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You searched for: Journal Journal of Proteome Research Remove constraint Journal: Journal of Proteome Research Publication Year 2012 Remove constraint Publication Year: 2012 Source 2012 v.11 no.3 Remove constraint Source: 2012 v.11 no.3
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1. Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

Author:
Weisbrod, Chad R.; Eng, Jimmy K.; Hoopmann, Michael R.; Baker, Tahmina; Bruce, James E.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1621-1632
ISSN:
1535-3907
Subject:
chromatography; computer software; ions; monitoring; peptides; proteome
Abstract:
... Fourier transform-all reaction monitoring (FT-ARM) is a novel approach for the identification and quantification of peptides that relies upon the selectivity of high mass accuracy data and the specificity of peptide fragmentation patterns. An FT-ARM experiment involves continuous, data-independent, high mass accuracy MS/MS acquisition spanning a defined m/z range. Custom software was developed to ...
DOI:
10.1021/pr2008175

2. Analysis of Folate Binding Protein N-linked Glycans by Mass Spectrometry

Author:
Jaiswal, Nidhi; Saraswat, Suraj; Ratnam, Manohar; Isailovic, Dragan
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1551-1560
ISSN:
1535-3907
Subject:
biomarkers; body fluids; breast milk; cattle; computer software; databases; desorption; drugs; folate receptors; folate-binding proteins; folic acid; fucose; glycomics; glycoproteins; ionization; milk; neoplasms; polysaccharides; sialic acid; tandem mass spectrometry
Abstract:
... The folate binding protein (FBP), also known as the folate receptor (FR), is a glycoprotein which binds the vitamin folic acid and its analogues. FBP contains multiple N-glycosilation sites, is selectively expressed in tissues and body fluids, and mediates targeted therapies in cancer and inflammatory diseases. Much remains to be understood about the structure, composition, and the tissue specific ...
DOI:
10.1021/pr2006044

3. Analysis of Seminal Plasma from Patients with Non-obstructive Azoospermia and Identification of Candidate Biomarkers of Male Infertility

Author:
Batruch, Ihor; Smith, Christopher R.; Mullen, Brendan J.; Grober, Ethan; Lo, Kirk C.; Diamandis, Eleftherios P.; Jarvi, Keith A.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1503-1511
ISSN:
1535-3907
Subject:
biomarkers; data collection; epididymis; females; male fertility; males; men; patients; proteins; proteome; seminal plasma; spermatozoa; testes
Abstract:
... Infertility affects approximately 15% of couples with equivalent male and female contribution. Absence of sperm in semen, referred to as azoospermia, accounts for 5–20% of male infertility cases and can result from pretesticular azoospermia, non-obstructive azoospermia (NOA), and obstructive azoospermia (OA). The current clinical methods of differentiating NOA cases from OA ones are indeterminate ...
DOI:
10.1021/pr200812p

4. Analysis of Tubulin Alpha-1A/1B C-Terminal Tail Post-translational Poly-glutamylation Reveals Novel Modification Sites

Author:
Sahab, Ziad J.; Kirilyuk, Alexander; Zhang, Lihua; Khamis, Zahraa I.; Pompach, Petr; Sung, YouMe; Byers, Stephen W.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1913-1923
ISSN:
1535-3907
Subject:
brain; cattle; glutamic acid; ions; mass spectrometry; mice; microtubules; mitosis; neoplasms; neurodegenerative diseases; peptidase K; physiological transport; proteome; synthetic peptides; trypsin; tubulin; tyrosine
Abstract:
... Tubulin-α₁A/₁B C-terminal tail (CTT) has seven glutamic acid residues among the last 11 amino acids of its sequence that are potential sites for glutamylation. Cleavage of C-terminal tyrosine resulting in the detyrosinated form of tubulin-α₁A/₁B is another major modification. These modifications among others bring about highly heterogeneous tubulin samples in brain cells and microtubules, play a m ...
DOI:
10.1021/pr2011044

