Comparative Identification of Prostanoid Inducible Proteins by LC-ESI-MS/MS and MALDI-TOF Mass Spectrometry

Person, Maria D.; Lo, Herng Hsiang; Towndrow, Kelly M.; Jia, Zhe; Monks, Terrence J.; Lau, Serrine S.

doi:10.1021/tx020049d

Cited by 29 publications

(17 citation statements)

References 33 publications

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“…The tryptic digests were analyzed on a Voyager-DE PRO matrix-assisted laser desorption/ionization time of flight MS (Applied Biosystems, Foster City, CA) as described previously (16,17) with minor modifications. The samples were desalted using a Ziptip -C18 pipette tip (Millipore, Billerica, MA).…”

Section: Methodsmentioning

confidence: 99%

Protein Expression Profiles in Pancreatic Adenocarcinoma Compared with Normal Pancreatic Tissue and Tissue Affected by Pancreatitis as Detected by Two-Dimensional Gel Electrophoresis and Mass Spectrometry

et al. 2004

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Pancreatic cancer is a rapidly fatal disease, and there is an urgent need for early detection markers and novel therapeutic targets. The current study has used a proteomic approach of two-dimensional (2D) gel electrophoresis and mass spectrometry (MS) to identify differentially expressed proteins in six cases of pancreatic adenocarcinoma, two normal adjacent tissues, seven cases of pancreatitis, and six normal pancreatic tissues. Protein extracts of individual sample and pooled samples of each type of tissues were separated on 2D gels using two different pH ranges. Differentially expressed protein spots were in-gel digested and identified by MS. Forty proteins were identified, of which five [i.e., ␣-amylase; copper zinc superoxide dismutase; protein disulfide isomerase, pancreatic; tropomyosin 2 (TM2); and galectin-1] had been associated previously with pancreatic disease in gene expression studies. The identified proteins include antioxidant enzymes, chaperones and/or chaperone-like proteins, calcium-binding proteins, proteases, signal transduction proteins, and extracellular matrix proteins. Among these proteins, annexin A4, cyclophilin A, cathepsin D, galectin-1, 14 -3-3, ␣-enolase, peroxiredoxin I, TM2, and S100A8 were specifically overexpressed in tumors compared with normal and pancreatitis tissues. Differential expression of some of the identified proteins was further confirmed by Western blot analyses and/or immunohistochemical analysis. These results show the value of a proteomic approach in identifying potential markers for early diagnosis and therapeutic manipulation. The newly identified proteins in pancreatic tumors may eventually serve as diagnostic markers or therapeutic targets.

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Section: Methodsmentioning

confidence: 99%

Protein Expression Profiles in Pancreatic Adenocarcinoma Compared with Normal Pancreatic Tissue and Tissue Affected by Pancreatitis as Detected by Two-Dimensional Gel Electrophoresis and Mass Spectrometry

et al. 2004

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“…It was previously reported that MALDI-TOF and LC-MS/MS are equally efficient at protein identification when comprehensive databases are available (Lim et al, 2003;Person et al, 2003). With plant species such as B. napus, for which database resources are limited, application of both MS methods may improve the identification rate.…”

Section: Lc-ms/ms Yielded Higher Percentage Of Protein Assignments Thmentioning

confidence: 99%

Proteomic Analysis of Seed Filling in Brassica napus. Developmental Characterization of Metabolic Isozymes Using High-Resolution Two-Dimensional Gel Electrophoresis

