Resume

• 2017

  Medical College of Wisconsin

• 2011

  Medical College of Wisconsin

• 1986

  Medical College of Wisconsin

  Medical College of Wisconsin

  Director Biotechnology and Bioengineering Center

  Medical College of Wisconsin

  Syracuse University

  Bachelor of Science (BS)

  Electrical and Electronics Engineering

  Johns Hopkins School of Medicine

  Doctor of Philosophy (Ph.D.)

  Bioengineering and Biomedical Engineering

• 1985

  Johns Hopkins University

  Johns Hopkins University

• Genomics

  Data Analysis

  Microsoft Office

  Confocal Microscopy

  Genetics

  Lifesciences

  Mass Spectrometry

  Research

  PCR

  Cell

  Western Blotting

  Computational Biology

  Biotechnology

  Clinical Research

  Microscopy

  Scientific Writing

  Biochemistry

  Molecular Biology

  Cell Culture

  Statistics

  Physiological genomics - where are we now?

  the first words of a new journal

  published in 1999

  promised us that we were “. . . in the midst of a revolution in biology and medicine: an information revolution

  Physiological genomics - where are we now?

  Memory formation requires de novo protein synthesis

  and memory disorders may result from misregulated synthesis of critical proteins that remain largely unidentified. Plasma membrane ion channels and receptors are likely candidates given their role in regulating neuron excitability

  a candidate memory mechanism. Here we conduct targeted molecular monitoring and quantitation of hippocampal plasma membrane proteins from mice with intact or impaired contextual fear memory to identify putative candidates. Here we report contextual fear memory deficits correspond to increased Trpc3 gene and protein expression

  and demonstrate TRPC3 regulates hippocampal neuron excitability associated with memory function. These data provide a mechanistic explanation for enhanced contextual fear memory reported herein following knockdown of TRPC3 in hippocampus. Collectively

  TRPC3 modulates memory and may be a feasible target to enhance memory and treat memory disorders.

  TRPC3 channels critically regulate hippocampal excitability and contextual fear memory.

  Eric Exner

  JD Bukowy

  OBJECTIVE: \n\nDiabetes Mellitus (DM) has reached epidemic levels globally. A contributing factor to the development of DM is high blood glucose (hyperglycemia). One complication associated with DM is a decreased angiogenesis. The Matrigel tube formation assay (TFA) is the most widely utilized in vitro assay designed to assess angiogenic factors and conditions. In spite of the widespread use of Matrigel TFAs

  quantification is labor-intensive and subjective

  often limiting experiential design and interpretation of results. This study describes the development and validation of an open source software tool for high throughput

  morphometric analysis of TFA images and the validation of an in vitro hyperglycemic model of DM.\n\nAPPROACH AND RESULTS: \n\nEndothelial cells mimic angiogenesis when placed onto a Matrigel coated surface by forming tube-like structures. The goal of this study was to develop an open-source software algorithm requiring minimal user input (Pipeline v1.3) to automatically quantify tubular metrics from TFA images. Using Pipeline

  the ability of endothelial cells to form tubes was assessed after culture in normal or high glucose for 1 or 2 weeks. A significant decrease in the total tube length and number of branch points was found when comparing groups treated with high glucose for 2 weeks versus normal glucose or 1 week of high glucose.\n\nCONCLUSIONS: \n\nUsing Pipeline

  it was determined that hyperglycemia inhibits formation of endothelial tubes in vitro. Analysis using Pipeline was more accurate and significantly faster than manual analysis. The Pipeline algorithm was shown to have additional applications

  such as detection of retinal vasculature\n

  Automated quantification reveals hyperglycemia inhibits endothelial angiogenic function.

  howard jacob

  mingyu liang

  Jamie Karcher

  daniella didier

  pengyuan liu

  anthony prisco

  tim stodola

  Endothelial progenitor cells (EPCs) promote angiogenesis

  and clinical trials suggest autologous EPC-based therapy may be effective in treatment of vascular diseases. Albeit promising

  variability in the efficacy of EPCs associated with underlying disease states has hindered the realization of EPC-based therapy. Here we first identify and characterize EPC dysfunction in a rodent model of vascular disease (SS/Mcwi rat) that exhibits impaired angiogenesis. To identify molecular candidates that mediate the angiogenic potential of these cells

