Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/Mascot_search_results_T141221_Park_RBC_iTRAQ_ABC_Xuniprot_HUMAN3_241_ProteinSummary_FDR.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_15_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_19_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_16_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_12_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_20_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_19_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_15_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_20_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_18_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_12_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_10_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_09_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_20_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_16_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_13_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_13_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_12_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_16_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_22_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_19_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_17_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_09_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_14_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_11_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_10_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_22_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_09_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_17_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_13_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_08_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_22_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_10_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_11_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_21_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_08_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_18_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_15_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_17_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_11_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_21_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_14_B.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_18_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_14_C.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_08_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/141221_Park_iTRAQ_21_A.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/T141221_Park_iTRAQ_B_Allpd_2D.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/T141221_Park_iTRAQ_A_Allpd_2D.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/T141221_Park_iTRAQ_C_Allpd_2D.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/T141221_Park_iTRAQ_CombinedABC_Allpd_2D.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/F037410.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/F037403.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/F037408.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD003851/F037409.datprimaryOK200002580Siu Kwan SzeNot availableBlood CellBloodSelection of CD71+ve reticulocytes from cord blood was performed using the MACS purification system (Miltenyi Biotec, Singapore). One to two mL of cord blood at 50% haematocrit in PBS was incubated with magnetic beads conjugated to CD71 antibody (MIltenyi Biotec) for 20 minutes at room temperature (200ul blood: 25ul CD71 microbeads). After incubation, the blood sample was passed through a MACS LS column followed by three times washing with PBS. Flow through (CD71-ve) and bound fractions (CD71 +ve) were collected and purity monitored by flow cytometry using Thiazole orange staining and/or sub-vital staining. Samples were verified for purity (>90%) prior to MS analyses.PrideNewman SzeQ ExactiveNanyang Technological UniveristyPARTIAL29094334 Chu TTT, Sinha A, Malleret B, Suwanarusk R, Park JE, Naidu R, Das R, Dutta B, Ong ST, Verma NK, Chan JK, Nosten F, Rénia L, Sze SK, Russell B, Chandramohanadas R. Quantitative mass spectrometry of human reticulocytes reveal proteome-wide modifications during maturation. Br J Haematol. 2017 10.1111/bjh.14976Nanyang Technical Universitysksze@ntu.edu.sgMass SpectrometryShotgun proteomicsPlasmodium Falciparum MalariaMature red blood cellMalariaReticulocytesItraqhttp://www.ebi.ac.uk/pride/archive/projects/PXD003851iTRAQiodoacetamide derivatized residuedeaminated residuemonohydroxylated residueCD71+ve and CD71-ve red cells were sub-fractionated to membrane and luminal contents and then digested using trypsin following standard shotgun proteomic sample preparation procedure. The tryptic peptides were labelled using 4-plex iTRAQ reagents. The Q Exactive raw files were converted to mgf file using Proteome Discoverer ver1.4. the combined data of all fractions in each replicate were searched Mascot against Uniprot Human protein DB using an in-house Mascot server 2.41. The Mascot results were exported to csv file, and further analyzed in MS