et al. 2006

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Brassica napus (cultivar Reston) seed proteins were analyzed at 2, 3, 4, 5, and 6 weeks after flowering in biological quadruplicate using two-dimensional gel electrophoresis. Developmental expression profiles for 794 protein spot groups were established and hierarchical cluster analysis revealed 12 different expression trends. Tryptic peptides from each spot group were analyzed in duplicate using matrix-assisted laser desorption ionization time-of-flight mass spectrometry and liquid chromatographytandem mass spectrometry. The identity of 517 spot groups was determined, representing 289 nonredundant proteins. These proteins were classified into 14 functional categories based upon the Arabidopsis (Arabidopsis thaliana) genome classification scheme. Energy and metabolism related proteins were highly represented in developing seed, accounting for 24.3% and 16.8% of the total proteins, respectively. Analysis of subclasses within the metabolism group revealed coordinated expression during seed filling. The influence of prominently expressed seed storage proteins on relative quantification data is discussed and an in silico subtraction method is presented. The preponderance of energy and metabolic proteins detected in this study provides an in-depth proteomic view on carbon assimilation in B. napus seed. These data suggest that sugar mobilization from glucose to coenzyme A and its acyl derivative is a collaboration between the cytosol and plastids and that temporal control of enzymes and pathways extends beyond transcription. This study provides a systematic analysis of metabolic processes operating in developing B. napus seed from the perspective of protein expression. Data generated from this study have been deposited into a web database (http://oilseedproteomics.missouri.edu) that is accessible to the public domain.Brassica napus (also known as rape and oilseed rape) is the third largest oilseed crop in the world, providing approximately 13% of the world's supply of vegetable oil. B. napus seeds produce oil and protein as the main storage compounds out of the three principal storage reserves (proteins, oil [triacylglycerols], and carbohydrates [starch]) found in plant seeds (Norton and Harris, 1975;Murphy et al., 1989;King et al., 1997;Schwender and Ohlrogge, 2002). These compounds support early seedling growth, and in nature the relative proportions of these compounds vary dramatically among different plant seeds. Seeds of legume species such as soybean (Glycine max) and pea (Pisum sativum) produce seeds with 20% to as much as 40% protein and 20% oil, while B. napus produces seeds with approximately 40% oil and 15% protein (Gunstone et al., 1995).Biochemical and molecular studies are beginning to define the biosynthetic pathways responsible for accumulation of these storage components in B. napus

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“…In MALDI, almost all peptides are singly-charged, while in ESI longer peptides usually involve doubly or triply-charged. [64][65][66] Furthermore the ESI analysis includes only those peptides definitively identified via MS/MS fragmentation, whereas the MALDI identification is by mass alone. 64 In summary, we have analyzed proteins from rat brain synaptic vesicles using two different separation methods and mass analysis techniques, cRPLC/MS/MS and 2DE-MALDI-TOF/MS.…”

Section: Discussionmentioning

confidence: 99%

A Comprehensive Identification of Synaptic Vesicle Proteins in Rat Brains by cRPLC/MS-MS and 2DE/MALDI-TOF-MS

Lee

Kim

Min³

et al. 2007

Bulletin of the Korean Chemical Society

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Proteomic analyses of synaptic vesicle fraction from rat brain have been performed for the better understanding of vesicle regulation and signal transmission. Two different approaches were applied to identify proteins in synaptic vesicle fraction. First, the isolated synaptic vesicle proteins were treated with trypsin, and the resulting peptides were analyzed using a high-pressure capillary reversed phase liquid chromatography/tandem mass spectrometry (cRPLC/MS/MS). Alternatively, proteins were separated by two-dimensional gel electrophoresis (2DE) and identified by matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF/MS). Total 18 and 52 proteins were identified from cRPLC/MS-MS and 2DE-MALDI-TOF-MS analysis, respectively. Among them only 2 proteins were identified by both methods. Of the proteins identified, 70% were soluble proteins and 30% were membrane proteins. They were categorized by their functions in vesicle trafficking and biogenesis, energy metabolism, signal transduction, transport and unknown functions. Among them, 27 proteins were not previously reported as synaptic proteins. The cellular functions of unknown proteins were estimated from the analysis of domain structure, expression profile and predicted interaction partners.

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Comparative Identification of Prostanoid Inducible Proteins by LC-ESI-MS/MS and MALDI-TOF Mass Spectrometry

Cited by 29 publications

References 33 publications

Protein Expression Profiles in Pancreatic Adenocarcinoma Compared with Normal Pancreatic Tissue and Tissue Affected by Pancreatitis as Detected by Two-Dimensional Gel Electrophoresis and Mass Spectrometry

Protein Expression Profiles in Pancreatic Adenocarcinoma Compared with Normal Pancreatic Tissue and Tissue Affected by Pancreatitis as Detected by Two-Dimensional Gel Electrophoresis and Mass Spectrometry

Proteomic Analysis of Seed Filling in Brassica napus. Developmental Characterization of Metabolic Isozymes Using High-Resolution Two-Dimensional Gel Electrophoresis

A Comprehensive Identification of Synaptic Vesicle Proteins in Rat Brains by cRPLC/MS-MS and 2DE/MALDI-TOF-MS

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