  we performed a broad analysis of cell surface protein expression using chemical labeling combined with mass spectrometry. Analysis revealed EPCs derived from SS/Mcwi rats express significantly more type 2 low-affinity immunoglobulin Fc-gamma (FCGR2) and natural killer 2B4 (CD244) receptors compared with controls. Genome-wide sequencing (RNA-seq) and qt-PCR confirmed isoforms of CD244 and FCGR2a transcripts were increased in SS/Mcwi EPCs. EPCs with elevated expression of FCGR2a and CD244 receptors are predicted to increase the probability of SS/Mcwi EPCs being targeted for death

  providing a mechanistic explanation for their reduced angiogenic efficacy in vivo. Pathway analysis supported this contention

  as \"key\" molecules annotated to cell death paths were differentially expressed in the SS/Mcwi EPCs. We speculate that screening and neutralization of cell surface proteins that \"tag\" and impair EPC function may provide an alternative approach to utilizing incompetent EPCs in greater numbers

  as circulating EPCs are depleted in patients with vascular disease. Overall

  novel methods to identify putative targets for repair of EPCs using discovery-based technologies will likely provide a major advance in the field of regenerative medicine.

  Targeting the endothelial progenitor cell surface proteome to identify novel mechanisms that mediate angiogenic efficacy in a rodent model of vascular disease

  Howard J. Jacob

  Mingyu Liang

  Daniela N. Didier

  Pengyuan Y. Liu

  Timothy J. Stodola

  Anthony Prisco

  Brian Hoffmann

  Endothelial progenitor cells (EPCs) promote angiogenesis

  and clinical trials suggest autologous EPC based therapy may be effective in treatment of vascular diseases. Albeit promising

  variability in the efficacy of EPCs associated with underlying disease states has hindered the realization of EPC-based therapy. Here we first identify and characterize EPC dysfunction in a rodent model of vascular disease (SS/Mcwi rat) that exhibits impaired angiogenesis. To identify molecular candidates that mediate the angiogenic potential of these cells

  we performed a broad analysis of cell surface protein expression using chemical labeling combined with mass spectrometry. Analysis revealed EPCs derived from SS/Mcwi rats express significantly more type 2 low-affinity immunoglobulin Fc-gamma (FCGR2) and Natural Killer 2B4 (CD244) receptors compared to controls. Genome-wide sequencing (RNA-seq) and qt-PCR confirmed isoforms of CD244 and FCGR2a transcripts were increased in SS/Mcwi EPCs. EPCs with elevated expression of FCGR2a and CD244 receptors are predicted to increase the probability of SS/Mcwi EPCs being targeted for death

  providing a mechanistic explanation for their reduced angiogenic efficacy in vivo. Pathway analysis supported this contention

  as ‘key’ molecules annotated to cell death paths were differentially expressed in the SS/Mcwi EPCs. We speculate that screening and neutralization of cell surface proteins that ‘tag’ and impair EPC function may provide an alternative approach to utilizing incompetent EPCs in greater numbers

  as circulating EPCs are depleted in patients with vascular disease. Overall

  novel methods to identify putative targets for repair of EPCs using discovery-based technologies will likely provide a major advance in the field of regenerative medicine.

  Targeting the endothelial progenitor cell surface proteome to identify novel mechanisms that mediateangiogenic efficacy in a rodent model of vascular disease

  Autologous bone marrow-derived mononuclear cell (BM-MNC) transplantation is a potential therapy for inducing revascularization in ischemic tissues providing the underlying disease process had not negatively affected BM-MNC function. Previously

  we have shown that skeletal muscle angiogenesis induced by electrical stimulation is impaired by a high-salt diet (HSD; 4% NaCl) in Sprague-Dawley (SD) rats. In this study we tested the hypothesis that BM-MNC angiogenic function is impaired by an elevated dietary sodium intake. Following 1 wk on HSD

  either vehicle or BM-MNCs derived from SD donor rats on HSD or normal salt diet (NSD; 0.4% NaCl) were injected into male SD rats undergoing hindlimb stimulation. Administration of BM-MNCs (intramuscular or intravenous) from NSD donors

  but not HSD donors

  restored the angiogenic response in HSD recipients. Angiotensin II (3 ng · kg(-1) · min(-1)) infusion of HSD donor rats restored angiogenic capacity of BM-MNCs

  and treatment of NSD donor rats with losartan

  an angiotensin II receptor-1 antagonist

  inhibited BM-MNC angiogenic competency. HSD BM-MNCs and NSD losartan BM-MNCs exhibited increased apoptosis in vitro following an acute 6-h hypoxic stimulus. HSD BM-MNCs also had increased apoptosis following injection into skeletal muscle. This study suggests that BM-MNC transplantation can restore skeletal muscle angiogenesis and that HSD impairs the angiogenic competency of BM-MNCs due to suppression of the renin-angiotensin system causing increased apoptosis.

