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- 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
- PubMed:
- 22288382
- PubMed Central:
- PMC3319072
-
http://dx.doi.org/10.1021%2Fpr2008175
- 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
-
http://dx.doi.org/10.1021%2Fpr2006044
- 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
-
http://dx.doi.org/10.1021%2Fpr200812p
- 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
- PubMed:
- 22296162
- PubMed Central:
- PMC3292626
-
http://dx.doi.org/10.1021%2Fpr2011044
- 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
- PubMed:
- 22320385
- PubMed Central:
- PMC3292799
-
http://dx.doi.org/10.1021%2Fpr2011439
- 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
- PubMed:
- 22224429
- PubMed Central:
- PMC3292622
-
http://dx.doi.org/10.1021%2Fpr200460s
- 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
-
http://dx.doi.org/10.1021%2Fpr2011632
- 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
-
http://dx.doi.org/10.1021%2Fpr2010605
- 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
-
http://dx.doi.org/10.1021%2Fpr200844d
- 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
-
http://dx.doi.org/10.1021%2Fpr2010692
- 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
-
http://dx.doi.org/10.1021%2Fpr200194p
- 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
-
http://dx.doi.org/10.1021%2Fpr2011268
- 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
-
http://dx.doi.org/10.1021%2Fpr200856w
- 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
-
http://dx.doi.org/10.1021%2Fpr2007895
- 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
-
http://dx.doi.org/10.1021%2Fpr200849v
- 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
-
http://dx.doi.org/10.1021%2Fpr201048c
- 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
-
http://dx.doi.org/10.1021%2Fpr201167n
- 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
-
http://dx.doi.org/10.1021%2Fpr201099u
- 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
-
http://dx.doi.org/10.1021%2Fpr2007494
- 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
-
http://dx.doi.org/10.1021%2Fpr201036j
