bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis of lymph
Authors: Leak Lee V. , Liotta Lance A. , Krutzsch Henry , Jones Michael , Fusaroa Vincent A. , Ross Sally J. , Zhao Yingming , Petricoin Emanuel F. 
Published: February 2004

AbstractThis report provides the first proteomic analysis of normal ovine lymph. By establishing the fact that lymph is more than an ultrafiltrate of blood plasma, it documents that the lymph proteome contains an array of proteins that differentiates it from plasma. The protein chip technology, surface‐enhanced laser desorption/ionization‐time of flight‐mass spectrometry (SELDI‐TOF‐MS), two‐dimensional gel electrophoresis (2‐D PAGE) and MS, were employed to examine the protein expression profiles of ovine lymph. Using a weak cation exchange chip surface to assay lymph and plasma samples by SELDI‐TOF‐MS showed that the analysis of peak maps from lymph contained three protein peaks that were found only in lymph, while analysis of peak maps from plasma samples showed that five protein peaks were found only in plasma. Lymph and plasma samples showed eight peaks that were common to both. There were also more ions present in plasma than in lymph, which is consistent with the 2‐D PAGE analysis. MS analysis of a large number of protein spots from 2‐D PAGE gels of lymph produced MS/MS sequences for 18 proteins that were identified by searching against a comprehensive protein sequence database. As in plasma, large protein spots of albumin dominated the protein pattern in lymph. Other major proteins identified in 2‐D PAGE gels of lymph included, fibrinogen α‐ and β‐chains, immunoglobulin G (IgG) heavy chain, serotransferrin precursor, lactoferrin, and apolipoprotein A‐1. Two proteins that were identified and were differentially expressed in lymph were glial fibrillary astrocyte acidic protein and neutrophil cytosol factor‐1. By bringing the technologies of proteomics to bear on the analysis of lymph, it is possible to detect proteins in lymph that are quantitatively and qualitatively differentially expressed from those of plasma.
Ovarian cancer detection by logical analysis of proteomic data
Authors: Alexe Gabriela , Alexe Sorin , Liotta Lance A. , Petricoin Emanuel , Reiss Michael , Hammer Peter L. 
Published: February 2004

AbstractA new type of efficient and accurate proteomic ovarian cancer diagnosis systems is proposed. The system is developed using the combinatorics and optimization‐based methodology of logical analysis of data (LAD) to the Ovarian Dataset 8‐7‐02 (http://clinicalproteomics.steem.com), which updates the one used by Petricoin et al. in The Lancet 2002, 359, 572–577. This mass spectroscopy‐generated dataset contains expression profiles of 15 154 peptides defined by their mass/charge ratios (m/z) in serum of 162 ovarian cancer and 91 control cases. Several fully reproducible models using only 7–9 of the 15 154 peptides were constructed, and shown in multiple cross‐validation tests (k‐folding and leave‐one‐out) to provide sensitivities and specificities of up to 100%. A special diagnostic system for stage I ovarian cancer patients is shown to have similarly high accuracy. Other results: (i) expressions of peptides with relatively low m/z values in the dataset are shown to be better at distinguishing ovarian cancer cases from controls than those with higher m/z values; (ii) two large groups of patients with a high degree of similarities among their formal (mathematical) profiles are detected; (iii) several peptides with a blocking or promoting effect on ovarian cancer are identified.
Effect of collagen substrates on proteomic modulation of breast cancer cells
Authors: Fontana Simona , Pucci‐Minafra Ida , Becchi Michel , Freyria Anne‐Marie , Minafra Salvatore 
Published: February 2004

AbstractWe have previously described the occurrence, in breast and colon cancer extra‐cellular matrix, of an oncofoetal form of collagen, OF/LB, able to induce an increase in cell proliferation and motility in the breast cancer cell line 8701‐BC. It also caused an increased amount of type V collagen which appears to exert an anti‐proliferative effect on the same cells. The aim of the present study was to investigate, at the proteomic level, the effect of OF/LB and type V collagens used as substrates for neoplastic cell growth. Due to the complexity of a whole proteomic profile, a subset of significant protein classes was used to assess variations in protein expression levels. For this study we adopted a multivariate statistical procedure that allows a global view of the variations induced by different growth conditions, when several variables have to be analyzed simultaneously. The results of this research indicate that in response to different growth substrates, chaperons and heat shock proteins contributed most to the dissimilarity in levels of expression of the selected protein spots. Moreover, we observed that different isoforms of the same protein showed independent levels of expression from one another in relation to the different collagen treatments.
Identification and characterization of phosphorylated proteins in the human pituitary
Authors: Giorgianni Francesco , Beranova‐Giorgianni Sarka , Desiderio Dominic M. 
Published: February 2004

