Protein Analysis

Access the human proteome on a microarray scale

ProtoArray Human Protein Microarray v5.0

Studyover9,000disease-relevantproteinsfromabroadrangeofgenefamilies Detectfemtomolelevelsofhighlyfunctionalproteinusingavarietyofsamplesources Identifyproteinsimmediatelyandaccesssequence-verifiedGatewayclonesforrapidfollow-upvalidationstudies Analyzeandmanagedatawithanadvancedsoftwarepackage

A high-content human protein microarray with new features and controls

TheProtoArrayHumanProteinMicroarrayv5.0isanadvanced,high-content,functionalproteinmicroarray(Figure1)thatenablesyoutoscanthousandsofproteinsfor biochemicalinteractionsinaslittleasoneday.Version5.0oftheProtoArrayHuman ProteinMicroarraycontainsmorethan9,000disease-relevanthumanproteinsrepresentingmultipleimportantproteinclasses(Table1).Proteinsarearrayedinduplicate ona1x3inchultrathinnitrocellulose-coatedslidewitha22x22formatthatallows roomforadditionalcustomcontentandcontrols.Controlfeaturesforv5.0include: Positionalmappingcontrolagenttoenableradiolabeledsmall-molecule profilingassays Positivecontrolsforubiquitinationandsumoylationstudies Controlcontenttofacilitateanoptimizeddatanormalizationalgorithmfor biomarkerdiscovery HumanIgAandantihumanIgAgradientstoallowforprofiling ofIgAserumantibodies
Table 1. ProtoArray v4.1 content and distribution by class. Figure 1. Image of more than 9,000 human proteins after probing of the ProtoArray Human Protein Microarray v5 with Alexa Fluor 647labeled anti-GST.

Class Proteinkinases(unique) Proteinkinases(including domains,splicevariants, andmutants) Transcriptionfactors Membraneproteins Nuclearproteins Signaltransduction Secretedproteins Cellcommunication Metabolism Celldeath Protease/peptidase activity

No. on array 268 776 328 2,635 2,252 1,526 192 1,687 3,862 505 219

Thepurifiedhumanproteinsareprintedinadust-free,temperature-andhumiditycontrolledenvironmenttomaintainconsistentquality.Thearraysareprintedbyan automated process on an instrument that is extensively calibrated and tested for printingProtoArrayHumanProteinMicroarrays.

Numbers are based on Gene Ontology classification and are subject to change. For a complete list of array proteins, visit www.invitrogen.com/protoarray.

Protein Analysis

Maximum protein functionality

TheProtoArrayHumanProteinMicroarrayisdesignedformaximumproteinqualityandfunctionality.Proteinsarederivedfrom sequence-validated open reading frames selected from Invitrogens extensive Ultimate ORF Clone Collection.* These fulllength proteins are expressed as N-terminal GST fusion proteins using a baculovirus-based expression system. All proteins are purified under nondenaturing conditions and printed at 4C to preservenativestructureandfunctionality.
* The Ultimate Human and Mouse ORF Clone Collection is the first and only clone resource to offer full-insert sequenced clones in a Gateway vector. To learnmore,visitorf.invitrogen.com.

Mappingofproteinproteininteractionsimportantinbiochemicalpathways Identificationofkinaseandubiquitinligasesubstratesfor targetdiscoveryandvalidation Antibodyspecificityprofilingforresearchandtherapeutic antibodydevelopment

Rapid and efficient data analysis

ProtoArrayHumanProteinMicroarrayscanbeeasilyreadwithmost commerciallyavailablefluorescentmicroarrayscanners(foralistof compatiblescanners,pleasevisitwww.invitrogen.com/protoarray). ProtoArray Prospector v5.2 software is a free data analysis tool

Each slide is labeled with a unique bar code for easy tracking. The nitrocellulose-coated slide provides high protein stability andyieldssensitiveresultsfordiscoverystudies,suchasimmune response biomarker profiling, small-molecule screening, and purifiedproteinprofiling.