  Bone marrow mononuclear cell angiogenic competency is suppressed by a high-salt diet.

  Ding X

  Liang M

  Kriegel AJ

  Liu S

  Cai J

  Rao S

  Liu H

  Yu X

  PLoS One. 2013 May 9;8(5):e62703. doi: 10.1371/journal.pone.0062703. Print 2013.

  Mesenchymal stem cell (MSC) administration is known to enhance the recovery of the kidney following injury. Here we tested the potential of hypoxic-preconditioned-MSC transplantation to enhance the efficacy of cell therapy on acute kidney injury (AKI) by improving MSC migration to the injured kidney. Cobalt was used as hypoxia mimetic preconditioning (HMP). MSC were subjected to HMP through 24 h culture in 200 µmol/L cobalt. Compared to normoxia cultured MSC (NP-MSC)

  HMP significantly increased the expression of HIF-1α and CXCR4 in MSC and enhanced the migration of MSC in vitro. This effect was lost when MSC were treated with siRNA targeting HIF-1α or CXCR4 antagonist. SPIO labeled MSC were administered to rats with I/R injury followed immediately by magnetic resonance imaging. Imaging clearly showed that HMP-MSC exhibited greater migration and a longer retention time in the ischemic kidney than NP-MSC. Histological evaluation showed more HMP-MSC in the glomerular capillaries of ischemic kidneys than in the kidneys receiving NP-MSC. Occasional tubules showed iron labeling in the HMP group

  while no tubules had iron labeling in NP group

  indicating the possibility of tubular transdifferentiation after HMP. These results were also confirmed by fluorescence microscopy study using CM-DiI labeling. The increased recruitment of HMP-MSC was associated with reduced kidney injury and enhanced functional recovery. This effect was also related to the increased paracrine action by HMP-MSC. Thus we suggest that by enhancing MSC migration and prolonging kidney retention

  hypoxic preconditioning of MSC may be a useful approach for developing AKI cell therapy.

  Hypoxic preconditioning with cobalt of bone marrow mesenchymal stem cells improves cell migration and enhances therapy for treatment of ischemic acute kidney injury

  Morse MM

  Amaral SL

  Angiogenesis induced by electrical stimulation is mediated by angiotensin II and VEGF.

  Jacob HJ

  North PE

  Geurts AM

  Lazar J

  Didier DN

  Hoffman M

  The renin-angiotensin system plays an important role in the control of blood pressure (BP) and renal function. To illuminate the importance of renin in the context of a disease background in vivo

  we used zinc-finger nucleases (ZFNs) designed to target the renin gene and create a renin knockout in the SS/JrHsdMcwi (SS) rat. ZFN against renin caused a 10-bp deletion in exon 5

  resulting in a frameshift mutation. Plasma renin activity was undetectable in the Ren-/- rat

  and renin protein was absent from the juxtaglomerular cells in the kidney. Body weight was lower in the Ren-/- rats (than in the Ren+/- or wild-type littermates)

  and conscious BP on low-salt diet (0.4% NaCl) was 58 ± 2 mm Hg in the Ren-/- male rats versus 117 mm Hg in the Ren+/- littermates

  a reduction of almost 50 mm Hg. Blood urea nitrogen (BUN) and plasma creatinine levels were elevated in the Ren-/- strain (BUN 112 ± 7 versus 23 ± 2 mg/dL and creatinine 0.53 ± 0.02 versus 0.26 ± 0.02 mg/dL)

  and kidney morphology was abnormal with a rudimentary inner renal medulla

  cortical interstitial fibrosis

  thickening of arterial walls

  and abnormally shaped glomeruli. The development of the first rat knockout in the renin-angiotensin system demonstrates the efficacy of the ZFN technology for creating knockout rats for cardiovascular disease on any genetic background and emphasizes the role of renin in BP regulation and kidney function even in the low-renin SS rat.

  Creation and characterization of a renin knockout rat.