AbstractPost‐translational modifications of proteins from the human pituitary gland play an important role in the regulation of different body functions. We report on the application of a liquid chromatography‐tandem mass spectrometry (MS/MS) based approach to detect and characterize phosphorylated proteins in a whole human pituitary digest. By combining an immobilized metal affinity column‐based enrichment method with MS/MS conditions that favor the neutral loss of phosphoric acid from a phosphorylated precursor ion, we identified several previously undescribed phosphorylated peptides. The identified peptides were matched to the sequences of six pituitary proteins: the human growth hormone, chromogranin A, secretogranin I, 60S ribosomal protein P1 and/or P2, DnaJ homolog subfamily C member 5, and galanin. The phosphorylation sites of these important regulatory proteins were determined by MS/MS and MS3 analysis.
Improved Ruthenium II tris (bathophenantroline disulfonate) staining and destaining protocol for a better signal‐to‐background ratio and improved baseline resolution
Authors: Lamanda Andreas , Zahn Alain , Röder Daniel , Langen Hanno 
Published: February 2004

AbstractIn proteomics the ability to visualize proteins from electropherograms is essential. Here a new protocol for staining and destaining gels treated with Ruthenium II tris (bathophenantroline disulfonate) is presented. The method is compared with the silver‐staining procedure of Swain and Ross, the Ruthenium II tris (bathophenantroline disulfonate) stain described by Rabilloud (Rabilloud T., Strub, S. M. Luche, S., Girardet, S. L. et al., Proteomics 2001, 1, 699–704) and the SYPRO Ruby gel stain. The method offers a better signal‐to‐background ratio with improved baseline resolution for both sodium dodecyl sulfate‐polyacrylamide gels and two‐dimensional gels.
About thiol derivatization and resolution of basic proteins in two‐dimensional electrophoresis
Authors: Luche Sylvie , Diemer Hélène , Tastet Chistophe , Chevallet Mireille , Van Dorsselaer Alain , Leize‐Wagner Emmanuelle , Rabilloud Thierry 
Published: February 2004

AbstractThe influence of thiol blocking on the resolution of basic proteins by two‐dimensional electrophoresis was investigated. Cysteine blocking greatly increased resolution and decreased streaking, especially in the basic region of the gels. Two strategies for cysteine blocking were found to be efficient: classical alkylation with maleimide derivatives and mixed disulfide exchange with an excess of a low molecular weight disulfide. The effect on resolution was significant enough to allow correct resolution of basic proteins with in‐gel rehydration on wide gradients (e.g. 3–10 and 4–12), but anodic cup‐loading was still required for basic gradients (e.g. 6–12 or 8–12). These results demonstrate that thiol‐related problems are not solely responsible for streaking of basic proteins on two‐dimensional gels.
Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data
Authors: Chamrad Daniel C. , Körting Gerhard , Stühler Kai , Meyer Helmut E. , Klose Joachim , Blüggel Martin 
Published: February 2004

AbstractIn this work, the commonly used algorithms for mass spectrometry based protein identification, Mascot, MS‐Fit, ProFound and SEQUEST, were studied in respect to the selectivity and sensitivity of their searches. The influence of various search parameters were also investigated. Approximately 6600 searches were performed using different search engines with several search parameters to establish a statistical basis. The applied mass spectrometric data set was chosen from a current proteome study. The huge amount of data could only be handled with computational assistance. We present a software solution for fully automated triggering of several peptide mass fingerprinting (PMF) and peptide fragmentation fingerprinting (PFF) algorithms. The development of this high‐throughput method made an intensive evaluation based on data acquired in a typical proteome project possible. Previous evaluations of PMF and PFF algorithms were mainly based on simulations.
Proteomic analysis of κ‐casein micro‐heterogeneity
Authors: Holland John W. , Deeth Hilton C. , Alewood Paul F. 
Published: February 2004

