Conference Program - ABRF 2011 - Association of Biomolecular ...

Poster AbstractsProteomics Core Facility. The data is processed and students examinetheir results and use bioinformatics tools to further understand thebiological implications of the results. The students than present theirfindings, describe specific proteins that showed differential expression.A hypothesis is presented explaining the biological relevance of theprotein expression change along with a plan for testing this hypothesis.This work was sponsored by Grant Number P20 RR16462, from theIDeA Networks of Biomedical Research Excellence (INBRE) Program ofthe National Center for Research Resources (NCRR), a component ofthe National Institutes of Health (NIH).186 Quantitative Western Blotting withAmersham ECL PrimeM. Winkvist, S. Grimsby, K. Söderquist,A. MarcussonGE Healthcare Bio-Sciences AB, Uppsala, SwedenWestern blotting is a well established technique used to study proteinsfrom a wide variety of sources. The technique is used throughout thelife sciences from basic research to medical diagnostic applications.Western Blot is at best considered as semi-quantitative and hencelimited to studies involving large protein differences.Here wedemonstrate the use of a new ECL TM reagent, Amersham TM ECL Primein a number of typical Western Blotting applications. The resultsdemonstrate that, Amersham ECL Prime can be used for detection oflow abundant proteins, that signals are very stable over time and covera broad dynamic range. These features make Amersham ECL Primehighly suitable for accurate quantitative analysis.187 New Approaches to QuantitativeWestern BlottingM. Winkvist, Å. Hagner-McWhirter,K. Söderquist, S. GrimsbyGE Healthcare Bio-Sciences AB, Uppsala, SwedenFluorescent detection in Western blotting offers high sensitivity, broaddynamic range and stability of signals. This makes it highly suitable forquantitative Western blotting. Here we show how fluorescent Westernblotting can be used for simultaneously detection of up to threedifferent proteins on the same blot at the same time and for detectionof proteins of the same molecular weight without stripping and reprobing.We also demonstrate how fluorescent Western blotting with3 layer probing can be used to increase sensitivity and thereby enablesdetection of very low abundant proteins. Finally we demonstrate thatit is possible to compare the total protein amount to the target proteinby using Deep Purple TM protein staining prior to ECLTM Plex TM Westernblotting.188 Rubicon PicoPlex-NGS Kits Availablefor Sequencing Single Cells Using theIllumina Genome AnalyzerJ. Langmore, T. Kurihara, E. Kamberov,J. M’Mwirichia, T. Tesmer, D. OldfieldRubicon Genomics, Ann Arbor, MI, United StatesRubicon Genomics has released its PicoPlex-NGS kits to prepare singlecells for NGS analysis on the Illumina Genome Analyzer. These kitsenable single eukaryotic or prokaryotic cells to be lysed, DNA extractedand amplified, and adapted for paired-end sequencing in a 1-tube,3-hr, 4-step process. Although the read coverage is poor in a single lane,the reproducibility of the reads allows single cells to be compared forSNP and CNV genotype, mutations. The same amplified samples canbe used for PCR and microarray analysis, including genome-wide SNPgenotyping, mutation, and copy number analysis. PRC amplification ortarget enrichment can be used for high accuracy and coverage singlecellgenomic analysis.189 PRG-2011: Defining the InteractionBetween Users and Suppliers ofProteomics Services/FacilitiesD.H. Hawke 1 , T.M. Andacht 2 , M.K. Bunger 3 ,C.E. Bystrom 4 , L.J. Dangott 5 , H. Molina 6 ,R.L. Moritz 7 , R.E. Settlage 8 , C.W. Turck 91University of Texas MD Anderson Cancer Center,Houston, TX, United States; 2 Centers for DiseaseControl and Prevention, Atlanta, GA, UnitedStates; 3 RTI International, Research TrianglePark, NC, United States; 4 Quest Diagnostics, SanJuan Capistrano, CA, United States; 5 Texas A&MUniversity, College Station, TX, United States;6Center for Genome Regulation, Barcelona,Spain; 7 Institute for Systems Biology, Seattle, WA,United States; 8 Virginia Bioinformatics Institute,Blacksburg, VA, United States; 9 Max Planck Instituteof Psychiatry, Munich, GermanyOver the last ten years the Proteomics Research Group (PRG) hasundertaken technical studies that have covered a wide range of issuesunique to the rapidly developing field of proteomics. These studieshaveincluded a range of qualitative and quantitative experiments. The PRGstudies have resulted in a great deal of attention not only within theABRF community but also outside as is evident from numerous articlesdealing with proteomics methods, procedures and standardization.As the field continues to develop, the diversity of instrumentationand laboratory workflows have grown in tandem. Therefore, for thePRG2011 study it seemed especially useful to perform a survey tohelp define future studies based on the current blend of sample typesand technologies and obtain a view of emerging trends. A survey wascreated to ascertain three main insights into core facility function: 1)How labs interact with their clients, 2) The capacity of labs to meet thedemands of their clients, and 3) The blend of experimental techniquesoffered to and requested by clients. Survey questions were designed toobtain information from both users of core facilities and the directorsand personnel of core facilities. Questions covered such topics as thetype and age of instruments in use, how data is analyzed and presentedto client, sources of funding, and emerging proteomics trends. Resultsare compiled en masse and presented without regard to institution.190 GlycoMaster — Software forGlycopeptide Identification withCombined ETD and CID/HCD SpectraP. Shan, L. XinBioinformatics Solutions Inc., Waterloo, ON,CanadaObjective: To automate the data analysis for the identification ofglycopeptides with combined ETD and CID/HCD fragmentation. Theinputs for GlycoMaster software include the raw mass spectrometry84 • ABRF 2011 — Technologies to Enable Personalized Medicine