gurgaon 122016, India.

Even though endoplasmic reticulum (ER) stress associated with mycobacterial infection has been well studied, the molecular basis of ER as a crucial organelle to determine the fate of Mtb is yet to be established. Here, we have studied the ability of Mtb to manipulate the ultrastructural architecture of macrophage ER and found that the ER-phenotypes associated with virulent (H37Rv) and avirulent (H37Ra) strains were different: a rough ER (RER) with the former against a smooth ER (SER) with the later. Further, the functional attributes of these changes were probed by MS-based quantitative proteomics (133 ER proteins) and lipidomics (8 phospholipids). Read More

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http://dx.doi.org/10.1155/2015/270438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4345262PMC
March 2015
5 Reads

Comparative proteomic study reveals the molecular aspects of delayed ocular symptoms induced by sulfur mustard.

Int J Proteomics 2015 21;2015:659241. Epub 2015 Jan 21.

Department of Ophthalmology, Chemical Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.

Objective. Sulfur mustard (SM) is a highly reactive alkylating agent which produces ocular, respiratory, and skin damages. Eyes are the most sensitive organ to SM due to high intrinsic metabolic and rapid turnover rate of corneal epithelium and aqueous-mucous interfaces of the cornea and conjunctiva. Read More

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http://dx.doi.org/10.1155/2015/659241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320800PMC
February 2015
6 Reads

A survey of computational intelligence techniques in protein function prediction.

Int J Proteomics 2014 11;2014:845479. Epub 2014 Dec 11.

Department of Computer Science & Engineering, Indian Institute of Technology (BHU), Varanasi 221005, India.

During the past, there was a massive growth of knowledge of unknown proteins with the advancement of high throughput microarray technologies. Protein function prediction is the most challenging problem in bioinformatics. In the past, the homology based approaches were used to predict the protein function, but they failed when a new protein was different from the previous one. Read More

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http://dx.doi.org/10.1155/2014/845479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4276698PMC
January 2015
3 Reads

Combined phosphoproteomics and bioinformatics strategy in deciphering drug resistant related pathways in triple negative breast cancer.

Int J Proteomics 2014 13;2014:390781. Epub 2014 Nov 13.

Gonda/UCLA Breast Cancer Research Laboratory and the Revlon/UCLA Breast Center, Department of Surgery, David Geffen School of Medicine, University of California at Los Angeles, 200 Med Plaza, Ste B265-1, Los Angeles, CA 90095-7028, USA.

Because of the absence of a clear therapeutic target for triple negative breast cancer (TNBC), conventional chemotherapy is the only available systemic treatment option for these patients. Despite chemotherapy treatment, TNBC patients still have worse prognosis when compared with other breast cancer patients. The study is to investigate unique phosphorylated proteins expressed in chemoresistant TNBC cell lines. Read More

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http://dx.doi.org/10.1155/2014/390781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247952PMC
December 2014
18 Reads

The influence of flanking secondary structures on amino Acid content and typical lengths of 3/10 helices.

Int J Proteomics 2014 13;2014:360230. Epub 2014 Oct 13.

Laboratory of Cellular Technologies, Institute of Physiology, The National Academy of Sciences of Belarus, Academicheskaya 28, 220072 Minsk, Belarus.

We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges-regions situated between any of two major elements of secondary structure (alpha helices and beta strands)-containing a pure random coil were compared with connecting bridges containing 3/10 helices. We included discovered trends in the original "VVTAK Connecting Bridges" algorithm, which is able to predict more probable conformation for a given connecting bridge. Read More

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http://dx.doi.org/10.1155/2014/360230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211214PMC
November 2014
3 Reads

Comparative Analysis of Sorghum bicolor Proteome in Response to Drought Stress and following Recovery.

Int J Proteomics 2014 1;2014:395905. Epub 2014 Oct 1.

Institute of Ecology, Evolution, and Diversity, Johann Wolfgang Goethe-University Frankfurt, Max-Von-Laue Straße 13, 60438 Frankfurt, Germany ; Biodiversity and Climate Research Centre (BiK-F), 60325, Frankfurt am Main, Germany.

