{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/x01/MSV000098333/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Gurjeet Kaur"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=3a3be663c16940da9dd99f237956fb6a"],"submitter_email":["g.virk@student.unsw.edu.au"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["1,153"],"ptm_modification":["MOD:00397 - \"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\"","MOD:00425 - \"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\"","MOD:00400 - \"A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen.\"","MOD:00399 - \"A protein modification that is produced by reaction with iodoacetic acid, usually replacement of a reactive hydrogen with a methylcarboxy group.\""],"data_protocol":[""],"omics_type":["Proteomics"],"instrument_platform":["Q Exactive HF"],"species":["Homo Sapiens (ncbitaxon:9606)"],"submitter_affiliation":["Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2052, Australia"],"description_synonyms":["Overall, Biological Markers, Viral Marker, Antemortem Diagnosis, Needs, Surrogate Endpoints, Activity, determination, Laboratory, Blood, Biochemical, Endpoint, protein, Overall Health, Serum, Diagnosis, Long Term, Status, School-Age, Laboratory Markers, protein polypeptide chains, Techniques, DSmurf, Biological, Method, B1, symptoms, SDS-PAGE, DGS, cytopathology, Research Activity, protein aggregate, Work Flow, Effect, Laboratory Research, Priorities, treatment, Fresh Frozen Plasmas, Fresh Frozen, me75, Divorced, Polyacrylamide, Target Populations, Man (Taxonomy), Biopsies, Tissue, proteins, Divorces, procedures, Estimated, D17Mit170, T1, allergic reaction, Immune, Markers, Methodological Studies, Smurf, DmelCG1106, Viral Markers, sample, D1, disease management, Therapies, Health Services Need, Blood Protein, Research Priority, Long-Term Effects, plasma, CG4943, Diagnose, D-smurf, Therapy, screening, Frozen Plasma, Viral, Surrogate Endpoint, PLATEST, Needs and Demand, Modern, Longterm Effect, Need, Research Priorities, Biochemical Markers, Lack, Procedure, Tl3, Plasmas, Biologic Marker, Tl2, Diagnoses, Workflows, Level of Health, Postmortem, Marker, School Age, Examinations and Diagnoses, Postmortem Diagnosis, General, Research and Development, Diagnoses and Examination, Populations, portion of blood plasma, Postmortem Diagnoses, histopathology, End Points, DmelCG4943, Sodium Dodecyl Sulfate-PAGE, Health Services Needs, signs, Immunologic, General Health Levels, Methodological, Laboratory Marker, Methodological Study, Treatments, human, CG1106, Activities, blood plasm, Health, Patient, Specificity and Sensitivity, Biochemical Marker, School-Age Population, Sodium Dodecyl Sulfate-PAGEs, Levels, Proteomes, Platelets, Work Flows, Fresh, human being, Fresh Frozen Plasma, Procedures, Clinical Markers, Peptidomics, Effects, Clinical Marker, dSmurf1, number, General Health, Gene, Serum Protein, Gel Electrophoresis, protein-containing complex, presence, Human, Surrogate End Points, Surrogate Markers, Sodium Dodecyl Sulfate PAGE, method, Homo sapiens, polypeptide chain, sensitive, method used in an experiment, Polyacrylamide Gel Electrophoresis, Gene Products, Studies, Low, Antemortem, Level, Separated, Man, sensitivity, Technique, Health Status, Biomarker, study, School-Age Populations, Health Services, Blood Plasma, Clinical, Longterm, Research, Flexibility, Biological Marker, gel, Target, Serum Proteins, Long-Term, Diagnoses and Examinations, Plasma Proteins, Population, man, General Health Level, Study, Plasma Protein, Immunologic Markers, d-smurf, Clients, Blood Plasmas, Sensitivity, Long-Term Effect, Development and Research, School Age Population, Immunologic Marker, Biologic, PTHB1, SDS PAGE, Antemortem Diagnoses, data, findings, cou, protein complex, Serum Markers, Proteins, End Point, total expressed protein, General Health Status, Dsmurf, Client, Examination and Diagnoses, Immune Marker, Frozen Plasmas, dSmurf, count in organism, Lr, Priority, native protein, natural protein, Surrogate End Point, C18, Health Level, Smurf ubiquitin ligase, chemical analysis, Protein, Long Term Effects, Research Activities, Overall Health Status, techniques, Biologic Markers, Plasma, School Age Populations., Separation, Serum Marker, Surrogate, Separations, Endpoints, Specificity, Target Population, portion of plasma, patient, Surrogate Marker, sample population, Longterm Effects, Protein Gene Products, plan specification, Gene Proteins, Therapeutic, Modern Man, Bra, Treatment, assay, biopsy, Health Levels, methodology, Immune Markers"],"name_synonyms":["Plasma, Fresh, Fresh Frozen Plasmas, Fresh Frozen, portion of blood plasma, Blood Plasma, achi/vis, Frozen Plasma, ach, Fresh Frozen Plasma, Procedures, dTGIFb, Blood, total expressed protein, portion of plasma, Methodological, procedures, Procedure, Plasmas, Methodological Study, zaa, CG8819, Achi, Study, vis, Frozen Plasmas, blood plasm, Techniques, Methodological Studies, DmelCG8819, Method, Blood Plasmas, Studies, techniques, methodology., Proteomes, Technique, plasma, methodology"],"additional_accession":["PXD022469"]},"is_claimable":false,"name":"Proteome-wide evaluation of plasma depletion methods vis-à-vis fractionation techniques","description":"Human plasma is one of the most widely used tissues in clinical analysis, and plasma-based biomarkers are used for monitoring patient health status and/or response to medical treatment to avoid unnecessary invasive biopsy. Data driven plasma proteomics has suffered from a lack of throughput and detection sensitivity, largely due to the complexity of the plasma proteome, and in particular the enormous quantitative dynamic range, estimated to be between 9-13 orders of magnitude between the lowest and highest abundance protein. A major challenge is to identify workflows which can achieve depth of plasma proteome coverage, while minimizing the complexity of sample workup and maximizing sample throughput. In this study, we have performed intensive depletion of high abundant plasma proteins or enrichment of low abundant proteins using Hu6, Hu14 and ProteoMiner followed by SDS PAGE and C18 prefractionation techniques. We compared the performance of each of these fractionation approaches to identify the method which satisfies requirements for analysis of clinical samples, and to include good plasma proteome coverage in combination with reasonable sample output. In this study, we have reported that gel-based prefractionation approaches can replace expensive and time-consuming chromatographic separation, thereby significantly accelerating analysis time. In addition, we showed that a variety of methodologies can achieve similarly high proteome coverage, allowing flexibility depending on project specific needs. These considerations are important in the effort to accelerate plasma proteomics research so as to provide efficient, reliable and accurate diagnoses for the population as a whole.","dates":{"publication":"Wed Jun 25 22:14:00 BST 2025"},"accession":"MSV000098333","cross_references":{}}