thatgeneratesalistofpositiveinteractionsbetweentheprobeof interestandtheimmobilizedproteinsonthearray.Newfeaturesof ProtoArrayProspectorv5.2softwareinclude: Optimizedreportoutputanddatanormalization Newalgorithmsforanalysisofsmall-moleculeprofilingdata Auto-updatefeature

Broad range of discovery applications

The ProtoArray Human Protein Microarray platform enables a widerangeofdiscoveryapplications(Figure2),including: Profilingofradiolabeledorfluorescentlylabeledmolecules fortargetidentificationorselectivity Rapiddiscoveryofdiseasemarkersformorethan9,000 antigensspecifictoavarietyofcancers,autoimmune,and otherdiseases You can download ProtoArray Prospector v5.2 at www.invitrogen.com/protoarray. Once you have identified your proteins of interest, you can obtain the corresponding ready-touse Ultimate ORF clones and get started on your downstream validationstudies.

Sera from healthy or untreated controls

Sera from diseased or treated patients

Ubiquitin ligase complex

E1 E2 E3
Ub Ub Ub Ub

Biomarker discovery

Profiling enzymatic activity

Kinase substrate identification and ubiquitin ligase profiling

G2-0

0123

Comparison

45

Proteinprotein interactions and antibody specificity profiling

Small-molecule protein profiling

Figure 2. Range of ProtoArray applications.

Ordering information
Product
ProtoArrayControlProteinMicroarrayv5.0 ProtoArrayHumanProteinMicroarrayv5.0 ProtoArrayHumanProteinMicroarrayv5.0,20-pack ProtoArrayHumanProteinMicroarrayv5.0PPIKit(forbiotinylatedproteins) ProtoArrayHumanProteinMicroarrayv5.0PPIKit(forV5-taggedproteins) ProtoArrayHumanProteinMicroarrayv5.0KSIKit ProtoArrayBlockingBufferKit 10XSyntheticBlock ArrayControlProtein AlexaFluor647Anti-V5AntibodyforProtoArray AlexaFluor647goatanti-humanIgM(chain) AlexaFluor647goatanti-humanIgG(H+L)

Cat. no.
PA10057 PAH052501 PAH0525020 PAH0525011 PAH0525013 PAH0525065 PA055 PA017 451096 451098 A21249 A21445

3
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Protein Analysis

References
1. Auger,I.etal.(2008)Newautoantigensinrheumatoidarthritis:screening8268proteinarrayswithRApatientssera.Ann Rheum Dis (Epubaheadofprint). 2. Schnack,C.etal.(2008)Proteinarrayanalysisofoligomerization-inducedchangesinalpha-synucleinprotein-proteininteractionspointstoaninterferencewithCdc42effector proteins.Neuroscience 154:14501457. 3. Gunawardana,C.etal.(2008)Identifyingnovelautoantibodysignaturesinovariancancerusinghigh-densityproteinmicroarrays.Clin Biochem(Epubaheadofprint). 4. Gnjatic,S.etal.(2008)Seromicanalysisofantibodyresponsesinnon-smallcelllungcancerpatientsandhealthydonorsusingconformationalproteinarrays.J Immunol Methods (availableonline). 5. 7. 9. Singh,J.etal.(2008)DcpSasatherapeutictargetforspinalmuscularatrophy.ACS Chem Biol3:711722. Marina,O.etal.(2008)Aconcentration-dependentanalysismethodforhighdensityproteinmicroarrays.J Proteome Res7:20592068. Li,Z.etal.(2008)Cdc34pubiquitin-conjugatingenzymeisacomponentofthetombusvirusreplicasecomplexandubiquitinatesp33replicationprotein.J Virol82:69116926. 6. Satoh,J.etal.(2008)Proteinmicroarrayanalysisidentifieshumancellularprionproteininteractors.Neuropathol Appl Neurobiol35:1635. 8. Schnack,C.etal.(2008)IdentificationofnovelsubstratesforCdk5andnewtargetsforCdk5inhibitorsusinghigh-densityproteinmicroarrays.Proteomics8:19801986. 10. Roche,S.etal.(2008)Autoantibodyprofilingonhigh-densityproteinmicroarraysforbiomarkerdiscoveryinthecerebrospinalfluid.J Immunol Methods338:7578.

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