5. Annotation of a Serum N-Glycan Library for Rapid Identification of Structures

Author:
Aldredge, Danielle; An, Hyun Joo; Tang, Ning; Waddell, Keith; Lebrilla, Carlito B.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1958-1968
ISSN:
1535-3907
Subject:
blood serum; databases; glycoproteins; glycosylation; humans; liquid chromatography; mass spectrometry; monosaccharides; neoplasms; pathological processes and conditions; polysaccharides
Abstract:
... Glycosylation is one of the most common post-translational modifications of proteins and has been shown to change with various pathological states including cancer. Global glycan profiling of human serum based on mass spectrometry has already led to several promising markers for diseases. The changes in glycan structure can result in altered monosaccharide composition as well as in the linkages be ...
DOI:
10.1021/pr2011439

6. Annotator: Postprocessing Software for Generating Function-based Signatures from Quantitative Mass Spectrometry

Author:
Sylvester, Juliesta E.; Bray, Tyler S.; Kron, Stephen J.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1521-1536
ISSN:
1535-3907
Subject:
computer software; gene ontology; mass spectrometry; models; proteins; proteome; proteomics; quantitative analysis; statistical analysis
Abstract:
... Mass spectrometry is used to investigate global changes in protein abundance in cell lysates. Increasingly powerful methods of data collection have emerged over the past decade, but this has left researchers with the task of sifting through mountains of data for biologically significant results. Often, the end result is a list of proteins with no obvious quantitative relationships to define the la ...
DOI:
10.1021/pr200460s

7. Assignment of Protein Interactions from Affinity Purification/Mass Spectrometry Data

Author:
Pardo, Mercedes; Choudhary, Jyoti S.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1462-1474
ISSN:
1535-3907
Subject:
antibodies; mass spectrometry; proteins; proteome
Abstract:
... The combination of affinity purification with mass spectrometry analysis has become the method of choice for protein complex characterization. With the improved performance of mass spectrometry technology, the sensitivity of the analyses is increasing, probing deeper into molecular interactions and yielding longer lists of proteins. These identify not only core complex subunits but also the more i ...
DOI:
10.1021/pr2011632

8. Association of Medication with the Human Plasma N-Glycome

Author:
Saldova, Radka; Huffman, Jennifer E.; Adamczyk, Barbara; Mužinić, Ana; Kattla, Jayesh J.; Pučić, Maja; Novokmet, Mislav; Abrahams, Jodie L.; Hayward, Caroline; Rudan, Igor; Wild, Sarah H.; Wright, Alan F.; Polašek, Ozren; Lauc, Gordan; Campbell, Harry; Wilson, James F.; Rudd, Pauline M.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1821-1831
ISSN:
1535-3907
Subject:
aspirin; biomarkers; blood groups; blood plasma; environmental factors; fucose; glycoproteins; glycosylation; hormone replacement therapy; hormones; humans; hydrophilic interaction chromatography; inflammation; islands; neoplasms; nonsteroidal anti-inflammatory agents; oral contraceptives; polysaccharides; prednisolone; Croatia; Scotland
Abstract:
... Glycosylation is highly variable depending on many environmental factors. Using our fully quantitative high-throughput normal phase hydrophilic interaction liquid chromatography platform we have identified glycosylation changes associated with medication in the plasma N-glycome from three different population cohorts: ORCADES from the Orkney Islands in Scotland and CROATIA-Vis and CROATIA-Korcula ...
DOI:
10.1021/pr2010605

9. Automated Workflow for Large-Scale Selected Reaction Monitoring Experiments

Author:
Malmström, Lars; Malmström, Johan; Selevsek, Nathalie; Rosenberger, George; Aebersold, Ruedi
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1644-1653
ISSN:
1535-3907
Subject:
Streptococcus pyogenes; computer software; databases; humans; mass spectrometry; models; monitoring; peptides; proteins; proteome; proteomics
Abstract:
... Targeted proteomics allows researchers to study proteins of interest without being drowned in data from other, less interesting proteins or from redundant or uninformative peptides. While the technique is mostly used for smaller, focused studies, there are several reasons to conduct larger targeted experiments. Automated, highly robust software becomes more important in such experiments. In additi ...
DOI:
10.1021/pr200844d