  MOTIVATION: \n\nRNA-Seq (also called whole-transcriptome sequencing) is an emerging technology that uses the capabilities of next-generation sequencing to detect and quantify entire transcripts. One of its important applications is the improvement of existing genome annotations. RNA-Seq provides rapid

  comprehensive and cost-effective tools for the discovery of novel genes and transcripts compared with expressed sequence tag (EST)

  which is instrumental in gene discovery and gene sequence determination. The rat is widely used as a laboratory disease model

  but has a less well-annotated genome as compared with humans and mice. In this study

  we incorporated deep RNA-Seq data from three rat tissues-bone marrow

  brain and kidney-with EST data to improve the annotation of the rat genome.\n\nRESULTS: \n\nOur analysis identified 32 197 transcripts

  including 13 461 known transcripts

  13 934 novel isoforms and 4802 new genes

  which almost doubled the numbers of transcripts in the current public rat genome database (rn5). Comparisons of our predicted protein-coding gene sets with those in public datasets suggest that RNA-Seq significantly improves genome annotation and identifies novel genes and isoforms in the rat. Importantly

  the large majority of novel genes and isoforms are supported by direct evidence of RNA-Seq experiments. These predicted genes were integrated into the Rat Genome Database (RGD) and can serve as an important resource for functional studies in the research community.\n\nAVAILABILITY AND IMPLEMENTATION: \n\nThe predicted genes are available at http://rgd.mcw.edu.\n

  Improved rat genome gene prediction by integration of ESTs with RNA-Seq information.

  A major challenge in the field of high-throughput proteomics is the conversion of the large volume of experimental data that is generated into biological knowledge. Typically

  proteomics experiments involve the combination and comparison of multiple data sets and the analysis and annotation of these combined results. Although there are some commercial applications that provide some of these functions

  there is a need for a free

  open source

  multifunction tool for advanced proteomics data analysis. We have developed the Visualize program that provides users with the abilities to visualize

  analyze

  and annotate proteomics data; combine data from multiple runs

  and quantitate differences between individual runs and combined data sets. Visualize is licensed under GNU GPL and can be downloaded from http://proteomics.mcw.edu/visualize. It is available as compiled client-based executable files for both Windows and Mac OS X platforms as well as PERL source code.

  Visualize: a free and open source multifunction tool for proteomics data analysis

  Jacob HJ

  Xiao B.

  Flister MJ

  Hoffman MJ

  Hypertension. 2013 Jul 1. [Epub ahead of print]

  3.7-Mb region of rat chromosome 13 (45.2-49.0 Mb) affects blood pressure (BP) in females only

  indicating the presence of sex-specific BP loci in close proximity to the Renin locus. In the present study

  we used a series of Dahl salt-sensitive/Mcwi-13 Brown Norway congenic rat strains to further resolve BP loci within this region. We identified 3 BP loci affecting female rats only

  of which the 2 smaller loci (line9BP3 and line9BP4) were functionally characterized by sequence and expression analysis. Compared with SS (SS/HsdMcwiCrl)

  the presence of a 591-kb region of BN (BN/NHsdMcwi) chromosome 13 (line9BP3) significantly lowered BP by 21 mm Hg on an 8% NaCl diet (153±7 versus 174±5 mm Hg; P<0.001). Unexpectedly

  the addition of 23 kb of Brown Norway chromosome 13 (line9BP4) completely erased the female-specific BP protection on 8% NaCl diet

  suggesting that BN hypertensive allele(s) reside in this region. The congenic interval of the protective line 9F strain contains 3 genes (Optc

  Prelp

  and Fmod)

  and the hypertensive line 9E contains 1 additional gene (Btg2). Sequence analysis of the 2 BP loci revealed a total of 282 intergenic variants

  with no coding variants. Analysis of gene expression by quantitative real-time polymerase chain reaction revealed strain- and sex-specific differences in Prelp

  Fmod

  and Btg2 expression

  implicating these as novel candidate genes for female-specific hypertension.

  Female-Specific Hypertension Loci on Rat Chromosome 13

  Distribution of angiotensin II receptor expression in the microcirculation of striated muscle.

  Rebro KJ

  Ward BD

  Schmainda KM

  Arvind P. Pathak

  MR-derived cerebral blood volume maps: issues regarding histological validation and assessment of tumor angiogenesis.

