MassIVEapplication/xmlftp://massive-ftp.ucsd.edu/v01/MSV000078763/primaryOK2000000ProteomicsRiitta LahesmaaLTQ Orbitrap VelosHomo Sapiens (ncbitaxon:9606)https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=d51d3a7e2c1d41399193a18ee4e557cfMassIVE56MS:1002864 - No post-translational-modifications are included in the identified peptides of this datasetWe determined longitudinal serum proteomics profiles from children with HLA-conferred diabetes susceptibility to identify changes that could be detected before seroconversion and positivity for disease-associated autoantibodies. Comparisons were made between children who seroconverted and progressed to type 1 diabetes (progressors) and those who remained autoantibody negative, matched by age, sex, sample periodicity, and risk group. The samples represented the prediabetic period and ranged from the age of 3 months to 12 years. After immunoaffinity depletion of the most abundant serum proteins, isobaric tags for relative and absolute quantification were used for sample labeling. Quantitative proteomic profiles were then measured for 13 case-control pairs by high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS). Additionally, a label-free LC-MS/MS approach was used to analyze depleted sera from six case-control pairs. Importantly, differences in abundance of a set of proteins were consistently detected before the appearance of autoantibodies in the progressors. Based on top-scoring pairs analysis, classification of such progressors was observed with a high success rate. Overall, the data provide a reference of temporal changes in the serum proteome in healthy children and children progressing to type 1 diabetes, including new protein candidates, the levels of which change before clinical diagnosis.Serum proteomes distinguish children developing type 1 diabetes in a cohort with HLA-conferred susceptibility.Moulder Robert R, Bhosale Santosh D SD, Erkkilä Timo T, Laajala Essi E, Salmi Jussi J, Nguyen Elizabeth V EV, Kallionpää Henna H, Mykkänen Juha J, Vähä-Mäkilä Mari M, Hyöty Heikki H, Veijola Riitta R, Ilonen Jorma J, Simell Tuula T, Toppari Jorma J, Knip Mikael M, Goodlett David R DR, Lähdesmäki Harri H, Simell Olli O, Lahesmaa Riitta Rl(4)17, moe, Bru, l(4)13, Gli, anon-WO03040301.161, Raw, l(1)G0415, Blood, Cid[Mel], Ci[D], number, Capillary, Serum, cont, presence, CENP-A, prevention, Dmoe, CENP-C, CenpA, l(4)102ABc, CG10701, Random., CONT, Beds, Capillary Bed, DmelCG10701, Del(8)44H, gma, prevention and control, Siah, DmelCG1084, CenH3[Cid], CG13329, CenH3[CID], Svc, ERM, CT1481, BcDNA:RE21270, reference sample, Sinusoidal Beds, DmelCG13329, free, Sinusoidal Bed, Bed, preventive measures, X-linked combined immunodeficiency, l(1)G0323, anon-WO03040301.155, CI, D17, anon-WO03040301.157, anon-WO03040301.159, Cenp-A, CG2125, blood capillary, Controlled, Sinusoid, CiD, Ce, Controlling, preventive therapy, Ci, cenH3, Sinusoids, Blood Serum, collisionally activated dissociation, Cid, CID, ciD, l(1)G0067, count in organism, capillary vessel, CAD, ci[D], DCONT, Ci155, ci-D, Sinusoidal, cenpA, D-Axonin, Col4a-1, DmelCG2125, CenH3, ci155, CenH3/CID, Ci/Gli, Ci/GLI, CENP-A/Cid, CENP-A/CID, prophylaxis, CENPA, dMoe, Randomization, Allocation, Emr1, EMR1, Capillary