{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/v05/MSV000091774/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Luca Fornelli"],"instrument_platform":["Orbitrap Eclipse"],"species":["Homo Sapiens (ncbitaxon:9606)"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=b44defaa01aa43b0bce1d3f12ce4fb9a"],"submitter_email":["luca.fornelli@ou.edu"],"submitter_affiliation":["University of Oklahoma"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["213"],"ptm_modification":["UNIMOD:1 - \"Acetylation.\""],"data_protocol":[""],"pubmed_abstract":["Existing mass spectrometric assays used for sensitive and specific measurements of target proteins across multiple samples, such as selected/multiple reaction monitoring (SRM/MRM) or parallel reaction monitoring (PRM), are peptide-based methods for bottom-up proteomics. Here, we describe an approach based on the principle of PRM for the measurement of intact proteoforms by targeted top-down proteomics, termed proteoform reaction monitoring (PfRM). We explore the ability of our method to circumvent traditional limitations of top-down proteomics, such as sensitivity and reproducibility. We also introduce a new software program, Proteoform Finder (part of ProSight Native), specifically designed for the easy analysis of PfRM data. PfRM was initially benchmarked by quantifying three standard proteins. The linearity of the assay was shown over almost 3 orders of magnitude in the femtomole range, with limits of detection and quantification in the low femtomolar range. We later applied our multiplexed PfRM assay to complex samples to quantify biomarker candidates in peripheral blood mononuclear cells (PBMCs) from liver-transplanted patients, suggesting their possible translational applications. These results demonstrate that PfRM has the potential to contribute to the accurate quantification of protein biomarkers for diagnostic purposes and to improve our understanding of disease etiology at the proteoform level."],"pubmed_title":["Targeted Quantification of Proteoforms in Complex Samples by Proteoform Reaction Monitoring."],"pubmed_authors":["Huang Che-Fan CF, Kline Jake T JT, Negrão Fernanda F, Robey Matthew T MT, Toby Timothy K TK, Durbin Kenneth R KR, Fellers Ryan T RT, Friedewald John J JJ, Levitsky Josh J, Abecassis Michael M I MMI, Melani Rafael D RD, Kelleher Neil L NL, Fornelli Luca L"],"pubmed_abstract_synonyms":["FBgn0003149, Biological Markers, Viral Marker, Surrogate Endpoints, determination, Laboratory, Blood, Biochemical, Endpoint, protein, Serum, limitations, peptide, Polypeptides, Techniques, Laboratory Markers, protein polypeptide chains, Readability, Para, peptido, diseases, Method, Biological, pathogenesis, diseases and disorders, Software Engineering, CG5939, study limitations, protein aggregate, WMS, Computer Program, me75, human disease, peptides, Open, Computer Programs and Programming, iecur, proteins, procedures, D17Mit170, T1, allergic reaction, reaction, Immune, Markers, Methodological Studies, scientific observation, Viral Markers, Homo sapiens disease, GPHYSD2, SGS, Viral, Surrogate Endpoint, DmelCG5939, Biochemical Markers, Procedure, SPDSY, Tl3, Tl2, Biologic Marker, Source Softwares, results, Software Tools, ACMICD, Multiple Reaction Monitoring, Programs, Program, Computer Applications, prm, Marker, Computer Applications Software, Diseases, Computer Applications Softwares, l(3)S010605, Softwares, Software Applications, End Points, 0106/05, Source Software, PM/mPM, fmol, MASS, Methodological, Immunologic, Laboratory Marker, Methodological Study, disease, Applications, Specificity and Sensitivity, Patient, Biochemical Marker, PBMCs, Polypeptide, Computer Software Applications, other disease, Procedures, SRML1, Clinical 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Markers, Serum Marker, Peripheral Blood, Surrogate, Endpoints, Engineering, Specificity, Understanding, Surrogate Marker, Protein Gene Products, plan specification, Reticuloendothelial System, Computer Programs, Gene Proteins, Livers, Applications Softwares, l(3)10631, Isolation of Nuclei TAgged in specific Cell Types, SSKS, Bra, Peptid, assay, pm, PM, methodology, Immune Markers"],"name_synonyms":["Human, reaction., human being, Man (Taxonomy), Homo sapiens, Man, human, Modern Man, humans, Modern"],"pubmed_title_synonyms":["reaction."],"description_synonyms":["Applications Software, FBgn0003149, Open Source, Computer Software, Procedures, determination, DmelCG5939, Computer, Procedure, Source Softwares, limitations, Software Tools, Tool, Programs, Program, Computer Applications, method, Techniques, Para, Software Tool, prm, mPM, Method, sensitive, method used in an experiment, Computer Applications Software, Studies, Computer Applications Softwares, l(3)S010605, Software Engineering, Softwares, CG5939, study limitations, Software, Technique, sensitivity, Computer Program, Application, Open Source Softwares, Software Applications, 0106/05, Source Software, Software Application, PM/mPM, Open, Engineering, Specificity, Open Source Software, Computer Programs and Programming, chemical analysis., Methodological, Methodological Study, Computer Software Application, plan specification, Study, allergic reaction, Computer Programs, reaction, Applications, Applications Softwares, l(3)10631, Methodological Studies, Tools, Specificity and Sensitivity, Isolation of Nuclei TAgged in specific Cell Types, Sensitivity, assay, pm, PM, Computer Software Applications"],"additional_accession":[]},"is_claimable":false,"name":"Targeted Quantification of Proteoforms in Human Samples by Proteoform Reaction Monitoring","description":"Here, we describe an approach based on the principle of PRM for the measurement of intact proteoforms by targeted top-down proteomics termed Proteoform Reaction Monitoring (PfRM). We explore the ability of our method to circumvent traditional limitations of top-down proteomics such as sensitivity and reproducibility. We also introduce a new software Proteoform Finder specifically designed for easy analysis of PfRM-MS data. ","dates":{"publication":"Fri Apr 21 14:37:00 BST 2023"},"accession":"MSV000091774","cross_references":{"pubmed":["38354049"]}}