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You searched for: Journal name Journal of Proteome Research Remove constraint Journal name: Journal of Proteome Research Publication year rev 7988-2012 Remove constraint Publication year rev: 7988-2012 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
PubMed:
22288382
PubMed Central:
PMC3319072

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 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
PubMed:
22296162
PubMed Central:
PMC3292626

4. 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

5. 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

6. 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

7. 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

8. Model Studies on iTRAQ Modification of Peptides: Sequence-dependent Reaction Specificity

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

9. Pepitome: Evaluating Improved Spectral Library Search for Identification Complementarity and Quality Assessment

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

10. Peptidomic Analysis of HEK293T Cells: Effect of the Proteasome Inhibitor Epoxomicin on Intracellular Peptides

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

11. Plasma Metabonomics as a Novel Diagnostic Approach for Major Depressive Disorder

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

12. Proteome Mapping of Human Skim Milk Proteins in Term and Preterm Milk

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

13. Proteomic Identification of Immunoproteasome Accumulation in Formalin-Fixed Rodent Spinal Cords with Experimental Autoimmune Encephalomyelitis

Author:
Jain Mohit Raja; Li Qing; Liu Tong; Rinaggio Joseph; Ketkar Amit; Tournier Vincent; Madura Kiran; Elkabes Stella; Li Hong
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1791-1803
ISSN:
1535-3907
Subject:
encephalitis; mice; models; peptides; proteasome endopeptidase complex; proteins; proteome; proteomics; rats; spinal cord
Abstract:
... Clinically relevant formalin-fixed and paraffin-embedded (FFPE) tissues have not been widely used in neuroproteomic studies because many proteins are presumed to be degraded during tissue preservation. Recent improvements in proteomics technologies, from the 2D gel analysis of intact proteins to the “shotgun” quantification of peptides and the use of isobaric tags for absolute and relative quantif ...
DOI:
10.1021/pr201043u
PubMed:
22188123
PubMed Central:
PMC3312875

14. Quantitative Protease Cleavage Site Profiling using Tandem-Mass-Tag Labeling and LC–MALDI-TOF/TOF MS/MS Analysis

Author:
Jakoby Thomas; van den Berg Bart HJ; Tholey Andreas
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1812-1820
ISSN:
1535-3907
Subject:
bicarbonates; peptide libraries; proteinases; proteolysis; proteome; proteomics; quantitative analysis; statistics; yeasts
Abstract:
... Knowledge of cleavage site specificity and activity are major prerequisites for understanding protease function. On the basis of a recently presented approach for proteomic identification of cleavage sites (PICS) in proteome-derived peptide libraries, we developed an isobaric labeling quantitative LC–MALDI-TOF/TOF MS/MS approach (Q-PICS) for simultaneous determination of cleavage site specificity ...
DOI:
10.1021/pr201051e

15. Relative Quantification of Serum Proteins from Pancreatic Ductal Adenocarcinoma Patients by Stable Isotope Dilution Liquid Chromatography–Mass Spectrometry

Author:
Wehr Angela Y.; Hwang Wei-Ting; Blair Ian A.; Yu Kenneth H.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1749-1758
ISSN:
1535-3907
Subject:
adenocarcinoma; binding proteins; biomarkers; blood proteins; blood serum; cell lines; humans; isotope dilution technique; liquid chromatography; mass spectrometry; monitoring; pancreatic neoplasms; patients; proteome; somatomedins; stable isotopes; trypsin
Abstract:
... We report an innovative multiplexed liquidchromatography–multiple reaction monitoring/mass spectrometry (LC–MRM/MS)-based assay for rapidly measuring a large number of disease specific protein biomarkers in human serum. Furthermore, this approach uses stable isotope dilution methodology to reliably quantify candidate protein biomarkers. Human serum was diluted using a stable isotope labeled proteo ...
DOI:
10.1021/pr201011f
PubMed:
22264027
PubMed Central:
PMC3292696

16. Semi-Automated Identification of N-Glycopeptides by Hydrophilic Interaction Chromatography, nano-Reverse-Phase LC–MS/MS, and Glycan Database Search

Author:
Pompach Petr; Chandler Kevin B.; Lan Renny; Edwards Nathan; Goldman Radoslav
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1728-1740
ISSN:
1535-3907
Subject:
computer software; databases; glycopeptides; glycosylation; haptoglobins; humans; hydrophilic interaction chromatography; ions; polysaccharides; proteome; tandem mass spectrometry; topology
Abstract:
... Glycoproteins fulfill many indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. Improved analytical methods are needed to allow a complete characterization of this complex and common post-translational modification. In this study, we present a workflow for the analysis of the microheterogeneity of N-glycoproteins that couples hydrophilic ...
DOI:
10.1021/pr201183w
PubMed:
22239659
PubMed Central:
PMC3292689

17. Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

Author:
Li Zhou; Adams Rachel M.; Chourey Karuna; Hurst Gregory B.; Hettich Robert L.; Pan Chongle
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1582-1590
ISSN:
1535-3907
Subject:
proteins; proteome; proteomics; spectrometers
Abstract:
... A variety of quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling using iTRAQ or TMT. Here, these methods were compared in terms of the depth of proteome coverage, quantification accuracy, precision, and reproducibility using a high-performance hybrid mass spectrometer, LTQ Orbitrap Velos. Our results show that (1) the spectr ...
DOI:
10.1021/pr200748h

18. Tumor Classification of Six Common Cancer Types Based on Proteomic Profiling by MALDI Imaging

Author:
Meding Stephan; Nitsche Ulrich; Balluff Benjamin; Elsner Mareike; Rauser Sandra; Schöne Cédrik; Nipp Martin; Maak Matthias; Feith Marcus; Ebert Matthias P.; Friess Helmut; Langer Rupert; Höfler Heinz; Zitzelsberger Horst; Rosenberg Robert; Walch Axel
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1996-2003
ISSN:
1535-3907
Subject:
adenocarcinoma; breasts; colon; colorectal neoplasms; diagnostic techniques; esophagus; hepatoma; image analysis; liver; metastasis; proteome; proteomics; stomach; support vector machines; thyroid gland
Abstract:
... In clinical diagnostics, it is of outmost importance to correctly identify the source of a metastatic tumor, especially if no apparent primary tumor is present. Tissue-based proteomics might allow correct tumor classification. As a result, we performed MALDI imaging to generate proteomic signatures for different tumors. These signatures were used to classify common cancer types. At first, a cohort ...
DOI:
10.1021/pr200784p

19. Worker Honeybee Brain Proteome

Author:
Hernández Liudy G.; Lu Bingwen; da Cruz Gabriel C. N.; Calábria Luciana K.; Martins Natalia F.; Togawa Roberto; Espindola Foued S.; Yates John R.; Cunha Ricardo B.; de Sousa Marcelo V.
Source:
Journal of Proteome Research 2012 v.11 no.3 pp. 1485-1493
ISSN:
1535-3907
Subject:
biogenesis; brain; energy; gene expression regulation; proteins; proteome; statistics; worker honey bees
Abstract:
... A large-scale mapping of the worker honeybee brain proteome was achieved by MudPIT. We identified 2742 proteins from forager and nurse honeybee brain samples; 17% of the total proteins were found to be differentially expressed by spectral count sampling statistics and a G-test. Sequences were compared with the EuKaryotic Orthologous Groups (KOG) catalog set using BLASTX and then categorized into t ...
DOI:
10.1021/pr2007818
PubMed:
22181811
PubMed Central:
PMC3321609

20. 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