AbstractThe proteome of bovine milk is dominated by just six gene products that constitute approximately 95% of milk protein. Nonetheless, over 150 protein spots can be readily detected following two‐dimensional electrophoresis of whole milk. Many of these represent isoforms of the major gene products produced through extensive post‐translational modification. Peptide mass fingerprinting of in‐gel tryptic digests (using matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry (MALDI‐TOF MS) in reflectron mode with α‐cyano‐4‐hydroxycinnamic acid as the matrix) identified 10 forms of κ‐casein with isoelectric point (pI) values from 4.47 to 5.81, but could not distinguish between them. MALDI‐TOF MS in linear mode, using sinapinic acid as the matrix, revealed a large tryptic peptide (mass > 5990 Da) derived from the C‐terminus that contained all the known sites of genetic variance, phosphorylation and glycosylation. Two genetic variants present as singly or doubly phosphorylated forms could be distinguished using mass data alone. Glycoforms containing a single acidic tetrasaccharide were also identified. The differences in electrophoretic mobility of these isoforms were consistent with the addition of the acidic groups. While more extensively glycosylated forms were also observed, substantial loss of N‐acetylneuraminic acid from the glycosyl group was evident in the MALDI spectra such that ions corresponding to the intact glycopeptide were not observed and assignment of the glycoforms was not possible. However, by analysing the pI shifts observed on the two‐dimensional gels in conjunction with the MS data, the number of N‐acetylneuraminic acid residues, and hence the glycoforms present, could be determined.
Construction of a two‐dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow‐2 cell suspension culture
Authors: Laukens Kris , Deckers Peter , Esmans Eddy , Van Onckelen Harry , Witters Erwin 
Published: February 2004

AbstractUsing two‐dimensional gel electrophoresis (2‐DE) and electrospray‐tandem mass spectrometry (ESI‐MS/MS), we have started the proteome analysis of the cell line Nicotiana tabacum cv. Bright Yellow‐2 (tobacco BY‐2). The BY‐2 cell suspension culture is widely used as a model system to study the growth and development of plant cells. We present a protocol describing the sample preparation and 2‐DE, enabling us to separate and display more than 1000 proteins from this cell culture. A reference gel was generated, using immobilized pH gradient isoelectric focusing in a linear gradient from pH 3 to 10 and 12% Sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE). Although the tobacco genome is not sequenced yet, a range of protein spots from this reference map was identified by means of a semi‐automated liquid chromatography‐ESI‐quadrupole time of flight‐tandem MS (LC‐ESI‐QTOF‐MS‐MS) setup and cross‐species matching. These data were integrated in a database, which can be accessed at http://tby2‐www.uia.ac.be/tby2/. On the on‐line reference map, the identified protein spots are hyperlinked to individual protein entries. Each protein entry contains all identification information, as well as links to relevant entries in other on‐line databases. Comprehensive search functions are implemented. Especially for an unsequenced but widespread model organism like tobacco BY‐2, such a reference database is a convenient source for protein information that brings protein identification within reach without the need for extensive MS. This publicly accessible database provides a solid basis for tobacco BY‐2 proteomics in the future.
Two‐dimensional gel electrophoresis pattern (pH 6–11) and identification of water‐soluble barley seed and malt proteins by mass spectrometry
Authors: Bak‐Jensen Kristian Sass , Laugesen Sabrina , Roepstorff Peter , Svensson Birte 
Published: February 2004

