hPOP Assays
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AssayMaterialGroupContact EmailHow much material is required
How many samples will be in one batch?
How many replicates will be ran for one sample?
Description of the assayNotes
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Degradome (protein termini)PBMCsLangephilipp.lange@ubc.ca
Enrichment of of protein N-termini by HUNTER, DIA analysis of proteins and termini on QE HF, quantification of proteins, protein fragments (identified by N terminus), prediction of proteolytic activities
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GenomePBMCsSnydersahadi@stanford.edu
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ImmunophenotypingPBMCsOrfao/Manuel Fuentes (mfuentes@usal.es)mfuentes@usal.es
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MetallomicsPBMCsRoberts (Blaine.roberts@florey.edu.au)Blaine.roberts@florey.edu.auenough for ~50ug of total proteinQuantitation of ~20 elements using 7700 ICP-MS using validated assays against SRM.
Protocol based on: https://actaneurocomms.biomedcentral.com/articles/10.1186/s40478-016-0390-8
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Proteome (DIA)PBMCsHauckhauck@helmholtz-muenchen.de300 000 cells per sample, equals appr 10µg total protein48 or 80
1 (additionally 4 to 8 pool samples will be analyszed for every batch)
LC-MSMS (Q Exactive HF-X), label-free quantification of MS2 intensities, matching to extensive human PBMC library containing >11 000 high conficent protein IDs (Lepper et al. 2018)
https://www.ncbi.nlm.nih.gov/pubmed/29182335
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Proteome (SWATH)PBMCsSnyder
Ranganathan (shoba.ranganathan@mq.edu.au)
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TranscriptomePBMCsSnydersahadi@stanford.edu
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Cytokines (62)PlasmaSnydersahadi@stanford.edu
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Degradome & ProteomePlasmaLangephilipp.lange@ubc.ca100 ul plasma
Enrichment of of protein N-termini by HUNTER, DIA analysis of proteins and termini on QE HF, quantification of proteins, protein fragments, prediction of proteolytic activities
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Glycome/ glycoproteomePlasmaMahal Lablkmahal@nyu.edu100 uL sera2-color lectin microarray analysis against a pooled biological reference.
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Immune Monitoring (65 proteins)PlasmaManuel Fuentes (mfuentes@usal.es)mfuentes@usal.es100 ul 384 or 962Beads suspension arrays targeting citokines, chemokines,.... providing immune system status
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LipidomePlasmaSnydersahadi@stanford.edu50 ul plasma
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MetabolomePlasmaSnydersahadi@stanford.edu100 ul plasma
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MetabolomePlasmaSlenosleno.lekha@uqam.ca100 uL plasmaMeOH ppt plasma, untargeted metabolomics with RP-LC-MS/MS (+/-) on tripleTOF 5600
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MetallomePlasmaUnwinr.unwin@manchester.ac.uk100ul plasmaICP-MS. Assay validated against NIST standard
Metals measured: Na, Mg, Al, K, Ca, Cr, Mn, Fe, Co, Cu, Zn, Se.   Protocol at https://link.springer.com/article/10.1007/s10534-018-0089-3
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MetallomicsPlasmaRoberts (Blaine.roberts@florey.edu.au)Blaine.roberts@florey.edu.au100uL plasma Quantitation of ~20 elements using 7700 ICP-MS using validated assays against SRM.
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Metalloproteomics SerumRoberts (Blaine.roberts@florey.edu.au)Blaine.roberts@florey.edu.au50 uL serumTransferin Fe and ceruloplasmin Cu saturation.
Protocol based on https://pubs.acs.org/doi/abs/10.1021/cn5003557
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PeptidomePlasmaLangephilipp.lange@ubc.ca500ul plasma
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Proteome (SRM)PlasmaUhlenfredrik.edfors@scilifelab.se
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Proteome (SWATH)PlasmaSnyder
Ranganathan (shoba.ranganathan@mq.edu.au)
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Proteome (SWATH)PlasmaThomas LAM (cclam@polyu.edu.hk)
cclam@polyu.edu.hk, hauck@helmholtz-muenchen.de
100µL plasma
LC-MSMS (nano-LC +Sciex 6600 Triple-TOF for DDA,SWATH,iTRAQ), Agilent 1260 infinity fraction collector for peptide fractionation. S-TRAP-micro,
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Proteome (SWATH)Plasma/ Whole bloodStoychevsstoychev@csir.co.za50ul plasma/ 50ul whole blood
SDS based protein extraction, HILIC-based clean-up and on-bead digestion followed by nanoLC Sciex 6600 DDA (spectral library) + SWATH (label free quant)
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Vesicle monitoring/phenotyping (40 proteins)PlasmaEV Array Team (Malene Møller Jørgensen)maljoe@rn.dk100µL plasma803
High-throughput phenotyping of extracellular vesicles present in plasma. The Assay is based on protein microarray technology. Each sample will be analyzed for the presence of 40 different surface antigens.