The adaptive response of Sorghum bicolor landraces from Egypt to drought stress and following recovery was analyzed using two-dimensional difference gel electrophoresis, 2D-DIGE. Physiological measurements and proteome alterations of accession number 11434, drought tolerant, and accession number 11431, drought sensitive, were compared to their relative control values after drought stress and following recovery. Differentially expressed proteins were analysed by Matrix assisted laser desorption ionisation time-of-flight mass spectrometry, MALDI-TOF-MS. Read More

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http://dx.doi.org/10.1155/2014/395905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198819PMC
October 2014
11 Reads

Dimerization of peptides by calcium ions: investigation of a calcium-binding motif.

Int J Proteomics 2014 14;2014:153712. Epub 2014 Sep 14.

Department of Neurology, Laboratory of Neuro-Oncology, Erasmus Medical Center, 3015 GE Rotterdam, The Netherlands.

We investigated calcium-binding motifs of peptides and their recognition of active functionalities for coordination. This investigation generates the fundamentals to design carrier material for calcium-bound peptide-peptide interactions. Interactions of different peptides with active calcium domains were investigated. Read More

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http://dx.doi.org/10.1155/2014/153712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177772PMC
October 2014
6 Reads

Mapping and Identification of the Urine Proteome of Prostate Cancer Patients by 2D PAGE/MS.

Int J Proteomics 2014 20;2014:594761. Epub 2014 Aug 20.

Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Krste Misirkov 2, 1000 Skopje, Macedonia.

Proteome analysis of the urine has shown that urine contains disease-specific information for a variety of urogenital system disorders, including prostate cancer (PCa). The aim of this study was to determine the protein components of urine from PCa patients. Urine from 8 patients with clinically and histologically confirmed PCa was analyzed by conventional 2D PAGE. Read More

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http://dx.doi.org/10.1155/2014/594761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4158146PMC
September 2014
24 Reads

A method to determine lysine acetylation stoichiometries.

Int J Proteomics 2014 20;2014:730725. Epub 2014 Jul 20.

Biological Science Division and Environmental, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

Lysine acetylation is a common protein posttranslational modification that regulates a variety of biological processes. A major bottleneck to fully understanding the functional aspects of lysine acetylation is the difficulty in measuring the proportion of lysine residues that are acetylated. Here we describe a mass spectrometry method using a combination of isotope labeling and detection of a diagnostic fragment ion to determine the stoichiometry of protein lysine acetylation. Read More

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http://dx.doi.org/10.1155/2014/730725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131070PMC
August 2014
14 Reads

Prediction of spontaneous regression of cervical intraepithelial neoplasia lesions grades 2 and 3 by proteomic analysis.

Int J Proteomics 2014 15;2014:129064. Epub 2014 Jun 15.

Pathology Department, Stavanger University Hospital, P.O. Box 8100, 4068 Stavanger, Norway ; The Gade Institute, University of Bergen, P.O. Box 1400, 5021 Bergen, Norway.

Regression of cervical intraepithelial neoplasia (CIN) 2-3 to CIN 1 or less is associated with immune response as demonstrated by immunohistochemistry in formaldehyde-fixed paraffin-embedded (FFPE) biopsies. Proteomic analysis of water-soluble proteins in supernatants of biopsy samples with LC-MS (LTQ-Orbitrap) was used to identify proteins predictive of CIN2-3 lesions regression. CIN2-3 in the biopsies and persistence (CIN2-3) or regression (≤CIN1) in follow-up cone biopsies was validated histologically by two experienced pathologists. Read More

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http://dx.doi.org/10.1155/2014/129064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082862PMC
July 2014
10 Reads

Characterisation of the Proteome of Leptospira interrogans Serovar Canicola as a Resource for the Identification of Common Serovar Immunogenic Proteins.

Int J Proteomics 2014 27;2014:572901. Epub 2014 May 27.

Animal Health and Veterinary Laboratories Agency, Addlestone, New Haw, Surrey KT15 3NB, UK.

Over 230 serovars of Leptospira interrogans have been identified; however few have been completely characterised. The aim of this study was to characterise the proteome of serovar Canicola and to compare this against the serovars of Copenhageni and Pomona. 2D-LC/MS analysis identified 1653 Leptospira proteins in serovar Canicola; 60 of these proteins were common to Copenhageni and Pomona, 16 of which are known to be immunogenic. Read More

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http://dx.doi.org/10.1155/2014/572901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058600PMC
July 2014
3 Reads

Enhanced Photosynthesis and Carbon Metabolism Favor Arsenic Tolerance in Artemisia annua, a Medicinal Plant as Revealed by Homology-Based Proteomics.

