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Journal of Proteome Research
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7988-2012
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2012 v.11 no.3
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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
- https://doi.org/10.1021/pr2008175
- 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
- https://doi.org/10.1021/pr2006044
- 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
- https://doi.org/10.1021/pr2011044
- 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
- https://doi.org/10.1021/pr2011439
- 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
- https://doi.org/10.1021/pr200460s
- 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
- https://doi.org/10.1021/pr2010605
- 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
- https://doi.org/10.1021/pr2010692
- 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
- https://doi.org/10.1021/pr200849v
- 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
- https://doi.org/10.1021/pr201048c
- 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
- https://doi.org/10.1021/pr201167n
- 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
- https://doi.org/10.1021/pr201099u
- 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
- https://doi.org/10.1021/pr201036j
- Author:
- Wiktorowicz John E.; English Robert D.; Wu Zheng; Kurosky Alexander
- Source:
- Journal of Proteome Research 2012 v.11 no.3 pp. 1512-1520
- ISSN:
- 1535-3907
- Subject:
- Escherichia coli; acylation; amino acids; hydroxylamine; models; proteome; synthetic peptides
- Abstract:
- ... A multiplexed peptide quantification strategy using the iTRAQ reagent has been described for relative measurements of peptides in digested protein mixtures. To validate the chemical specificity of the iTRAQ reaction, we have performed a detailed study of iTRAQ reactivity with two sets of synthetic peptides. The first set of peptides had sequences of Tyr-Xaa-Ser-Glu-Gly-Leu-Ser-Lys and Tyr-Xaa-Ser- ...
- DOI:
- 10.1021/pr2003165
- PubMed:
- 22335824
- PubMed Central:
- PMC3310887
- https://doi.org/10.1021/pr2003165
- Author:
- Deutscher Ania T.; Tacchi Jessica L.; Minion F. Chris; Padula Matthew P.; Crossett Ben; Bogema Daniel R.; Jenkins Cheryl; Kuit Tracey A.; Walker Mark J.; Djordjevic Steven P.
- Source:
- Journal of Proteome Research 2012 v.11 no.3 pp. 1924-1936
- ISSN:
- 1535-3907
- Subject:
- Mycoplasma hyopneumoniae; adhesins; cilia; collagen; epithelium; fibronectins; glycosaminoglycans; mass spectrometry; peptides; plasminogen; proteinases; proteome; surface proteins; swine
- Abstract:
- ... P97 and P102 paralogues occur as endoproteolytic cleavage fragments on the surface of Mycoplasma hyopneumoniae that bind glycosaminoglycans, plasminogen, and fibronectin and perform essential roles in colonization of ciliated epithelia. We show that the P102 paralogue Mhp384 is efficiently cleaved at an S/T-X-F↓X-D/E-like site, creating P60₃₈₄ and P50₃₈₄. The P97 paralogue Mhp385 is inefficiently ...
- DOI:
- 10.1021/pr201115v
- https://doi.org/10.1021/pr201115v
- Author:
- Victor Bjorn; Gabriël Sarah; Kanobana Kirezi; Mostovenko Ekaterina; Polman Katja; Dorny Pierre; Deelder André M.; Palmblad Magnus
- Source:
- Journal of Proteome Research 2012 v.11 no.3 pp. 1991-1995
- ISSN:
- 1535-3907
- Subject:
- amino acid sequences; databases; humans; models; peptides; proteome; tandem mass spectrometry
- Abstract:
- ... Tandem mass spectrometry is commonly used to identify peptides, typically by comparing their product ion spectra with those predicted from a protein sequence database and scoring these matches. The most reported quality metric for a set of peptide identifications is the false discovery rate (FDR), the fraction of expected false identifications in the set. This metric has so far only been used for ...
- DOI:
- 10.1021/pr201035r
- https://doi.org/10.1021/pr201035r
- Author:
- Dasari Surendra; Chambers Matthew C.; Martinez Misti A.; Carpenter Kristin L.; Ham Amy-Joan L.; Vega-Montoto Lorenzo J.; Tabb David L.
- Source:
- Journal of Proteome Research 2012 v.11 no.3 pp. 1686-1695
- ISSN:
- 1535-3907
- Subject:
- algorithms; amino acid sequences; automation; data collection; databases; mass spectrometry; peptides; proteome; proteomics; quality control; sequence analysis
- Abstract:
- ... Spectral libraries have emerged as a viable alternative to protein sequence databases for peptide identification. These libraries contain previously detected peptide sequences and their corresponding tandem mass spectra (MS/MS). Search engines can then identify peptides by comparing experimental MS/MS scans to those in the library. Many of these algorithms employ the dot product score for measurin ...