  Endothelial progenitor cells (EPCs) are a rare population of cells that participate in angiogenesis. To effectively use EPCs for regenerative therapy

  the mechanisms by which they participate in tissue repair must be elucidated. This study focused on the process by which activated EPCs bind to a target tissue. It has been demonstrated that EPCs can bind to endothelial cells (ECs) through the tumore necrosis factor-α (TNF-α)-regulated vascular cell adhesion molecule 1/very-late antigen 4 (VLA4) interaction. VLA4 can bind in a high or low affinity state

  a process that is difficult to experimentally isolate from bond expression upregulation. To separate these processes

  a new parallel plate flow chamber was built

  a detachment assay was developed

  and a mathematical model was created that was designed to analyze the detachment assay results. The mathematical model was developed to predict the relative expression of EPC/EC bonds made for a given bond affinity distribution. EPCs treated with TNF-α/vehicle were allowed to bind to TNF-α/vehicle-treated ECs in vitro. Bound cells were subjected to laminar flow

  and the cellular adherence was quantified as a function of shear stress. Experimental data were fit to the mathematical model using changes in bond expression or affinity as the only free parameter. It was found that TNF-α treatment of ECs increased adhesion through bond upregulation

  whereas TNF-α treatment of EPCs increased adhesion by increasing bond affinity. These data suggest that injured tissue could potentially increase recruitment of EPCs for tissue regeneration via the secretion of TNF-α.

  TNF-α increases endothelial progenitor cell adhesion to the endothelium by increasing bond expression and affinity.

  Jordan R. Wagnera

  Bone marrow-derived endothelial progenitor cells (BM-EPCs) are stimulated by vascular endothelial growth factor-A (VEGF-A) and other potent proangiogenic factors. During angiogenesis

  an increase in VEGF-A expression stimulates BM-EPCs to enhance endothelial tube formation and contribute to an increase in microvessel density. Hypoxia is known to produce an enhanced angiogenic response and heightened levels of VEGF-A have been seen in oxygen deprived epithelial and endothelial cells

  yet the pathways for VEGF-A signaling in BM-EPCs have not been described. This study explores the influence of hypoxia on VEGF-A signaling in rat BM-EPCs utilizing a novel proteomic strategy to directly identify interacting downstream components of the combined VEGF receptor(s) signaling pathways

  gene expression analysis

  and functional phenotyping. VEGF-A signaling network analysis following liquid chromatographic separation and tandem mass spectrometry revealed proteins related to inositol/calcium signaling

  nitric oxide signaling

  cell survival

  cell migration

  and inflammatory responses. Alterations in BM-EPC expression of common angiogenic genes and tube formation in response to VEGF-A during hypoxia were measured and combined with the proteomic analysis to enhance and support the signaling pathways detected. BM-EPC tube formation assays in response to VEGF-A exhibited little tube formation; however

  a cell projection/migratory phenotype supported the signaling data. Additionally

  a novel assay measuring BM-EPC incorporation into preformed endothelial cell tubes indicated a significant increase of incorporated BM-EPCs after pretreatment with VEGF-A during hypoxia. This study verifies known VEGF-A pathway components and reveals several unidentified mechanisms of VEGF-A signaling in BM-EPCs during hypoxia that may be important for migration to sites of vascular regeneration.

  Vascular endothelial growth factor-A signaling in bone marrow-derived endothelial progenitor cells exposed to hypoxic stress.

  EL-Mansy MF

  Hoffmann BR

  J Med Chem. 2012 Oct 11;55(19):8260-71. doi: 10.1021/jm301204r. Epub 2012 Sep 28.

  Drugs exert desired and undesired effects based on their binding interactions with protein target(s) and off-target(s)

  providing evidence for drug efficacy and toxicity. Pioglitazone and rosiglitazone possess a common functional core

  glitazone

  which is considered a privileged scaffold upon which to build a drug selective for a given target--in this case

  PPARγ. Herein

  we report a retrospective analysis of two variants of the glitazone scaffold

  pioglitazone and rosiglitazone

  in an effort to identify off-target binding events in the rat heart to explain recently reported cardiovascular risk associated with these drugs. Our results suggest that glitazone has affinity for dehydrogenases

  consistent with known binding preferences for related rhodanine cores. Both drugs bound ion channels and modulators

  with implications in congestive heart failure

  arrhythmia

  and peripheral edema. Additional proteins involved in glucose homeostasis

  synaptic transduction

  and mitochondrial energy production were detected and potentially contribute to drug efficacy and cardiotoxicity

  Chemical proteomics-based analysis of off-target binding profiles for rosiglitazone and pioglitazone: clues for assessing potential for cardiotoxicity.