Int J Proteomics 2014 29;2014:163962. Epub 2014 Apr 29.

Laboratory of Morphogenesis, Center of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India.

This paper provides the first proteomic evidence of arsenic (As) tolerance and interactive regulatory network between primary and secondary metabolism in the medicinal plant, Artemisia annua. While chlorophyll fluorescence and photosynthetic rate depicted mild inhibition, there was a significant enhancement in PSI activity, whole chain, ATP, and NADPH contents in 100  μ M As treatments compared to the control plants. However, a decrease in the above variables was recorded under 150  μ M treatments. Read More

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https://www.hindawi.com/archive/2014/163962/
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http://dx.doi.org/10.1155/2014/163962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4020366PMC
May 2014
6 Reads

In-depth profiling of the peripheral blood mononuclear cells proteome for clinical blood proteomics.

Int J Proteomics 2014 3;2014:129259. Epub 2014 Mar 3.

Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany.

Peripheral blood mononuclear cells (PBMCs) are an easy accessible cellular part of the blood organ and, along with platelets, represent the only site of active gene expression in blood. These cells undergo immunophenotypic changes in various diseases and represent a peripheral source of monitoring gene expression and posttranslational modifications relevant to many diseases. Little is known about the source of many blood proteins and we hypothesise that release from PBMCs through active and passive mechanisms may account for a substantial part of the plasma proteome. Read More

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http://dx.doi.org/10.1155/2014/129259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3958665PMC
April 2014
7 Reads

Comparison of Heavy Labeled (SIL) Peptide versus SILAC Protein Internal Standards for LC-MS/MS Quantification of Hepatic Drug Transporters.

Int J Proteomics 2014 25;2014:451510. Epub 2014 Feb 25.

Department of Pharmaceutics, University of Washington, P.O. Box 357610, Seattle, WA 98195, USA.

We studied the precision of quantification of organic anion-transporting polypeptide 1B1 (OATP1B1), OATP1B3, OATP2B1, and P-glycoprotein (P-gp) in human livers by surrogate peptide based LC-MS/MS approach using two different internal standards: stable isotope labeled peptide (SIL) versus stable isotope labeled protein (SILAC). The SIL peptides were procured commercially and the SILAC proteins were generated in-house by labeling arginine and/or lysine residues in cells expressing these transporters. Liver tissue (n = 20) was homogenized and the membrane fraction was isolated. Read More

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http://dx.doi.org/10.1155/2014/451510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3955635PMC
April 2014
13 Reads

Protein-protein interaction detection: methods and analysis.

Int J Proteomics 2014 17;2014:147648. Epub 2014 Feb 17.

Department of CSE, VR Siddhartha Engineering College, Vijayawada 520007, India.

Protein-protein interaction plays key role in predicting the protein function of target protein and drug ability of molecules. The majority of genes and proteins realize resulting phenotype functions as a set of interactions. The in vitro and in vivo methods like affinity purification, Y2H (yeast 2 hybrid), TAP (tandem affinity purification), and so forth have their own limitations like cost, time, and so forth, and the resultant data sets are noisy and have more false positives to annotate the function of drug molecules. Read More

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http://dx.doi.org/10.1155/2014/147648DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947875PMC
June 2014
17 Reads

A colorimetric method for monitoring tryptic digestion prior to shotgun proteomics.

Int J Proteomics 2014 10;2014:125482. Epub 2014 Feb 10.

Windber Research Institute, 620 Seventh Street, Windber, PA 15963, USA.

Tryptic digestion is an important preanalytical step in shotgun proteomics because inadequate or excessive digestion can result in a failed or incomplete experiment. Unfortunately, this step is not routinely monitored before mass spectrometry because methods available for protein digestion monitoring either are time/sample consuming or require expensive equipment. To determine if a colorimetric method (ProDM Kit) can be used to identify the extent of tryptic digestion that yields the best proteomics outcome, plasma and serum digested for 8 h and 24 h were screened with ProDM, Bioanalyzer, and LC/MS/MS, and the effect of digestion on the number of proteins identified and sequence coverage was compared. Read More

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https://www.hindawi.com/archive/2014/125482/
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http://dx.doi.org/10.1155/2014/125482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941143PMC
March 2014
16 Reads

The effect of alendronate on proteome of hepatocellular carcinoma cell lines.