10. Broad Identification of Bacterial Type in Urinary Tract Infection Using 1H NMR Spectroscopy

Author:
Gupta, Ashish; Dwivedi, Mayank; Mahdi, Abbas Ali; Khetrapal, Chunni Lal; Bhandari, Mahendra
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1844-1854
ISSN:
1535-3907
Subject:
Acinetobacter; Citrobacter; Enterobacter; Enterococcus faecalis; Escherichia coli; Klebsiella pneumoniae; Proteus mirabilis; Pseudomonas aeruginosa; Staphylococcus saprophyticus; acetates; citrates; creatinine; discriminant analysis; ethanol; formates; lactic acid; magnetism; microorganisms; nuclear magnetic resonance spectroscopy; patients; screening; succinic acid; trimethylamine; urea; urinary tract diseases; urine
Abstract:
... To address the shortcomings of urine culture for the rapid identification of urinary tract infection (UTI), we applied ¹H-nuclear magnetic resonance (NMR) spectroscopy as a surrogate method for fast screening of microorganisms. Study includes 682 urine samples from suspected UTI patients, 50 healthy volunteers, and commercially available standard strains of gram negative bacilli (GNB) (Escherichia ...
DOI:
10.1021/pr2010692

11. BuildSummary: Using a Group-Based Approach To Improve the Sensitivity of Peptide/Protein Identification in Shotgun Proteomics

Author:
Sheng, Quanhu; Dai, Jie; Wu, Yibo; Tang, Haixu; Zeng, Rong
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1494-1502
ISSN:
1535-3907
Subject:
computer software; data collection; databases; proteinases; proteins; proteome; proteomics
Abstract:
... The target-decoy database search strategy is widely accepted as a standard method for estimating the false discovery rate (FDR) of peptide identification, based on which peptide-spectrum matches (PSMs) from the target database are filtered. To improve the sensitivity of protein identification given a fixed accuracy (frequently defined by a protein FDR threshold), a postprocessing procedure is ofte ...
DOI:
10.1021/pr200194p

12. Chemical Deamidation: A Common Pitfall in Large-Scale N-Linked Glycoproteomic Mass Spectrometry-Based Analyses

Author:
Palmisano, Giuseppe; Melo-Braga, Marcella N.; Engholm-Keller, Kasper; Parker, Benjamin L.; Larsen, Martin R.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1949-1957
ISSN:
1535-3907
Subject:
Escherichia coli; asparagine; biomarkers; cell lines; deamidation; glycoproteins; glycoproteomics; glycosylation; mammals; mass spectrometry; membrane proteins; microorganisms; models; oxygen; peptides; proteolysis; proteome; stable isotopes
Abstract:
... N-Linked glycoproteins are involved in several diseases and are important as potential diagnostic molecules for biomarker discovery. Therefore, it is important to provide sensitive and reliable analytical methods to identify not only the glycoproteins but also the sites of glycosylation. Recently, numerous strategies to identify N-linked glycosylation sites have been described. These strategies ha ...
DOI:
10.1021/pr2011268

13. Comparative Proteomic Analysis of Auxin-Induced Embryogenic and Nonembryogenic Tissues of the Solanaceous Tree Cyphomandra betacea (Tamarillo)

Author:
Correia, Sandra; Vinhas, Raquel; Manadas, Bruno; Lourenço, Ana Sofia; Veríssimo, Paula; Canhoto, Jorge M.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1666-1675
ISSN:
1535-3907
Subject:
2,4-D; Solanum betaceum; callus; fruits; gene expression; leaves; messenger RNA; pathogenesis-related proteins; phosphopyruvate hydratase; picloram; protein synthesis; proteome; proteomics; quantitative polymerase chain reaction; ribosomal proteins; somatic embryogenesis; trees
Abstract:
... Cyphomandra betacea (tamarillo) is a tree that produces edible, highly nutritional fruits. In tamarillo, somatic embryogenesis (SE) is achieved through a two-step process starting with the formation of an embryogenic tissue on an auxin-rich medium and further development of embryos, following tissue transfer to an auxin-free medium. During the induction stage, both embryogenic (EC) and nonembryoge ...
DOI:
10.1021/pr200856w

