Applied Biosystems

There are many protocols and different types of platforms available, e.g. GeneChips from Affymetrix, Illumina Bead Arrays, Arrays from Agilent, Applied Biosystems, GE Healthcare, customized spotted cDNA microarrays etc. the basic procedure for a large-scale measurement of gene expression involves the preparation of total or mRNA from the biological sample(s) under investigation (e.g. candidate tissue) and the hybridization of copied labelled RNA or cDNA to the DNA elements on the array surface (Fig. 1). 

Figure 4.6 Schematic of a thermospray LC-MS interface. From applications literature published by Vestec (Applied Biosystems), Foster City, CA, and reproduced with permission.

Applied Biosystems, Foster City, CA, http //www.appliedbiosystems.com. 

MIT Lincoln Laboratory Midwest Research Institute Applied Biosystems Navy Research Lab Cepheid... 

Aclara BioSciences Applied Biosystems BioVigilant Fibertek Innovatek... 

The LCQ and LCQ DECA are products of Thermo Electron Corporation (San Jose, CA) the Q-TOF is a product of Waters (Beverly, MA) the QSTAR, ProQUANT, and ProICAT are products of Applied Biosystems (Foster City, CA) and Spectrum Mill and the MSD TRAP XCT are products of Agilent Technologies (Palo Alto, CA). 

The PCR primers and the fluorogenic probes for the studied targets were designed using the Primer Express Software 1.7 (PE Applied Biosystem, Foster City, CA, USA). To normalize the quantitative data, specific probes for the TATA-bind-ing protein mRNA were used as an internal control. 

Applied Biosystems Q q TOF analyser equipped with a nanoelectrospray ion source for nano ESI MS and nano ESI MS/ MS analysis... 

The following protocol describes the use of an acid-cleavable ICAT reagent, currently available from Applied Biosystems. This is not meant to be a detailed method describing every aspect concerning the use of mass spectrometry, but only to describe the modification reaction of the ICAT compound with proteins. 

Dissolve one vial of heavy isotope, cleavable ICAT reagent (Applied Biosystems) in 20 pi acetonitrile (use a fume hood for handling solvents). Dissolve a second vial containing the normal isotope ICAT compound in 20 pi acetonitrile. Vortex mix each vial to dissolve. 

Figure 7.6 Photograph of a modern protein sequencing system. Photograph courtesy of Perkin Elmer Applied Biosystems Ltd, UK...

Mass spectrometric analysis was performed with a hybrid triple quadrupole/ linear ion trap Applied Biosystem MSD Sciex 4000QTRAP (Applied Biosystems, Foster City, USA) instrument equipped with a Turbospray ESI interface. For target quantitative analyses, data acquisition was performed in SRM, recording the transitions between the precursor ion and the two most abundant fragment ions. The developed instrumental method display excellent LODs in SRM mode between 0.5 and 1.2 pg (Table 2). 

MS condition — An API 4000 equipped with a Turbo Ionspray from Applied Biosystems was used as the mass detector and [M + NH4]+ was chosen as the precursor ion for multiple reaction monitoring (MRM) due to the lack of protonated molecular ions. A transition of m/z 434.4 — 273.2 was chosen for paricalcitol and m/z 450.5 —> 379.2 was selected for the structure analog internal standard. 

MS condition — An API 3000 equipped with a Turbo Ionspray from Applied Biosystems was used as the mass detector. [M - II was chosen as the precursor ion for multiple reaction monitoring... 

FIGU RE 5.1 Ion path for 4000 QTRAP, showing linear ion trap design in Q3. (Courtesy of Applied Biosystems, Foster City, California.)... 

One of the best tools for metabolite profiling is the hybrid QTRAP MS/MS system (Applied Biosystems).119-121 While the hybrid QTRAP MS/MS was initially considered a premier tool for metabolite identification, it has more recently been seen as a tool for quantitation and metabolite profiling. Li et al.122 described the use of a hybrid QTRAP MS/MS system for discovery PK assays plus metabolite profiling in the same analytical procedure. Because QTRAP MS/MS may be used as a triple quadrupole MS system, it can be used as part of a quantitative HPLC/MS/MS system. Because QTRAP MS/MS also has linear ion trap capabilities, it can be used for metabolite screening and characterization—essentially it combines the capabilities of a triple quadrupole mass spectrometer and a linear ion trap mass spectrometer. 

Chovan et al.30 described a system that integrates different components of bioanalysis including automatic in vitro incubation, automatic method development (mainly SRM transitions for LC/MS/ MS analysis), and a generic LC method for sample analysis to minimize human intervention and streamline information flow. Automaton software (Applied Biosystems) was used for automatic MS method development. Flow injection was used instead of a HPLC column to decrease run time to 0.8 min per injection. Two injections were performed. The first was performed to locate the precursor ion and optimal declustering potential (DP). The second injection was performed to locate the product ion and optimal collision energy (CE). 

Koal et al. (2004) measured four immunosuppressants (cyclosporine A, tacrolimus, sirolimus, and everolimus) in whole blood samples from transplant recipients. The samples were treated first with a protein precipitation step. The supernatant was extracted with a Poros Rl/20 perfusion column (30 x 2.1 mm, 20 tm, Applied Biosystems, Darmstadt, Germany) online. A Luna phenyl hexyl column (2 x 50 mm, Phenomenex, Schaffenburg, Germany) was used for separation. The total run time was 2.5 min. The lower limit of quantitation was 10 ng/mL for cyclosporine A and 1 ng/mL for the other three analytes. 

The first commercial CE instruments were introduced in 1988 by Applied Biosystems (Foster City, CA) and Beckman Coulter (Fullerton, CA). The main challenge during these days was to find out how to overcome poor reproducibility and improve separation efficiency. In the early 1990s, many instrument-building companies introduced CE systems (e.g. Isco (Lincoln, NE), Bio-Rad (Hercules, CA), Waters (Milford, MA), Applied Biosystems, ThermoQuest (Santa Fe, NM) and Dionex (Sunnyvale, CA)), but at the end of the decade only Beckman Coulter... 

Technologies Applied Biosystems Prism 310 Genetic Analyzer... 

Figure 10.3 Whole-mass analysis of a monoclonal antibody. (A) Direct infusion of the antibody generates an envelope of high m/z ions ranging from 2000 to 3500. Deconvolution of the ion current signal gives the mass of the complete native molecule (147, 100.97 Da) and resolves some heterogeneity linked to the A-glycan structures. The major forms are consistent with molecules carrying biantennary structures capped with 0, 1, or 2 hexose (G = galactose) residues. (Data generated on an ESI-Q-Star instrument, Sciex-Applied Biosystems.)...

Note Unfortunately, establishing patents and trademarks has caused redundant names for almost the same thing Time Lag Focusing (TLF, Micromass) Delayed Extraction (DE, Applied Biosystems) Pulsed Ion Extraction (PIE, Bru-ker Daltonik). 

LITs capable of scanning, axial or radial excitation of ions, and precursor ion selection for MS/MS experiments [118,134-136] have lately been incorporated in commercial mass spectrometers (Fig. 4.39). The replacement of Q3 in a QqQ instrument with a scanning LIT, for example, enhances its sensitivity and offers new modes of operation (Applied Biosystems Q-Trap). Introduction of a scanning LIT [118,135] as MSI in front of an FT-ICR instrument (Thermo Electron LTQ-FT) shields the ultrahigh vacuum of the FT-ICR from collision gas and decomposition products in order to operate under optimum conditions. In addition, the LIT accumulates and eventually mass-selects ions for the next cycle while the ICR cell is still busy with the previous ion package. 

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