Unique scanning capabilities of a new hybrid linear ion trap mass spectrometer (Q TRAP) used for high sensitivity proteomics applications

Blanc, J. C. Yves Le; Hager, James W.; Ilisiu, A. M. Patricia; Hunter, Christie L.; Feng, Zhouming; Chu, Ivan K.

doi:10.1002/pmic.200300415

Cited by 138 publications

(109 citation statements)

References 8 publications

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“…To address the tremendous time commitment and multiple rounds of analyses, sometimes on different instruments, required for the development of MRM-MS methodologies, a novel hybrid instrument (4000 QTRAP, Applied Biosystems) is now available which is both a triple quadrupole and a linear trap and offers a unique opportunity to design MRM-MS methods [20]. Termed the MIDAS (MRM-initiated detection and sequencing) workflow [21], when significant signal in a specific MRM transition is detected (both the parent mass in Q1 and fragment mass in Q3 are isolated and detected), the instrument switches the third quadrapole to ion trap mode and collects a full scan tandem mass spectrum.…”

Section: Methods Developmentmentioning

confidence: 99%

Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry

Yocum¹,

Chinnaiyan²

2009

Briefings in Functional Genomics and Proteomics

109

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Quantitative targeted proteomics has recently taken front stage in the proteomics community. Centered on multiple reaction monitoring^mass spectrometry (MRM^MS) methodologies, quantitative targeted proteomics is being used in the verification of global proteomics data, the discovery of lower abundance proteins, protein post-translational modifications, discrimination of select highly homologous protein isoforms and as the final step in biomarker discovery. An older methodology utilized with small molecule analysis, the proteomics community is making great technological strides to develop MRM^MS as the next method to address previously challenging issues in global proteomics experimentation, namely dynamic range, identification of post-translational modifications, sensitivity and selectivity of measurement which will undoubtedly further biomedical knowledge.This brief review will provide a general introduction of MRM^MS and highlight its novel application for targeted quantitative proteomic experimentations.

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Section: Methods Developmentmentioning

confidence: 99%

Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry

Yocum¹,

Chinnaiyan²

2009

Briefings in Functional Genomics and Proteomics

109

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“…Amino acid sequence similarity searches were performed against the available databanks using the BLAST program 47 at http://www.bork.embl-heidelberg.de. The molecular masses of the purified proteins were determined by SDS-PAGE (on 12-15% polyacrylamide gels) and by electrospray ionization (ESI) mass spectrometry using an Applied Biosystems QTrap 2000 mass spectrometer 48 operated in Enhanced Multiple Charge mode in the range m/z 600-1700.…”

Section: Methodsmentioning

confidence: 99%

Snake Venomics of the Lancehead Pitviper Bothrops asper: Geographic, Individual, and Ontogenetic Variations

et al. 2008

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We report the comparative proteomic characterization of the venoms of adult and newborn specimens of the lancehead pitviper Bothrops asper from two geographically isolated populations from the Caribbean and the Pacific versants of Costa Rica. The crude venoms were fractionated by reverse-phase HPLC, followed by analysis of each chromatographic fraction by SDS-PAGE, N-terminal sequencing, MALDI-TOF mass fingerprinting, and collision-induced dissociation tandem mass spectrometry of tryptic peptides. The two B. asper populations, separated since the late Miocene or early Pliocene (8-5 mya) by the Guanacaste Mountain Range, Central Mountain Range, and Talamanca Mountain Range, contain both identical and different (iso)enzymes from the PLA 2 , serine proteinase, and SVMP families. Using a similarity coefficient, we estimate that the similarity of venom proteins between the two B. asper populations may be around 52%. Compositional differences between venoms among different geographic regions may be due to evolutionary environmental pressure acting on isolated populations. To investigate venom variability among specimens from the two B. asper populations, the reverse-phase HPLC protein profiles of 15 venoms from Caribbean specimens and 11 venoms from snakes from Pacific regions were compared. Within each B. asper geographic populations, all major venom protein families appeared to be subjected to individual variations. The occurrence of intraspecific individual allopatric variability highlights the concept that a species, B. asper in our case, should be considered as a group of metapopulations. Analysis of pooled venoms of neonate specimens from Caribbean and Pacific regions with those of adult snakes from the same geographical habitat revealed prominent ontogenetic changes in both geographical populations. Major ontogenetic changes appear to be a shift from a PIII-SVMP-rich to a PI-SVMP-rich venom and the secretion in adults of a distinct set of PLA 2 molecules than in the neonates. In addition, the ontogenetic venom composition shift results in increasing venom complexity, indicating that the requirement for the venom to immobilize prey and initiate digestion may change with the size (age) of the snake. Besides ecological and taxonomical implications, the geographical venom variability reported here may have an impact in the treatment of bite victims and in the selection of specimens for antivenom production. The occurrence of intraspecies variability in the biochemical composition and symptomatology after envenomation by snakes from different gegraphical location and age has long been apreciated by herpetologist and toxinologists, though detailed comparative proteomic analysis are scarce. Our study represents the first detailed characterization of individual and ontogenetic venom protein profile variations in two geographical isolated B. asper populations, and highlights the necessity of using pooled venoms as a statistically representative venom for antivenom production.