http://evarray.dk/  https://www.tandfonline.com/doi/full/10.3402/jev.v2i0.20920
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Proteome (Autoantibody)PlasmaPeter Nilssonpeter.nilsson@scilifelab.se50 µl
planar protein arrays with 42.000 protein fragments for a selected set of samples followed by targeted bead based assays with 380 antigens on 380 samples
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Obesity ( 12 proteins) Plasma/serumManuel Fuentes ( mfuentes@usal.es)mfuentes@usal.es100 uL384 or 962Beads suspension arrays targeting proteins related to obesity
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Metallomics
Red blood cells if available
Roberts (Blaine.roberts@florey.edu.au)Blaine.roberts@florey.edu.au
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Clinical Chemistry/ImmunoassaySerumAlex J. Raiajr2170@cumc.columbia.edu500-1000 ul serum
we will be able to perform a number of clinical chemistry and immunoassay tests allowing for clinical correlation of health and disease states- everything from basic/comprehensive metabolic panels, kidney/liver/thyroid function testing, cholesterol level determination, cardiac risk, and many others. We can discuss further which ones are most useful and should be prioritized, based on sample availability.
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Clinical TestsSerumSnydersahadi@stanford.edu
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Protease activitySerumKönigkoenigs@uni-muenster.de200 µlhttps://www.sciencedirect.com/science/article/abs/pii/S0731708517310671?via%3Dihub
measuring bradykinin degradation by serum proteases using dabsylation and TLC, article in PAIN just accepted; www.medizin.uni-muenster.de/cu-proteomics
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Protease activityPlasmaKönigkoenigs@uni-muenster.de201 µloptional, see Email
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Proteome (Autoantibody)SerumHeng Zhuhzhu4@jhmi.edu
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MetagenomeStool
Snyder, Gibbons (sgibbons@systemsbiology.org)
sgibbons@systemsbiology.org1-3 gramsgDNA extraction, Nextera library prep, Illumina sequencing
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MetaproteomeStoolMoritz-Deutsch5-10 gramsSTrap digestion, MS/MS analysis, metaproteomic analysis
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Degradome & ProteomeUrineLangephilipp.lange@ubc.ca
S-TRAP, Enrichment of of protein N-termini by HUNTER, DIA analysis of proteins and termini on QE HF, quantification of proteins, protein fragments, prediction of proteolytic activities
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LipidomeUrine?
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MetabolomeUrineSlenosleno.lekha@uqam.ca300 uL urineSPE urine, untargeted metabolomics with RP-LC-MS/MS (+/-) on tripleTOF 5600
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MetallomicsUrineRoberts (Blaine.roberts@florey.edu.au)Blaine.roberts@florey.edu.au400uL urineQuantitation of ~20 elements using 7700 ICP-MS using validated assays against SRM.
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PeptidomeUrineLangephilipp.lange@ubc.ca
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ProteomeUrineArthurjmarthur@uams.edu500 ul urine
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Proteome UrineSingh_FSU (rakesh.singh@med.fsu.edu)rakesh.singh@med.fsu.edu0.5 ml Urine48
Modified FASP method will be used to digest the extracted proteins. Digested peptides will be run on nEasy-Thermo Orbitrap Velos. Label free quantification will be performed using Maxquant/Perseus
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Proteome (DIA/DDA)UrineSuttonc.w.sutton@bradford/ac/uk2ml
high throughput MTP trypsin digest method, each sample prepared in duplicate, each digest analysed in triplicate by 1D HPLC/Orbitrap Fusion MS for label-free quantification
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Proteome (SWATH)UrineStoychevsstoychev@csir.co.zaNo capacity to process Urine at this point
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Proteome [sample processing]AllWilsonjohn@protifi.com< 100 ug, 100 - 300 ug
ProtiFi will offer discounts on S-Traps to analyze the samples of this study. Especially where sample is limited, groups may be interested in the ability to do metabolomics and proteomics from the same sample cf. https://www.protifi.com/wp-content/uploads/2018/12/S-Trap-ASMS-2018-metabolomics-proteomics.pdf . Please write John if interested.
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PTM/EV profiling (PASEF)
Plasma; urine, maybe stool
Stensballeas@hst.aau.dk50uL plasma; 150uL urineEnrichment/subfractionation; In-sol/S-trap; LC-MSMS (Bruker timsTOF PRO PASEF); PTM focused datamining
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ProteomePlasmaJochen Schwenkjochen.schwenk@scilifelab.se50 µl384 per batch2Antibody suspension bead arrays (± 200 proteins)
Additional use of samples sent to Peter Nilsson
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Global Epi-proteome (histone PTMs)PBMCsBen Garcia lab (UPenn)
bgarci@pennmedicine.upenn.edu
500,000 to 1 million cells96 per batch2
Cellular fractionation of nuclei from cells followed by isolation of histones by precipitation. Quantification of 100 -150 histone PTMs and variants using DIA-MS/MS on an Orbitrap Fusion
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