Beds, control, CG1084, label, cardinality, l(1)G0404, CenpA/CID, Ci-155, Serums, moesin/ezrin/radixin homolog mRNA, CID/CENP-Al(1)G0067, ERM, moe, l(1)G0323, anon-WO03040301.155, anon-WO03040301.161, Emr1, CG10701, EMR1, D17, anon-WO03040301.157, l(1)G0415, anon-WO03040301.159, l(1)G0404, dMoe, DmelCG10701, gma, moesin/ezrin/radixin homolog mRNA., DmoeModb1, liquid chromatography tandem mass spectroscopy, Diabetes Type 1, IPP2A2, PHGDHD, determination, Insulin Dependent Diabetes Mellitus 1, Blood, protein, Serum, Insulin Dependent Diabetes, prevention, temporal, A10, 5730420M11Rik, Classifications, Insulin dependent diabetes mellitus, protein polypeptide chains, phosphoglyceric acid dehydrogenase activity, hierarchies, SerA, SERA, hierarchy, diseases, Biological, systematics, Biorhythm, Juvenile onset diabetes mellitus, 1, diseases and disorders, not stated as uncontrolled, Biorhythms, insulin dependent diabetes, with unspecified complication, Sudden Onset, protein aggregate, Leprb, Autoimmune, prevention and control, DM - Diabetes mellitus, 3-phosphoglyceric acid dehydrogenase activity, Juvenile Onset Diabetes, SET, human disease, Sex, LCMSMS, Biological Rhythms, reference sample, TAF-I, Sudden-Onset Diabetes, NLS, proteins, 4930479N23, NLS1, free, Phenotypic, phosphoglycerate oxidoreductase activity, 3-phosphoglycerate:NAD+ 2-oxidoreductase activity, DmelCG4299, preventive measures, IGAAD, set, Diabetes mellitus, sex, Autoantibody, DmelCG10574, SerA 3PG dehydrogenase activity, Rhythms, sample, Homo sapiens disease, Bioperiodicity, associated, juvenile diabetes, Type 1 Diabetes Mellitus, db, PGAD, LC-MS2, phapii, Juvenile Onset, preventive therapy, DM, LC-MS/MS, Systematics, Brittle, StF-IT-1, uncontrolled, Blood Serum, PGDH, OB-RGRP, Juvenile-Onset, Menstruation, Taxonomies, Diabetes mellitus type I, Rhythmicity, PGDH activity, RENBP, Insulin-dependent diabetes, Diseases, NOS, immune mediated diabetes, type I diabetes mellitus, Genotypic, Sudden-Onset, Autoimmune Diabetes, IDDM, HLA-DR-associated protein II, IDDM - Insulin-dependent diabetes mellitus, DI-2, Diabetes mellitus type 1, I-2Dm, Sudden-Onset Diabetes Mellitus, PDG, Diabetes mellitus type I [insulin dependent type] [IDDM] [juvenile type], CG4299, Juvenile Diabetes, Children, Obr, Diabetes NOS, Type 1, AGE, I-2PP1, disease, TAF-IBETA, liquid chromatography-tandem mass spectroscopy, label, Seroconversions, Rhythmicities, Biological Rhythm, Insulin-Dependent Diabetes Mellitus 1, TAF-Ibeta, obl, i2pp2a, Proteomes, Juvenile-Onset Diabetes Mellitus, DMI UNSPF NT ST UNCNTRLD, Ketosis-Prone Diabetes Mellitus, other disease, Juvenile diabetes, Bioperiodicities, Type I Diabetes, Peptidomics, taxonomy, glycerate 3-phosphate dehydrogenase activity, Periodicities, number, Gene, Diabetes mellitus type 1 (disorder), DIABETES MELLITUS TYPE 01, protein-containing complex, presence, 3PHP reductase activity, PHAPII, LC-MS-MS, Autoimmune Diabete, alpha-phosphoglycerate dehydrogenase activity, polypeptide chain, PGD, Insulin-Dependent, LC-MSMS, Diabetes mellitus (disorder), Gene Products, disease or disorder, 3-phosphate dehydrogenase activity, Type I, D-3-phosphoglycerate:NAD+ oxidoreductase activity, Taxonomy, Insulin-Dependent Diabetes Mellitus, Genotypic Sex, Type I