AbstractA protocol was established for two‐dimensional gel electrophoresis (2‐DE) of barley seed and malt proteins in the pH range of 6–11. Proteins extracted from flour in a low‐salt buffer were focused after cup‐loading onto IPG strips. Successful separation in the second dimension was achieved using gradient gels in a horizontal SDS‐PAGE system. Silver staining of gels visualized around 380 (seed) and 500 (malt) spots. Thirty‐seven different proteins from seeds were identified in 60 spots, among these 46 were visualized also in the malt 2‐D pattern. Proteins were identified by peptide mass fingerprinting and by tandem MS sequencing after in‐gel digestion by trypsin. In addition, the N‐terminal sequence of 10 different proteins from 11 spots was determined after electroblotting to a polyvinylidene difluoride (PVDF) membrane. Five identified proteins (in 9 spots) are involved in glycolysis, 12 in defence against pathogens (21 spots), 4 in storage, folding, and synthesis of proteins, and in nitrogen metabolism (5 spots), 6 in carbohydrate metabolism (11 spots), and 4 in stress and detoxification (9 spots). Six proteins (7 spots) were not grouped in these categories, and 3 were not ascribed a function. The presented 2‐D patterns and identifications will be used to describe proteome differences between cultivars and changes during malting.
Comparative proteome analysis of thalamus in MK‐801‐treated rats
Authors: Paulson Linda , Martin Peter , Nilsson Carol L. , Ljung Elisabeth , Westman‐Brinkmalm Ann , Blennow Kaj , Davidsson Pia 
Published: February 2004

AbstractTwo‐dimensional gel‐electrophoresis in combination with mass spectrometry is a powerful approach to compare protein expression in brain tissues. Using this proteomic approach, and based on the hypothesis that schizophrenia involves hypoglutamergic brain function, alterations in protein levels in the thalamus of rats treated with the N‐methyl‐D‐aspartate (NMDA) receptor antagonist [+]‐5‐methyl‐10,11‐dihydro‐5H‐dibenzo‐[a,d]‐cycloheptene‐5,10‐iminehydrogenmaleate (MK‐801), as compared to saline‐treated animals, were assessed in an unbiased fashion. The rats were divided into two groups; group 1 (short‐term treated) and group 2 (long‐term treated). In group 1, the levels of seven proteins were increased and four proteins reduced. In group 2, the levels of six proteins were reduced. Several of the altered proteins (heat shock proteins 60 and 72, albumin, dihydropyrimidinase related protein‐2, aldolase c, and malate dehydrogenase) have previously been connected to schizophrenia. Alterations of other proteins (dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex E2, guanine deaminase, α‐enolase, aconitase, ATP‐synthase and α‐internexin), have not, to the best of our knowledge, earlier been implicated in schizophrenia pathology. Our results show the high potential of using proteomic methods for the validation of animal models of schizophrenia and to identify new proteins involved in the pathophysiological mechanisms of schizophrenia.
Comparative proteomic analysis of de‐N‐glycosylated serum from hepatitis B carriers reveals polypeptides that correlate with disease status
Authors: Comunale Mary Ann , Mattu Taj S. , Lowman Melissa A. , Evans Alison A. , London W. Thomas , Semmes O. John , Ward Michael , Drake Richard , Romano Patrick R. , Steel Laura F. , Block Timothy M. , Mehta Anand 
Published: February 2004

AbstractAnalysis of the polypeptide profile in tissues, cells, and sera by high‐resolution two‐dimensional (2‐D) gel electrophoresis offers promise in the identification of biomarkers that correlate with disease. However, sera contain many polypeptides bearing N‐linked glycosylation that can complicate interpretation. Therefore, we tested the possibility that de‐N‐glycosylation of the polypeptides present in human serum would result in a simplification of serum proteome profiles. Briefly, polypeptides present in human serum were left untreated or subjected to de‐N‐glycosylation by incubation with PNGase F and resolved by high‐resolution 2‐D gel electrophoresis. De‐N‐glycosylation reduced the number of glycoform variants, enhanced the resolution of many polypeptides and allowed other polypeptides to become visible. As an initial test of concept, clinically relevant serum samples from individuals with or without diagnosis of hepatocellular carcinoma were compared. Several polypeptides, apparent only after de‐N‐glycosylation, were shown to correlate with disease. Although the results are preliminary and the identities of all the putative biomarkers not yet known, the data suggest that de‐N‐glycosylation offers a method to enhance the resolution of serum polypeptide profiles and has value in comparative proteomic studies.
Protein profiling and identification of modulators regulated by the E7 oncogene in the C33A cell line by proteomics and genomics
Authors: Lee Kyung‐Ae , Shim Jung‐Hyun , Kho Chang Won , Park Sung Goo , Park Byoung Chul , Kim Jae‐Wha , Lim Jong‐Seok , Choe Yong‐Kyung , Paik Sang‐Gi , Yoon Do‐Young 
Published: February 2004

