{"database":"panorama","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Aleksandra Binek"],"species":["Homo Sapiens"],"full_dataset_link":["https://panoramaweb.org/im1z39.url"],"submitter_email":["aleksandra.binek@cshs.org"],"submitter_affiliation":["Cedars-Sinai Medical Center"],"sample_protocol":[""],"repository":["PanoramaPublic"],"data_protocol":[""],"pubmed_abstract":["<h4>Background</h4>Accurate discovery assay workflows are critical for identifying authentic circulating protein biomarkers in diverse blood matrices. Maximizing the commonalities in the proteomic workflows between different biofluids simplifies the approach and increases the likelihood for reproducibility. We developed a workflow that can accommodate 3 blood-based proteomes: naive plasma, depleted plasma and dried blood.<h4>Methods</h4>Optimal conditions for sample preparation and data independent acquisition-mass spectrometry analysis were established in plasma then automated for depleted plasma and dried blood. The mass spectrometry workflow was modified to facilitate sensitive high-throughput analysis or deeper profiling with mid-throughput analysis. Analytical performance was evaluated by the linear response of peptides and proteins to a 6- or 7-point dilution curve and the reproducibility of the relative peptide and protein intensity for 5 digestion replicates per day on 3 different days for each biofluid.<h4>Results</h4>Using the high-throughput workflow, 74% (plasma), 93% (depleted), and 87% (dried blood) displayed an inter-day CV <30%. The mid-throughput workflow had 67% (plasma), 90% (depleted), and 78% (dried blood) of peptides display an inter-day CV <30%. Lower limits of detection and quantification were determined for peptides and proteins observed in each biofluid and workflow. Based on each protein and peptide's analytical performance, we could describe the observable, reliable, reproducible, and quantifiable proteomes for each biofluid and workflow.<h4>Conclusion</h4>The standardized workflows established here allows for reproducible and quantifiable detection of proteins covering a broad dynamic range. We envisage that implementation of this standard workflow should simplify discovery approaches and facilitate the translation of candidate markers into clinical use."],"pubmed_title":["Standardized Workflow for Precise Mid- and High-Throughput Proteomics of Blood Biofluids."],"pubmed_authors":["Mc Ardle Angela A, Binek Aleksandra A, Moradian Annie A, Chazarin Orgel Blandine B, Rivas Alejandro A, Washington Kirstin E KE, Phebus Conor C, Manalo Danica-Mae DM, Go James J, Venkatraman Vidya V, Coutelin Johnson Casey W CW, Fu Qin Q, Cheng Susan S, Raedschelders Koen K, Fert-Bober Justyna J, Pennington Stephen R SR, Murray Christopher I CI, Van Eyk Jennifer E JE"],"description_synonyms":["protein translation, CDF, scale tissue, Biological Markers, Viral Marker, Surrogate Endpoints, determination, Laboratory, PNT-P1, Blood, DmelCG17077, Biochemical, Mbp1, Endpoint, EY3-1, protein, Pnt, Serum, Mid(H15), Polypeptides, protein synthesis., Laboratory Markers, Techniques, POF, png, peptido, Biological, Method, AGAMOUS-like 61, D-ets-2, 3520, protein aggregate, Work Flow, myd, DiA, Pnt-P1, Fresh Frozen Plasmas, Fresh Frozen, l(2)k07135, peptides, plant peltate hair, Mbp-1, procedures, DIASP, DIA, Dia, allergic reaction, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, Immune, Markers, Methodological Studies, scientific observation, Viral Markers, 38E.16, plasma, protein anabolism, Frozen Plasma, Viral, protein biosynthetic process, wide/broad, Surrogate Endpoint, gyltl1b-b, D-Ets-2, Biochemical Markers, ets94F, 0123/09, Procedure, Biologic Marker, Plasmas, ms(2)04138, Workflows, Desmoplastic infantile astrocytoma, Marker, MDDGA6, mKIAA0609, protein formation, KIAA0609, H15r/nmr2, fg, pntP2, gyltl1b, Pointed-P1, End Points, POF2, F27C12_24, F27C12.24, Ets94F, mdc1d, expanded, Immunologic, Methodological, Laboratory Marker, Methodological Study, ptd, PntP2, MDC1D, wide, enr, enlarged, Biochemical Marker, PntP1, PBMCs, E(E2F)3D, DIANA, PNTP2, Polypeptide, Proteomes, PNTP1, Work Flows, Fresh, big, 0998/12, Fresh Frozen Plasma, Procedures, Clinical Markers, Clinical Marker, ETS2, Ets2, peltate hair, number, Gene, broad, protein-containing complex, froggy, Gyltl1a, Surrogate End Points, Surrogate Markers, large, DMPOINT1A, pntegfr, 0608/07, sensitive, DmelCG1768, PBMC, Gene Products, Studies, HILDA, Technique, sensitivity, portion of blood, Biomarker, Blood Plasma, Clinical, pointed-RC, Flexibility, MDDGB6, Biological Marker, los, LARGE, EK3-2, Study, l(3)07825, BPFD#36, Immunologic Markers, DmelCG6634, Blood Plasmas, great, CG17077, peptidos, DIA2, Immunologic Marker, l(3)j1B7, Biologic, measuring, Ets, whole blood, protein complex, vertebrate blood, Desmoplastic astrocytoma of infancy, Proteins, Serum Markers, End Point, CG1768, DRF2, Peptide, Immune Marker, Frozen Plasmas, H15r, native protein, Surrogate End Point, chemical analysis, Protein, MLPLI, protein biosynthesis, background, techniques, Dias, scales, pnt-P1, pnt-P2, l(3)s118306, Biologic