diabetes, ipp2a2, obese-like, 2pp2a, labeling, CG10574, non-neoplastic, Brittle Diabetes Mellitus, 2PP2A, Rhythm, taf-ibeta, Diabetes Mellitus, Type 1 Diabetes, dSET, dSet, disorder, Diabetes, diabetes, incidence, Controlled, T1DM, HEL-S-113, Controlling, T1D, Diabete, RnBP, protein complex, Proteins, alpha-KG reductase activity, disorders, igaad, GlcNAc 2-epimerase, total expressed protein, Cyclicity, medical condition, 3PGDH, DMI UNSPF UNCNTRLD, Ketosis Prone, type I diabetes, group, diabetes mellitus (disease), insulin-dependent diabetes mellitus, count in organism, N-acetyl-D-glucosamine 2-epimerase, LC/MS/MS, native protein, Period, natural protein, I-2PP2A, D-3-phosphoglycerate dehydrogenase activity, Protein, D- and L-HGA, Dm I-2, chemical analysis, I2PP2A, condition, 3-PGDH, Mellitus, LEPROT, susceptibility, diabetes mellitis type I, diabetes mellitus, ensemble, prophylaxis, glycerate-1, alphaKG reductase activity, diabetes mellitis type 1, sample population, Ketosis-Prone, Protein Gene Products, 3-phosphoglycerate dehydrogenase activity, type 1 diabetes, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, 3-phospho-D-glycerate:NAD+ 2-oxidoreductase activity, Juvenile-Onset Diabetes, control, Phenotypic Sex, Cyclicities, renin-binding protein, liquid chromatography tandem mass spectrometry, assay, AA407739, Serums, clinical diagnosis., Insulin DependentT1DM, Ketosis-Prone Diabetes Mellitus, Diabetes Type 1, Juvenile diabetes, T1D, Juvenile Onset, Diabete, Type I Diabetes, Insulin Dependent Diabetes Mellitus 1, Blood, Brittle, uncontrolled, Diabetes mellitus type 1 (disorder), Blood Serum, Serum, DIABETES MELLITUS TYPE 01, Insulin Dependent Diabetes, DMI UNSPF UNCNTRLD, Ketosis Prone, type I diabetes, Juvenile-Onset, insulin-dependent diabetes mellitus, Autoimmune Diabete, Insulin dependent diabetes mellitus, Diabetes mellitus type I, Insulin-Dependent, Insulin-dependent diabetes, Juvenile onset diabetes mellitus, 1, not stated as uncontrolled, immune mediated diabetes, insulin dependent diabetes, Type I, with unspecified complication, Sudden Onset, Autoimmune, Mellitus, type I diabetes mellitus, Juvenile Onset Diabetes, Sudden-Onset, diabetes mellitis type I, Autoimmune Diabetes, IDDM, Insulin-Dependent Diabetes Mellitus, IDDM - Insulin-dependent diabetes mellitus, Diabetes mellitus type 1, Type I diabetes, Sudden-Onset Diabetes, Sudden-Onset Diabetes Mellitus, Diabetes mellitus type I [insulin dependent type] [IDDM] [juvenile type], Juvenile Diabetes, susceptibility., Children, diabetes mellitis type 1, Type 1, Ketosis-Prone, type 1 diabetes, Brittle Diabetes Mellitus, Juvenile-Onset Diabetes, Diabetes Mellitus, Type 1 Diabetes, Insulin-Dependent Diabetes Mellitus 1, Proteomes, Diabetes, juvenile diabetes, Serums, Juvenile-Onset Diabetes Mellitus, Type 1 Diabetes Mellitus, DMI UNSPF NT ST UNCNTRLD, Insulin Dependent0trueD17_LFThermo RAW files Case9TS and Control9TS (Case and Cont) represent D17 and Control-17 and are marked by their visit number. These are label free analyses of depleted serum samples conducted with an Orbitrap Velos - Proxeon capillary LC combination. CID fragmentation was used. The samples were analyzed in quadruplicate with randomization.Wed Jun 25 02:36:00 BST 2014MSV00007876325616278