AbstractHuman papillomaviruses (HPVs) have been recognized as the primary cause of cervical cancer. HPV 16 E7 binds to tumor suppressor retinoblastoma protein, and interferes with its function, causing release of the transcription factor E2F, which influences expression of cell cycle‐related genes. This study was performed to identify the genes and proteins modulated by the HPV E7 oncogene. An HPV‐negative cervical cancer cell line (C33A) was prepared to establish a stable cell line expressing E7. In order to analyze the target molecules modulated by E7 expression, we used two approaches: matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry (MALDI‐TOF MS) and DNA microarrays. Forty‐seven spots were identified in C33A/E7 by two‐dimensional electrophoresis and MALDI/TOF MS. Protein disulfide isomerase A3, integrase interactor 1 protein, growth inhibitory protein, glutathione S‐transferase P, and vav proto‐oncogene were down‐regulated, whereas heat shock 60 kDa protein 1, Ku70 binding protein, alpha enolase, 26S proteasome subunit were up‐regulated. A genomic approach using a microarray kit showed that IL‐12Rβ1, cytochrome c, and tumor necrosis factor receptor II were induced by the E7 oncogene. These results suggest that E7 can evade immune surveillance by suppressing or inducing these cell signaling factors, cell cycle regulators, and chaperones.
A map of WW domain family interactions
Authors: Hu Hai , Columbus John , Zhang Yi , Wu Dongying , Lian Lubing , Yang Song , Goodwin Jennifer , Luczak Christine , Carter Mark , Chen Lin , James Michael , Davis Roger , Sudol Marius , Rodwell John , Herrero Juan J. 
Published: February 2004

AbstractWW domains are protein modules that bind proline‐rich ligands. WW domain‐ligand complexes are of importance as they have been implicated in several human diseases such as muscular dystrophy, cancer, hypertension, Alzheimer's, and Huntington's diseases. We report the results of a protein array aimed at mapping all the human WW domain protein‐protein interactions. Our biochemical approach integrates parallel synthesis of peptides, protein expression, and high‐throughput screening methodology combined with tools of bioinformatics. The results suggest that the majority of the bioinformatically predicted WW peptide ligands and most WW domains are functional, and that only about 10% of the measured domain‐ligand interactions are positive. The analysis of the WW domain protein arrays also underscores the importance of the amino acid residues surrounding the WW ligand core motifs for specific binding to WW domains. In addition, the methodology presented here allows for the rapid elucidation of WW domain‐ligand interactions with multiple applications including prediction of exact WW ligand binding sites, which can be applied to the mapping of other protein signaling domain families. Such information can be applied to the generation of protein interaction networks and identification of potential drug targets. To our knowledge, this report describes the first protein‐protein interaction map of a domain in the human proteome.
Cell wall proteomics of the green alga Haematococcus pluvialis (Chlorophyceae)
Authors: Wang Sheng‐Bing , Hu Qiang , Sommerfeld Milton , Chen Feng 
Published: February 2004

AbstractThe green microalga Haematococcus pluvialis can synthesize and accumulate large amounts of the ketocarotenoid astaxanthin, and undergo profound changes in cell wall composition and architecture during the cell cycle and in response to environmental stresses. In this study, cell wall proteins (CWPs) of H. pluvialis were systematically analyzed by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) coupled with peptide mass fingerprinting (PMF) and sequence‐database analysis. In total, 163 protein bands were analyzed, which resulted in positive identification of 81 protein orthologues. The highly complex and dynamic composition of CWPs is manifested by the fact that the majority of identified CWPs are differentially expressed at specific stages of the cell cycle along with a number of common wall‐associated ‘housekeeping’ proteins. The detection of cellulose synthase orthologue in the vegetative cells suggested that the biosynthesis of cellulose occurred during primary wall formation, in contrast to earlier observations that cellulose was exclusively present in the secondary wall of the organism. A transient accumulation of a putative cytokinin oxidase at the early stage of encystment pointed to a possible role in cytokinin degradation while facilitating secondary wall formation and/or assisting in cell expansion. This work represents the first attempt to use a proteomic approach to investigate CWPs of microalgae. The reference protein map constructed and the specific protein markers obtained from this study provide a framework for future characterization of the expression and physiological functions of the proteins involved in the biogenesis and modifications in the cell wall of Haematococcus and related organisms.