14. Comprehensive Description of the N-Glycoproteome of Mouse Pancreatic β-Cells and Human Islets

Author:
Danzer, Carsten; Eckhardt, Katrin; Schmidt, Alexander; Fankhauser, Niklaus; Ribrioux, Sebastien; Wollscheid, Bernd; Müller, Lukas; Schiess, Ralph; Züllig, Richard; Lehmann, Roger; Spinas, Giatgen; Aebersold, Rudolf; Krek, Wilhelm
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1598-1608
ISSN:
1535-3907
Subject:
G-protein coupled receptors; biomarkers; diabetes; drugs; glucose; glycoproteins; homeostasis; humans; insulin secretion; islets of Langerhans; mice; protein kinases; proteinases; proteome; proteomics; surface proteins
Abstract:
... Cell surface N-glycoproteins provide a key interface of cells to their environment and therapeutic entry points for drug and biomarker discovery. Their comprehensive description denotes therefore a formidable challenge. The β-cells of the pancreas play a crucial role in blood glucose homeostasis, and disruption of their function contributes to diabetes. By combining cell surface and whole cell cap ...
DOI:
10.1021/pr2007895

15. Detergent-resistant Plasma Membrane Proteome in Oat and Rye: Similarities and Dissimilarities between Two Monocotyledonous Plants

Author:
Takahashi, Daisuke; Kawamura, Yukio; Yamashita, Tetsuro; Uemura, Matsuo
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1654-1665
ISSN:
1535-3907
Subject:
Arabidopsis; Avena sativa; Secale cereale; oats; physicochemical properties; plasma membrane; prediction; proteins; proteome; proteomics; rye; tobacco
Abstract:
... The plasma membrane (PM) is involved in important cellular processes that determine the growth, development, differentiation, and environmental signal responses of plant cells. Some of these dynamic reactions occur in specific domains in the PM. In this study, we performed comparable nano-LC–MS/MS-based large-scale proteomic analysis of detergent-resistant membrane (DRM) fractions prepared from th ...
DOI:
10.1021/pr200849v

16. Enhanced Separation and Characterization of Deamidated Peptides with RP-ERLIC-Based Multidimensional Chromatography Coupled with Tandem Mass Spectrometry

Author:
Hao, Piliang; Qian, Jingru; Dutta, Bamaprasad; Cheow, Esther Sok Hwee; Sim, Kae Hwan; Meng, Wei; Adav, Sunil S.; Alpert, Andrew; Sze, Siu Kwan
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1804-1811
ISSN:
1535-3907
Subject:
deamidation; liver; physicochemical properties; proteins; proteome; rats; reversed-phase liquid chromatography; synthetic peptides; tandem mass spectrometry
Abstract:
... Deamidation of asparaginyl residues in proteins produces a mixture of asparaginyl, n-aspartyl, and isoaspartyl residues, which affects the proteins’ structure, function, and stability. Thus, it is important to identify and quantify the products to evaluate the effects in biological systems. It is still a challenging task to distinguish between the n-Asp and isoAsp deamidation products in a proteom ...
DOI:
10.1021/pr201048c