Int J Proteomics 2014 6;2014:532953. Epub 2014 Feb 6.

National Center for Proteomics, University of Karachi, Karachi 75270, Pakistan.

Cancer is a life threatening disorder effecting 11 million people worldwide annually. Among various types of cancers, Hepatocellular carcinoma (HCC) has a higher rate of mortality and is the fifth leading cause of cancer related deaths around the world. Many chemotherapeutic drugs have been used for the treatment of HCC with many side effects. Read More

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https://www.hindawi.com/archive/2014/532953/
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http://dx.doi.org/10.1155/2014/532953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932719PMC
March 2014
12 Reads

Periodontal proteomics: wonders never cease!

Int J Proteomics 2013 31;2013:850235. Epub 2013 Dec 31.

Department of Periodontology, Faculty of Dental Sciences, SGT University, Budhera, Gurgaon, Haryana 122505, India.

Proteins are vital parts of living organisms, as they are integral components of the physiological metabolic pathways of cells. Periodontal tissues comprise multicompartmental groups of interacting cells and matrices that provide continuous support, attachment, proprioception, and physical protection for the teeth. The proteome map, that is, complete catalogue of the matrix and cellular proteins expressed in alveolar bone, cementum, periodontal ligament, and gingiva, is to be explored for more in-depth understanding of periodontium. Read More

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http://dx.doi.org/10.1155/2013/850235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893808PMC
June 2014
4 Reads

The Human Urinary Proteome Fingerprint Database UPdb.

Int J Proteomics 2013 9;2013:760208. Epub 2013 Oct 9.

BHF Glasgow Cardiovascular Research Centre, University of Glasgow, 126 University Place, Joseph Black Building, Room B2-21, Glasgow G12 8TA, UK ; Tissue Injury and Repair Group, School of Clinical Sciences and Community Health, University of Edinburgh, 1st Floor Chancellors Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK.

The use of human urine as a diagnostic tool has many advantages, such as ease of sample acquisition and noninvasiveness. However, the discovery of novel biomarkers, as well as biomarker patterns, in urine is hindered mainly by a lack of comparable datasets. To fill this gap, we assembled a new urinary fingerprint database. Read More

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http://dx.doi.org/10.1155/2013/760208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809596PMC
November 2013
7 Reads
3 Citations

Proteomic Analysis and Label-Free Quantification of the Large Clostridium difficile Toxins.

Int J Proteomics 2013 27;2013:293782. Epub 2013 Aug 27.

Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention (CDC), MS F-50, 4770 Buford Hwy NE, Atlanta, GA 30341, USA.

Clostridium difficile is the leading cause of antibiotic-associated diarrhea in hospitals worldwide, due to hypervirulent epidemic strains with the ability to produce increased quantities of the large toxins TcdA and TcdB. Unfortunately, accurate quantification of TcdA and TcdB from different toxinotypes using small samples has not yet been reported. In the present study, we quantify C. Read More

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http://dx.doi.org/10.1155/2013/293782DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771451PMC
September 2013
12 Reads

Proteomic Analysis of the Ontogenetic Variability in Plasma Composition of Juvenile and Adult Bothrops jararaca Snakes.

Int J Proteomics 2013 22;2013:135709. Epub 2013 Apr 22.

Laboratório de Herpetologia, Instituto Butantan, Avenida Vital Brazil 1500, 05503-900 São Paulo, SP, Brazil ; Programa de Pós-Graduação Interunidades em Biotecnologia, Universidade de São Paulo, Avenida Professor Lineu Prestes 2415, 05508-900 São Paulo, SP, Brazil.

The ontogenetic variability in venom composition of some snake genera, including Bothrops, as well as the biological implications of such variability and the search of new molecules that can neutralize the toxic components of these venoms have been the subject of many studies. Thus, considering the resistance of Bothrops jararaca to the toxic action of its own venom and the ontogenetic variability in venom composition described in this species, a comparative study of the plasma composition of juvenile and adult B. jararaca snakes was performed through a proteomic approach based on 2D electrophoresis and mass spectrometry, which allowed the identification of proteins that might be present at different levels during ontogenetic development. Read More

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http://dx.doi.org/10.1155/2013/135709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654370PMC
September 2013
4 Reads

Advances in quantitative mass spectrometry.