Markers, Plasma, Serum Marker, Peripheral Blood, scale, Surrogate, nmr2, Endpoints, CG6634, portion of plasma, TBX20, extra, Surrogate Marker, introduction, Protein Gene Products, Reticuloendothelial System, Gene Proteins, Ets58AB, cardinality, Peptid, assay, POINT, methodology, Immune Markers, CG8705"],"pubmed_title_synonyms":["portion of blood, Workflows, DmelCG6634, H15r, whole blood, Peptidomics, vertebrate blood., nmr2, los, CG6634, TBX20, extra, Work Flow, Work Flows, H15r/nmr2, Mid(H15)"],"name_synonyms":["portion of blood, Workflows, DmelCG6634, H15r, whole blood, Peptidomics, vertebrate blood., nmr2, los, CG6634, TBX20, extra, Work Flow, Work Flows, H15r/nmr2, Mid(H15)"],"pubmed_abstract_synonyms":["Fresh, protein translation, 0998/12, Biological Markers, Viral Marker, Surrogate Endpoints, Fresh Frozen Plasma, Procedures, determination, Clinical Markers, Laboratory, Clinical Marker, PNT-P1, Blood, ETS2, Ets2, DmelCG17077, Biochemical, Gene, Endpoint, EY3-1, protein, Pnt, Spectrum Analyses, broad, Serum, protein-containing complex, Mid(H15), Surrogate End Points, peptide, Surrogate Markers, Polypeptides, protein synthesis., Laboratory Markers, Techniques, DMPOINT1A, pntegfr, 0608/07, peptido, png, Biological, Method, sensitive, responsivity, Gene Products, Studies, Mass, Analysis, D-ets-2, 3520, protein aggregate, Work Flow, Technique, sensitivity, Mass Spectroscopy, Pnt-P1, portion of blood, Mass Spectrum Analysis, Biomarker, reactivity, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, Clinical, peptides, pointed-RC, Analyses, Biological Marker, los, procedures, EK3-2, Study, allergic reaction, l(3)07825, Immunologic Markers, Immune, DmelCG6634, Markers, Methodological Studies, scientific observation, Viral Markers, Blood Plasmas, peptidos, CG17077, Immunologic Marker, plasma, l(3)j1B7, Biologic, close to, measuring, protein anabolism, Ets, Frozen Plasma, Viral, protein biosynthetic process, wide/broad, Surrogate Endpoint, whole blood, protein complex, vertebrate blood, Proteins, Serum Markers, End Point, D-Ets-2, Biochemical Markers, ets94F, 0123/09, Procedure, Biologic Marker, Plasmas, Spectrum Analysis, Peptide, results, Immune Marker, Spectroscopy, near to, Frozen Plasmas, polypeptide, Workflows, MS, H15r, native protein, Marker, Surrogate End Point, chemical analysis, Protein, protein formation, protein biosynthesis, background, techniques, pnt-P1, pnt-P2, Mass Spectrum Analyses, l(3)s118306, H15r/nmr2, Biologic Markers, Plasma, Mass Spectrum, Serum Marker, pntP2, Pointed-P1, End Points, Surrogate, nmr2, Endpoints, Ets94F, Spectrometry, CG6634, portion of plasma, Immunologic, Methodological, TBX20, extra, Laboratory Marker, Methodological Study, Surrogate Marker, introduction, Protein Gene Products, ptd, Gene Proteins, PntP2, wide, Ets58AB, Biochemical Marker, approaches, PntP1, E(E2F)3D, vicinity of, Peptid, PNTP2, assay, Polypeptide, response, Proteomes, PNTP1, Work Flows, POINT, methodology, Immune Markers, CG8705"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Standardized workflow for precise mid- and high-throughput proteomics of blood biofluids","description":"Background: Accurate discovery assay workflows are critical for identifying authentic circulating protein biomarkers in diverse blood matrices. Maximizing the commonalities in the proteomic workflows between different biofluids simplifies the approach and increases the likelihood for reproducibility. We developed a workflow that allows flexibility for high and mid-throughput analysis for three blood-based proteomes: naïve plasma, plasma depleted of the 14 most abundant proteins, and dried blood. \nMethods: Optimal conditions for sample preparation and DIA-MS analysis were established in plasma then automated and adapted for depleted plasma and whole blood. The MS workflow was modified to facilitate sensitive high-throughput or deep profile analysis with mid-throughput analysis. Analytical performance was evaluated from 5 complete workflows repeated over 3 days as well as a linearity analysis of an 8-point dilution curve.  \nResult: Using our high-throughput workflow, 74%, 93%, 87% of peptides displayed an inter-day CV<30% in plasma, depleted plasma and whole blood. While the mid-throughput workflow had 67%, 90%, 78% of peptides in plasma, depleted plasma and whole blood meeting the CV<30% standard. \nNaive plasma samples had the highest rates of identifications where a lower limit of detection or quantitation could be determined. Combining the analysis of both high-throughput plasma fractions exceed the number of reliably identified proteins for individual biofluids in the mid-throughput workflows. \nConclusion: The workflow established here allowed for reliable detection of proteins covering a broad dynamic range. We envisage that implementation of this standard workflow on a large scale will facilitate the translation of candidate markers into clinical use.","dates":{"publication":"Wed May 11 00:00:00 GMT+01:00 2022"},"accession":"PXD024884","cross_references":{"TAXONOMY":["9606"],"pubmed":["34687543"]}}