  Lazar J

  Li P

  Didier DN

  Kriegel AJ

  Physiological Genomics

  The SS-16(BN)/Mcwi consomic rat was produced by the introgression of chromosome 16 from the Brown Norway (BN/NHsdMcwi) rat onto the genetic background of the Dahl salt-sensitive (SS/Mcwi) rat by marker-assisted breeding. Microarray analysis of SS-16(BN)/Mcwi and SS/Mcwi left ventricle tissue and subsequent protein pathway analysis were used to identify alterations in gene expression in signaling pathways involved with the observed cardioprotection on the SS background. The SS-16(BN)/Mcwi rats exhibited much higher mRNA levels of expression of transcription factor JunD

  a gene found on chromosome 16. Additionally

  high levels of differential gene expression were found in pathways involved with angiogenesis

  oxidative stress

  and growth factor signaling. We tested the physiological relevance of these pathways by experimentally determining the responsiveness of neonatal cardiomyocytes to factors from identified pathways and found that cells isolated from SS-16(BN)/Mcwi rats had a greater growth response to epidermal growth factor and endothelin-1 than those from parental SS/Mcwi. We also demonstrate that the SS-16(BN)/Mcwi is better protected from developing fibrosis with surgically elevated afterload than other normotensive strains

  indicating that gene-gene interactions resulting from BN chromosomal substitution confer specific cardioprotection. When combined with our previous findings

  these data suggest that that SS-16(BN)/Mcwi may have an increased angiogenic potential and better protection from oxidative stress than the parental SS/Mcwi strain. Additionally

  the early transient idiopathic left ventricular hypertrophy in the SS-16(BN)/Mcwi may be related to altered myocyte sensitivity to growth factors.

  Mechanisms of cardioprotection resulting from Brown Norway chromosome 16 substitution in the salt-sensitive Dahl rat.

  Endres B

  stodola TJ

  Didier DN

  Parker SJ

  Physiol Genomics.

  Bone marrow mononuclear cells (BMMNCs) increase capillary density and reduce fibrosis in rodents after myocardial infarction

  resulting in an overall improvement in left ventricular function. Little is known about the effectiveness of BMMNC therapy in hypertensive heart disease. In the current study

  we show that delivery of BMMNCs from hypertension protected SS-13(BN)/MCWi donor rats

  but not BMMNC from hypertension susceptible SS/MCWi donor rats

  resulted in 57.2 and 83.4% reductions in perivascular and interstitial fibrosis

  respectively

  as well as a 60% increase in capillary-to-myocyte count in the left ventricles (LV) of hypertensive SS/MCWi recipients. These histological changes were associated with improvements in LV compliance and relaxation (103 and 46.4% improvements

  respectively). Furthermore

  improved diastolic function in hypertensive SS/MCWi rats receiving SS-13(BN)/MCWi derived BMMNCs was associated with lower clinical indicators of heart failure

  including reductions in end diastolic pressure (65%) and serum brain natriuretic peptide levels (49.9%) with no improvements observed in rats receiving SS/MCWi BMMNCs. SS/MCWi rats had a lower percentage of endothelial progenitor cells in their bone marrow relative to SS-13(BN)/MCWi rats. These results suggest that administration of BMMNCs can prevent or reverse pathological remodeling in hypertensive heart disease

  which contributes to ameliorating diastolic dysfunction and associated symptomology. Furthermore

  the health and hypertension susceptibility of the BMMNC donor are important factors influencing therapeutic efficacy

  possibly via differences in the cellular composition of bone marrow.

  Bone marrow mononuclear cells induce beneficial remodeling and reduce diastolic dysfunction in the left ventricle of hypertensive SS/MCWi rats.

  Simon Twigger

  Andrew Vallejos

  joey Geiger

  One of the major difficulties for many laboratories setting up proteomics programs has been obtaining and maintaining the computational infrastructure required for the analysis of the large flow of proteomics data. We describe a system that combines distributed cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without the investment in computational hardware or software licensing fees. Additionally

  the pricing structure of distributed computing providers

  such as Amazon Web Services

  allows laboratories or even individuals to have large-scale computational resources at their disposal at a very low cost per run. We provide detailed step-by-step instructions on how to implement the virtual proteomics analysis clusters as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases on the Medical College of Wisconsin Proteomics Center Web site (http://proteomics.mcw.edu/vipdac).

  Low cost

  scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms. Journal of proteome research.

  Greene