17. Insights into the Molecular Composition of Endogenous Unanchored Polyubiquitin Chains

Author:
Strachan, Joanna; Roach, Lucy; Sokratous, Kleitos; Tooth, David; Long, Jed; Garner, Thomas P.; Searle, Mark S.; Oldham, Neil J.; Layfield, Robert
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1969-1980
ISSN:
1535-3907
Subject:
ions; mass spectrometry; moieties; proteomics; skeletal muscle; ubiquitin
Abstract:
... The diverse influences of ubiquitin, mediated by its post-translational covalent modification of other proteins, have been extensively investigated. However, more recently roles for unanchored (nonsubstrate linked) polyubiquitin chains have also been proposed. Here we describe the use of ubiquitin-binding domains to affinity purify endogenous unanchored polyubiquitin chains and their subsequent ch ...
DOI:
10.1021/pr201167n

18. Mass Spectrometrical Identification of Hippocampal NMDA Receptor Subunits NR1, NR2A–D and Five Novel Phosphorylation Sites on NR2A and NR2B

Author:
Ghafari, Maryam; Höger, Harald; Keihan Falsafi, Soheil; Russo-Schlaff, Nina; Pollak, Arnold; Lubec, Gert
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1891-1896
ISSN:
1535-3907
Subject:
antibodies; chymotrypsin; computer software; mass spectrometry; nervous system; peptides; phosphorylation; post-translational modification; precipitin tests; protein-protein interactions; proteins; proteome; rats; synaptic transmission; trypsin
Abstract:
... The NMDA receptor (NMDA-R) is a key element in neural transmission and mediating a vast variety of physiological and pathological processes in the nervous system. It is well-known that phosphorylation is required for functioning of the NMDA–R, and we therefore decided to study this post-translational modification in subunits NR1 and NR2A–D. Immunoprecipitation with an antibody against NR1 was carr ...
DOI:
10.1021/pr201099u

19. Measuring H218O Tracer Incorporation on a QQQ-MS Platform Provides a Rapid, Transferable Screening Tool for Relative Protein Synthesis

Author:
Conway, James P.; Johns, Douglas G.; Wang, Sheng-Ping; Walker, Nykia D.; McAvoy, Thomas A.; Zhou, Haihong; Zhao, Xuemei; Previs, Stephen F.; Roddy, Thomas P.; Hubbard, Brian K.; Yates, Nathan A.; Hendrickson, Ronald C.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1591-1597
ISSN:
1535-3907
Subject:
amino acids; coronary disease; drugs; low density lipoprotein; mass spectrometry; mice; models; protein synthesis; proteinase inhibitors; proteome; rapid methods; risk; screening; triacylglycerols; very low density lipoprotein
Abstract:
... Intracellular proteins are in a state of flux, continually being degraded into amino acids and resynthesized into new proteins. The rate of this biochemical recycling process varies across proteins and is emerging as an important consideration in drug discovery and development. Here, we developed a triple-stage quadrupole mass spectrometry assay based on product ion measurements at unit resolution ...
DOI:
10.1021/pr2007494

20. Metabolic Diversity of Progressive Kidney Disease in 325 Patients with Type 1 Diabetes (the FinnDiane Study)

Author:
Mäkinen, Ville-Petteri; Tynkkynen, Tuulia; Soininen, Pasi; Peltola, Tomi; Kangas, Antti J.; Forsblom, Carol; Thorn, Lena M.; Kaski, Kimmo; Laatikainen, Reino; Ala-Korpela, Mika; Groop, Per-Henrik
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1782-1790
ISSN:
1535-3907
Subject:
albumins; albuminuria; blood lipids; blood serum; cross-sectional studies; data analysis; excretion; glycemic control; high density lipoprotein; inflammation; insulin-dependent diabetes mellitus; kidney diseases; kidneys; low density lipoprotein; metabolites; models; nuclear magnetic resonance spectroscopy; patients; phenotype; phospholipids; saturated fatty acids; sphingomyelins
Abstract:
... Type 1 diabetic patients with varying severity of kidney disease were investigated to create multimetabolite models of the disease process. Urinary albumin excretion rate was measured for 3358 patients with type 1 diabetes. Prospective records were available for 1051 patients, of whom 163 showed progression of albuminuria (8.3-year follow-up), and 162 were selected as stable controls. At baseline, ...
DOI:
10.1021/pr201036j