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“…The tryptic peptide mixtures were analyzed with an Applied Biosystems Voyager-DE-Pro matrix-assisted laser-desorption ionization time of flight mass spectrometer. For peptide sequencing, the protein digest mixture was subjected to electrospray ionization mass spectrometric analysis (QTrap 2000 [Applied Biosystems] with a nanoelectrospray source [Protana]; Le Blanc et al, 2003). Collision-induced dissociation spectra were interpreted manually or using a licensed version of the MASCOT program (http://www.matrixscience.com) against the SwissProt/TrEMBL database (http://us.expasy.org/sprot/).…”

Section: Proteomic Characterizationmentioning

confidence: 99%

Mitochondrial and Nuclear Localization of a Novel Pea Thioredoxin: Identification of Its Mitochondrial Target Proteins

et al. 2009

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Plants contain several genes encoding thioredoxins (Trxs), small proteins involved in the regulation of the activity of many enzymes through dithiol-disulfide exchange. In addition to chloroplastic and cytoplasmic Trx systems, plant mitochondria contain a reduced nicotinamide adenine dinucleotide phosphate-dependent Trx reductase and a specific Trx o, and to date, there have been no reports of a gene encoding a plant nuclear Trx. We report here the presence in pea (Pisum sativum) mitochondria and nuclei of a Trx isoform (PsTrxo1) that seems to belong to the Trx o group, although it differs from this Trx type by its absence of introns in the genomic sequence. Western-blot analysis with isolated mitochondria and nuclei, immunogold labeling, and green fluorescent protein fusion constructs all indicated that PsTrxo1 is present in both cell compartments. Moreover, the identification by tandem mass spectrometry of the native mitochondrial Trx after gel filtration using the fast-protein liquid chromatography system of highly purified mitochondria and the in vitro uptake assay into isolated mitochondria also corroborated a mitochondrial location for this protein. The recombinant PsTrxo1 protein has been shown to be reduced more effectively by the Saccharomyces cerevisiae mitochondrial Trx reductase Trr2 than by the wheat (Triticum aestivum) cytoplasmic reduced nicotinamide adenine dinucleotide phosphate-dependent Trx reductase. PsTrxo1 was able to activate alternative oxidase, and it was shown to interact with a number of mitochondrial proteins, including peroxiredoxin and enzymes mainly involved in the photorespiratory process.

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Unique scanning capabilities of a new hybrid linear ion trap mass spectrometer (Q TRAP) used for high sensitivity proteomics applications

Cited by 138 publications

References 8 publications

Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry

Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry

Snake Venomics of the Lancehead Pitviper Bothrops asper: Geographic, Individual, and Ontogenetic Variations

Mitochondrial and Nuclear Localization of a Novel Pea Thioredoxin: Identification of Its Mitochondrial Target Proteins

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