Int J Proteomics 2013 29;2013:621029. Epub 2013 Apr 29.

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.1155/2013/621029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657455PMC
June 2013
6 Reads

Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion with Data-Dependent (MS1) and Data-Independent (MS2) Acquisitions.

Int J Proteomics 2013 4;2013:791985. Epub 2013 Apr 4.

The Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA.

The receptor tyrosine kinase ErbB2 is a breast cancer biomarker whose posttranslational modifications (PTMs) are a key indicator of its activation. Quantifying the expression and PTMs of biomarkers such as ErbB2 by selected reaction monitoring (SRM) mass spectrometry has several limitations, including minimal coverage and extensive assay development time. Therefore, we assessed the utility of two high resolution, full scan mass spectrometry approaches, MS1 Filtering and SWATH MS2, for targeted ErbB2 proteomics. Read More

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http://dx.doi.org/10.1155/2013/791985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654371PMC
May 2013
7 Reads

Quantitative Proteomics via High Resolution MS Quantification: Capabilities and Limitations.

Int J Proteomics 2013 23;2013:674282. Epub 2013 Apr 23.

Global Discovery and Development Statistics, Lilly Research Laboratories, Indianapolis, IN 46285, USA ; Lilly Corporate Center, DC 0720, Indianapolis, IN 46285, USA.

Recent improvements in the mass accuracy and resolution of mass spectrometers have led to renewed interest in label-free quantification using data from the primary mass spectrum (MS1) acquired from data-dependent proteomics experiments. The capacity for higher specificity quantification of peptides from samples enriched for proteins of biological interest offers distinct advantages for hypothesis generating experiments relative to immunoassay detection methods or prespecified peptide ions measured by multiple reaction monitoring (MRM) approaches. Here we describe an evaluation of different methods to post-process peptide level quantification information to support protein level inference. Read More

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http://dx.doi.org/10.1155/2013/674282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3655581PMC
May 2013
3 Reads

iTRAQ-Based and Label-Free Proteomics Approaches for Studies of Human Adenovirus Infections.

Int J Proteomics 2013 11;2013:581862. Epub 2013 Mar 11.

Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland ; Life Science Zurich Graduate School, Molecular Life Science Program, Switzerland.

Both isobaric tags for relative and absolute quantitation (iTRAQ) and label-free methods are widely used for quantitative proteomics. Here, we provide a detailed evaluation of these proteomics approaches based on large datasets from biological samples. iTRAQ-label-based and label-free quantitations were compared using protein lysate samples from noninfected human lung epithelial A549 cells and from cells infected for 24 h with human adenovirus type 3 or type 5. Read More

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http://dx.doi.org/10.1155/2013/581862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608280PMC
April 2013
5 Reads

Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans.

Int J Proteomics 2013 10;2013:279590. Epub 2013 Mar 10.

Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, P.O. Box 999/MS K8-98, Richland, WA 99352, USA.

The periplasm of Gram-negative bacteria is a dynamic and physiologically important subcellular compartment where the constant exposure to potential environmental insults amplifies the need for proper protein folding and modifications. Top-down proteomics analysis of the periplasmic fraction at the intact protein level provides unrestricted characterization and annotation of the periplasmic proteome, including the post-translational modifications (PTMs) on these proteins. Here, we used single-dimension ultra-high pressure liquid chromatography coupled with the Fourier transform mass spectrometry (FTMS) to investigate the intact periplasmic proteome of Novosphingobium aromaticivorans. Read More

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http://dx.doi.org/10.1155/2013/279590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608174PMC
April 2013
8 Reads

Current status and advances in quantitative proteomic mass spectrometry.

Int J Proteomics 2013 6;2013:180605. Epub 2013 Mar 6.

Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia.

The accurate quantitation of proteins and peptides in complex biological systems is one of the most challenging areas of proteomics. Mass spectrometry-based approaches have forged significant in-roads allowing accurate and sensitive quantitation and the ability to multiplex vastly complex samples through the application of robust bioinformatic tools. These relative and absolute quantitative measures using label-free, tags, or stable isotope labelling have their own strengths and limitations. Read More

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http://dx.doi.org/10.1155/2013/180605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606794PMC
March 2013
7 Reads

Additions to the Human Plasma Proteome via a Tandem MARS Depletion iTRAQ-Based Workflow.

