{"id":39,"date":"2007-04-24T15:34:23","date_gmt":"2007-04-24T19:34:23","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/proteomics-core-laboratory\/instrumentation-in-the-core-laboratory\/"},"modified":"2019-06-28T12:46:15","modified_gmt":"2019-06-28T16:46:15","slug":"instrumentation-in-the-core-laboratory","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/proteomics-core-laboratory\/instrumentation-in-the-core-laboratory\/","title":{"rendered":"Instrumentation in the Core Laboratory"},"content":{"rendered":"<div><img loading=\"lazy\" src=\"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/files\/Images\/LANdiagram\/LANdiagram.jpg\" width=\"341\" height=\"265\" alt=\"LAN diagram\" class=\"aligncenter\" \/><\/p>\n<ul>\n<li>Waters\/Micromass Electrospray Ionization (ESI) Quadrupole Time-of-Flight (qTOF) orthogonal mass spectrometer, equipped with Nano-lockspray and a Z-spray interface, mated with a dedicated Waters nanoACQUITY ultra performance liquid chromatography system for subsequent detailed proteomics analysis by capillary and nano LC-MS\/MS.<\/li>\n<li>An additional Waters nanoACQUITY ultra performance liquid chromatography system for high-resolution separations for columns ranging from 320 to 75 microns, plus an ACQUITY UPLC core for off-line protein and peptide fractionation.<\/li>\n<li>High-throughput Matrix-Assisted Laser Desorption Ionization (MALDI) cryogenic Fourier Transform Mass Spectrometry (cryoFTMS) system, currently being constructed in-house. FTMS technology, the basis of building such a cryoFTMS instrument, has been shown to be useful for detailed protein analyses and capable of detecting the relative abundance and complete coverage of oxidative modifications.<\/li>\n<\/ul>\n<\/div>\n<p>&nbsp;<\/p>\n<ul>\n<li>Bruker Reflex IV MALDI TOF instrument for preliminary high throughput mass spectrometry analysis of samples of peptides and proteins derived from biological samples.<\/li>\n<li>Beckman Coulter Proteome Lab (PF2D) for two-dimensional protein fractionation based on pI and size of protein. This system affords automated protein fractionation in the liquid phase and yields samples ready for characterization directly by MS. Targeted sample analysis may be performed using the Core&#8217;s built-in software suite (see below).<\/li>\n<li>Beckman Coulter ProteomeLab IgY, a plasma\/serum proteome partitioning system, for depletion of abundant proteins from plasma and serum samples prior to 2D-gel electrophoresis by PF2D separation.<\/li>\n<li>A high performance computer cluster (above, <a href=\"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/files\/PDFs\/LANdiagram.pdf\">LANdiagram<\/a>) for high-intensity bioinformatics processing, consisting of two 4-way data processing computers and a redundant data storage array server. The 4-way data processors each utilize four AMD Opteron 880 processors (2.4 GHz), 32 GB RAM, dual gigabit data ports, with 2 TB of local disk space in a RAID 5 single parity configuration and a separate 400 GB RAID 1 mirrored array for the operating system and applications. The redundant data storage array server utilizes two AMD Opteron 2216 processors (2.4 GHz), 4 GB RAM, dual gigabit data ports, with 4 TB of local disk space in a RAID 6 double parity configuration and a separate 40 GB RAID 1 mirrored array for its operating system.<\/li>\n<li>Global computer network comprising 17 workstations for secure online and offline data processing and analysis. The workstations are located in laboratories and in a dedicated data processing room, linked by the network described above<\/li>\n<li>A suite of Core technology advancements that facilitate proteomics studies include new analytical tools: High Performance Liquid Chromatography-Mass Spectrometry (HPLC-MS) workflow, based on multi-dimensional protein chromatography coupled with MS; a software tool that uses nominal and exact mass databases for MS analyses of post-translational modifications; and another that is a stand alone graphical user interface-based software shell for automated MS data file conversion and database searches. Core researchers use an advanced statistical approach for mapping sequence variants and post-translational modifications and have developed software to automate a proteomics platform to facilitate pattern-based identification of important protein structural changes in biological samples by MALDI TOF-MS and nanoLiquid Chromatography-Electrospray Ionization-MS\/MS.<\/li>\n<li>A Mascot Server (Matrix Science) and a ProteinLynx Global Server (Waters Corp.) are used for data analyses. Data are searched against custom annotated and programmed protein databases using advanced search algorithms.<\/li>\n<li><a href=\"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/cardiovascular-proteomics-archive-2003-2010\/bioinformatics\/\">Bioinformatics<\/a> researchers working with the Core Lab have built a web-bsed protein identification server. BU-PID is operational, accepting data from CPC projects and from commercial databases, and being fine-tuned.<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<h3>Instrumentation, BUSM Mass Spectrometry Resource<\/h3>\n<p>The <a href=\"http:\/\/www.bumc.bu.edu\/msr\/\">mass spectrometry laboratory<\/a> is an NIH-NCRR Research Resource. Major equipment includes:<\/p>\n<ul>\n<li>Micromass Quattro II ESI triple quadrupole HPLC-tandem MS system with Z-spray source;<\/li>\n<li>Tandem ESI-MS analyses can also be performed with the Bruker esquire3000 ESI-quadrupole ion trap (QIT);<\/li>\n<li>ThermoQuest GCQplus gas chromatograph\/QIT MS system, equipped for electron ionization and chemical ionization;<\/li>\n<li>Finnigan-MAT Vision 2000;<\/li>\n<li>Bruker Reflex IV MALDI reflectron time-of-flight MS system;<\/li>\n<li>Ultraviolet (nitrogen, 337 nm) laser on the Finnegan and Bruker systems;<\/li>\n<li>Infrared (Er-YAG, 2.94 \u00b5m) laser on the Finnegan and Bruker systems;<\/li>\n<li>IonSpec Ultima Fourier transform ion cyclotron resonance mass spectrometer, with a 7-Tesla active-shielded magnet, equipped for both ESI and IR\/UV MALDI. The mass spectrometer has very high resolution, several ion dissociation modes, and capability for multistage tandem MS. A second 7-Tesla active-shielded magnet is now being installed, so that dedicated systems will be available for both ESI and MALDI. The isntrument&#8217;s MALDI ion source has been modified for high-pressure MALDI and for accommodation of a large (4\u201d x 4\u201d) X-Y stage. The ESI source has a quadrupole ion trap as an intermediate stage for ion separation and accumulation;<\/li>\n<li>Two Applied Biosystems Q-STAR Pulsar&#x2122; MALDI and ESI-Q-TOF mass spectrometers for dedicated ESI and MALDI systems. The ESI Q-Star system works well with capillary HPLC and will be equipped for CE-MS. These instruments are designed for analysis of the intact proteins and glycoproteins and the oligosaccharides, peptides and glycopeptides that can be obtained by enzymic digestion;<\/li>\n<li>Digilab Multimode Atomic Force Microscope, installed in June 2003.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Waters\/Micromass Electrospray Ionization (ESI) Quadrupole Time-of-Flight (qTOF) orthogonal mass spectrometer, equipped with Nano-lockspray and a Z-spray interface, mated with a dedicated Waters nanoACQUITY ultra performance liquid chromatography system for subsequent detailed proteomics analysis by capillary and nano LC-MS\/MS. An additional Waters nanoACQUITY ultra performance liquid chromatography system for high-resolution separations for columns ranging from 320 [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":35,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/39"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/comments?post=39"}],"version-history":[{"count":9,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/39\/revisions"}],"predecessor-version":[{"id":2584,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/39\/revisions\/2584"}],"up":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/35"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/media?parent=39"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}