- DOI:
- 10.1021/pr200874e
- PubMed:
- 22217208
- PubMed Central:
- PMC3292681
- https://doi.org/10.1021/pr200874e
- Author:
- Fricker Lloyd D.; Gelman Julia S.; Castro Leandro M.; Gozzo Fabio C.; Ferro Emer S.
- Source:
- Journal of Proteome Research 2012 v.11 no.3 pp. 1981-1990
- ISSN:
- 1535-3907
- Subject:
- animal tissues; cell lines; hydrophobicity; mass spectrometry; mitochondria; nuclear proteins; peptides; proteasome endopeptidase complex; proteasome inhibitors; protein degradation; proteome; sequence analysis
- Abstract:
- ... Peptides derived from cytosolic, mitochondrial, and nuclear proteins have been detected in extracts of animal tissues and cell lines. To test whether the proteasome is involved in their formation, HEK293T cells were treated with epoxomicin (0.2 or 2 μM) for 1 h and quantitative peptidomics analysis was performed. Altogether, 147 unique peptides were identified by mass spectrometry sequence analysi ...
- DOI:
- 10.1021/pr2012076
- PubMed:
- 22304392
- PubMed Central:
- PMC3315381
- https://doi.org/10.1021/pr2012076
- Author:
- Zheng Peng; Gao Hong C.; Li Qi; Shao Wei H.; Zhang Mei L.; Cheng Ke; Yang De Y.; Fan Song H.; Chen Liang; Fang Liang; Xie Peng
- Source:
- Journal of Proteome Research 2012 v.11 no.3 pp. 1741-1748
- ISSN:
- 1535-3907
- Subject:
- behavior disorders; discriminant analysis; least squares; mental depression; metabolomics; nuclear magnetic resonance spectroscopy; patients; suicide
- Abstract:
- ... Major depressive disorder (MDD) is a socially detrimental psychiatric disorder, contributing to increased healthcare expenditures and suicide rates. However, no empirical laboratory-based tests are available to support the diagnosis of MDD. In this study, a NMR-based plasma metabonomic method for the diagnosis of MDD was tested. Proton nuclear magnetic resonance (¹H NMR) spectra of plasma sampled ...
- DOI:
- 10.1021/pr2010082
- https://doi.org/10.1021/pr2010082
- Author:
- Anderson N. Leigh; Razavi Morteza; Pearson Terry W.; Kruppa Gary; Paape Rainer; Suckau Detlef
- Source:
- Journal of Proteome Research 2012 v.11 no.3 pp. 1868-1878
- ISSN:
- 1535-3907
- Subject:
- antibodies; biomarkers; humans; matrix-assisted laser desorption-ionization mass spectrometry; peptides; proteome; stable isotopes; statistical analysis
- Abstract:
- ... We have investigated the precision of peptide quantitation by MALDI-TOF mass spectrometry (MS) using six pairs of proteotypic peptides (light) and same-sequence stable isotope labeled synthetic internal standards (heavy). These were combined in two types of dilution curves spanning 100-fold and 2000-fold ratios. Coefficients of variation (CV; standard deviation divided by mean value) were examined ...
- DOI:
- 10.1021/pr201092v
- https://doi.org/10.1021/pr201092v
- Author:
- Molinari Claire E.; Casadio Ylenia S.; Hartmann Ben T.; Livk Andreja; Bringans Scott; Arthur Peter G.; Hartmann Peter E.
- Source:
- Journal of Proteome Research 2012 v.11 no.3 pp. 1696-1714
- ISSN:
- 1535-3907
- Subject:
- breast milk; dairy protein; electrophoresis; gene expression regulation; humans; immune response; liquid chromatography; mothers; pregnancy; premature birth; protein composition; protein synthesis; proteome; skim milk
- Abstract:
- ... The abundant proteins in human milk have been well characterized and are known to provide nutritional, protective, and developmental advantages to both term and preterm infants. However, relatively little is known about the expression of the low abundance proteins that are present in human milk because of the technical difficulties associated with their detection. We used a combination of electrop ...
- DOI:
- 10.1021/pr2008797
- https://doi.org/10.1021/pr2008797
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