Int J Proteomics 2013 19;2013:654356. Epub 2013 Feb 19.

Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.

Robust platforms for determining differentially expressed proteins in biomarker and discovery studies using human plasma are of great interest. While increased depth in proteome coverage is desirable, it is associated with costs of experimental time due to necessary sample fractionation. We evaluated a robust quantitative proteomics workflow for its ability (1) to provide increased depth in plasma proteome coverage and (2) to give statistical insight useful for establishing differentially expressed plasma proteins. Read More

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http://dx.doi.org/10.1155/2013/654356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590782PMC
March 2013
5 Reads

A Novel Peptide-Based SILAC Method to Identify the Posttranslational Modifications Provides Evidence for Unconventional Ubiquitination in the ER-Associated Degradation Pathway.

Int J Proteomics 2013 3;2013:857918. Epub 2013 Feb 3.

Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, USA ; Department of Protein Chemistry, Genentech Inc., South San Francisco, CA 94080, USA.

The endoplasmic reticulum-associated degradation (ERAD) pathway is responsible for disposing misfolded proteins from the endoplasmic reticulum by inducing their ubiquitination and degradation. Ubiquitination is conventionally observed on lysine residues and has been demonstrated on cysteine residues and protein N-termini. Ubiquitination is fundamental to the ERAD process; however, a mutant T-cell receptor α (TCRα) lacking lysine residues is targeted for the degradation by the ERAD pathway. Read More

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http://dx.doi.org/10.1155/2013/857918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574754PMC
February 2013
4 Reads

An Internal Standard-Assisted Synthesis and Degradation Proteomic Approach Reveals the Potential Linkage between VPS4B Depletion and Activation of Fatty Acid β-Oxidation in Breast Cancer Cells.

Int J Proteomics 2013 4;2013:291415. Epub 2013 Feb 4.

Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

The endosomal/lysosomal system, in particular the endosomal sorting complexes required for transport (ESCRTs), plays an essential role in regulating the trafficking and destination of endocytosed receptors and their associated signaling molecules. Recently, we have shown that dysfunction and down-regulation of vacuolar protein sorting 4B (VPS4B), an ESCRT-III associated protein, under hypoxic conditions can lead to the abnormal accumulation of epidermal growth factor receptor (EGFR) and aberrant EGFR signaling in breast cancer. However, the pathophysiological consequences of VPS4B dysfunction remain largely elusive. Read More

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http://dx.doi.org/10.1155/2013/291415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575666PMC
February 2013
13 Reads

Issues and applications in label-free quantitative mass spectrometry.

Int J Proteomics 2013 16;2013:756039. Epub 2013 Jan 16.

Department of Cellular & Integrative Physiology, Biotechnology Research & Training Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

To address the challenges associated with differential expression proteomics, label-free mass spectrometric protein quantification methods have been developed as alternatives to array-based, gel-based, and stable isotope tag or label-based approaches. In this paper, we focus on the issues associated with label-free methods that rely on quantitation based on peptide ion peak area measurement. These issues include chromatographic alignment, peptide qualification for quantitation, and normalization. Read More

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http://dx.doi.org/10.1155/2013/756039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562690PMC
February 2013
5 Reads

Protein target quantification decision tree.

Int J Proteomics 2013 15;2013:701247. Epub 2013 Jan 15.

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS 4053, Indianapolis, IN 46202, USA.

The utility of mass spectrometry-(MS-) based proteomic platforms and their clinical applications have become an emerging field in proteomics in recent years. Owing to its selectivity and sensitivity, MS has become a key technological platform in proteomic research. Using this platform, a large number of potential biomarker candidates for specific diseases have been reported. Read More

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http://dx.doi.org/10.1155/2013/701247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562589PMC
February 2013
5 Reads

Serum biomarkers identification by mass spectrometry in high-mortality tumors.

Int J Proteomics 2013 15;2013:125858. Epub 2013 Jan 15.

Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio Coppito 2, 67100 L'Aquila, Italy.

Cancer affects millions of people worldwide. Tumor mortality is substantially due to diagnosis at stages that are too late for therapies to be effective. Advances in screening methods have improved the early diagnosis, prognosis, and survival for some cancers. Read More

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http://dx.doi.org/10.1155/2013/125858DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562576PMC
February 2013
5 Reads

Advantageous uses of mass spectrometry for the quantification of proteins.

Authors:
John E Hale

Int J Proteomics 2013 8;2013:219452. Epub 2013 Jan 8.

Hale Biochemical Consulting, 6341 Wyatt Lane, Klamath Falls, OR 97601, USA.

Quantitative protein measurements by mass spectrometry have gained wide acceptance in research settings. However, clinical uptake of mass spectrometric protein assays has not followed suit. In part, this is due to the long-standing acceptance by regulatory agencies of immunological assays such as ELISA assays. Read More

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http://dx.doi.org/10.1155/2013/219452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556832PMC
February 2013
3 Reads

Proteomics sample preparation, preservation, and fractionation.

Authors:
Gary B Smejkal

Int J Proteomics 2012 30;2012:701230. Epub 2012 Dec 30.

Covaris Inc., 14 Gill Street, Suite H, Woburn, MA 01801, USA ; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA.

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http://dx.doi.org/10.1155/2012/701230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546479PMC
January 2013
3 Reads

Functional Proteomic Profiling of Phosphodiesterases Using SeraFILE Separations Platform.

Int J Proteomics 2012 25;2012:515372. Epub 2012 Nov 25.

ProFACT Proteomics Inc., 1 Deer Park Drive, Suite M, Monmouth Junction, NJ 08852, USA.

Functional proteomic profiling can help identify targets for disease diagnosis and therapy. Available methods are limited by the inability to profile many functional properties measured by enzymes kinetics. The functional proteomic profiling approach proposed here seeks to overcome such limitations. Read More

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http://dx.doi.org/10.1155/2012/515372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3512300PMC
December 2012
4 Reads

Optimization of an Efficient Protein Extraction Protocol Compatible with Two-Dimensional Electrophoresis and Mass Spectrometry from Recalcitrant Phenolic Rich Roots of Chickpea (Cicer arietinum L.).

Int J Proteomics 2012 31;2012:536963. Epub 2012 Oct 31.

Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme VII-M, Kankurgachi, West Bengal, Kolkata 700054, India.

Two-dimensional electrophoresis and mass spectrometry are undoubtedly two essential tools popularly used in proteomic analyses. Utilization of these techniques however largely depends on efficient and optimized sample preparation, regarded as one of the most crucial steps for recovering maximum amount of reliable information. The present study highlights the optimization of an effective and efficient protocol, capable of extraction of root proteins from recalcitrant phenolic rich tissues of chickpea. Read More

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http://dx.doi.org/10.1155/2012/536963DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502011PMC
November 2012
6 Reads
5 Citations

Reconstruction of Sugar Metabolic Pathways of Giardia lamblia.

Int J Proteomics 2012 18;2012:980829. Epub 2012 Oct 18.

Institute of Molecular BioSciences, Massey University, Palmerston North 4442, New Zealand.

Giardia lamblia is an "important" pathogen of humans, but as a diplomonad excavate it is evolutionarily distant from other eukaryotes and relatively little is known about its core metabolic pathways. KEGG, the widely referenced site for providing information of metabolism, does not yet include many enzymes from Giardia species. Here we identify Giardia's core sugar metabolism using standard bioinformatic approaches. Read More

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http://dx.doi.org/10.1155/2012/980829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483818PMC
November 2012
27 Reads

Miniaturized mass-spectrometry-based analysis system for fully automated examination of conditioned cell culture media.

Int J Proteomics 2012 4;2012:290457. Epub 2012 Oct 4.

Department of Biotechnology, Netherlands Proteomics Centre, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands ; Institute of Sensor and Actuator Systems, Vienna University of Technology, Gusshausstrasse 27-29/E366, 1040 Vienna, Austria.

We present a fully automated setup for performing in-line mass spectrometry (MS) analysis of conditioned media in cell cultures, in particular focusing on the peptides therein. The goal is to assess peptides secreted by cells in different culture conditions. The developed system is compatible with MS as analytical technique, as this is one of the most powerful analysis methods for peptide detection and identification. Read More

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http://dx.doi.org/10.1155/2012/290457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471440PMC
October 2012
3 Reads