Excel.ProteomicsHomo Sapiens (human)sksze@ntu.edu.sgBiologicalSingaporeErythropoiesis is marked by progressive changes in morphological, biochemical and mechanical properties of erythroid precursors to generate red blood cells (RBC). The earliest enucleated forms derived in this process, known as reticulocytes, are multi-lobular and spherical. As reticulocytes mature, they undergo a series of dynamic cytoskeletal re-arrangements and the expulsion of residual organelles, resulting in highly deformable biconcave RBCs (normocytes). To understand the significant, yet neglected proteome-wide changes associated with reticulocyte maturation, we undertook a quantitative proteomics approach. Immature reticulocytes (marked by the presence of surface transferrin receptor, CD71) and mature RBCs (devoid of CD71) were isolated from human cord blood using a magnetic separation procedure. After sub-fractionation into triton-extracted membrane proteins and luminal samples (isobaric tags for relative and absolute quantitation), quantitative mass spectrometry was conducted to identify more than 1800 proteins with good confidence and coverage. While most structural proteins (such as Spectrins, Ankyrin and Band 3) as well as surface glycoproteins were conserved, proteins associated with microtubule structures, such as Talin-1/2 and ß-Tubulin, were detected only in immature reticulocytes. Atomic force microscopy (AFM)-based imaging revealed an extended network of spectrin filaments in reticulocytes (with an average length of 48 nm), which shortened during reticulocyte maturation (average spectrin length of 41 nm in normocytes). The extended nature of cytoskeletal network may partly account for increased deformability and shape changes, as reticulocytes transform to normocytes.Quantitative mass spectrometry of human reticulocytes reveal proteome-wide modifications during maturation.Chu Trang T T TTT, Sinha Ameya A, Malleret Benoit B, Suwanarusk Rossarin R, Park Jung E JE, Naidu Renugah R, Das Rupambika R, Dutta Bamaprasad B, Ong Seow Theng ST, Verma Navin K NK, Chan Jerry K JK, Nosten François F, Rénia Laurent L, Sze Siu K SK, Russell Bruce B, Chandramohanadas Rajesh RMacs, BPBS, TfR, AI426448, TFRC, sarcoma of the breast, selection process, Histological Labelings, RASSF4, TfR1, B-cell receptor complex, body system, TFR, Fluorescence-Activated, antibody, Fluorescence-Activated Cell Sortings, Microfluorometry, BCR complex, MACS, AU015758, E430033M20Rik, Histological, system, 2610028K12Rik, Flow Microfluorimetry, TFR1, 1-methyl-4-((3-methyl-2(3H)-benzothiazolylidene)methyl)-, Reticulocyte, immunoglobulin complex, Cell Sortings, Cytofluorometry, portion of blood, anatomical systems, Staining, sarcoma of breast, Fluorescence Activated Cell Sorting, Flow Cytofluorometries, membrane bound, Microfluorometries, IBP, pk18, Mtvr-1, MBR, T9, column, sample, Flow, Flow Microfluorometries, PTBR, Cytometry, Bladder pain syndrome, B-lymphocyte receptor complex, Transferrin receptor protein 1, Flow Cytofluorometry, Acas3, Histological Labeling, TR, 80K-L, Cytometries, Sortings, cord blood, Cell Sorting, serum form, p90, Fluorescence-Activated Cell Sorting, BZRP, whole blood, DBI, PKCSL, vertebrate blood, Labeling and Staining, Flow Cytometries, Stainings, sTfR, PRKCSL, breast sarcoma, antibodies, fetal blood, Labeling, PBS, PBR, Microfluorimetry, AI195355, Temperatures, PKBS, Histological Labeling., Bucs1, connected anatomical system, Flow Microfluorometry, Mtvr1, salt with 4-methylbenzenesulfonic acid (1:1), opsonin activity, Cytofluorometries, Painful Bladder Syndrome, Trfr, Magnetic, umbilical cord blood, mDRC, Fluorescence-Activated Cell, sample population, organ system, CD71, immunoglobulin, Painful bladder syndrome, B cell receptor accessory molecule complex, Labelings, Quinolinium, TRFR, B lymphocyte receptor complex, Sorting, B cell receptor activity, Bladder Pain SyndromeMass Spectrum Analysis, Mass Spectrum, human being, wide/broad, Analyses, number, Spectrometry, total expressed protein, Spectrum Analyses, broad., man, presence, Spectrum Analysis, human, Spectroscopy, count in organism, wide, Mass, quantitative, Analysis, Reticulocyte, Proteomes, Mass Spectrum Analyses, Mass Spectroscopy, presence or absence in organismTfR, AI426448, Phenylethylbarbiturate, TFRC, Bru, d230, Clo, Raw, AW549739, Slf, SLF, Somatomedin-C, dTAFII250, FPH2, TfR1, CSV., PHENYLETHYLMALONYLUREA, EfW1, contrasted, Intervention or Procedure, TFR, dmTAF[[II]]230, peptide, Polypeptides, AU015758, Phenylethylbarbituric Acid, peptido, dmTAF1, E430033M20Rik, Taf230, integral component of membrane, phenobarbital, 6-trione, 4, 2610028K12Rik, Del(8)44H, TFR1, Phenylethylbarbitursaeure, TAF250, C79691, Svc, hYAK3-2, Taf200, dTAF[[II]]250, TFIID TAF250, peptides, cel, interventionDescription, cell, membrane region, beta-Trypsin, human protein, somatomedin-C, 5-Phenyl-5-ethylbarbituric acid, SF, Interventional, Taf1p, Kitl, 5-ethyl-5-phenyl-2, Mtvr-1, Mast cell growth factor, SURGICAL AND MEDICAL PROCEDURES, Lccp, dTAF250, mKIAA0989, Con, Phenobarbitol, T9, 5H)-pyrimidinetrione, IGF1, Mechano growth factor, RED, Red, region of membrane, 6(1H, blz, peptidos, 3H, Soluble KIT ligand, TAF, Transferrin receptor protein 1, Sl, TR, DYRK5, Intervention Strategies, IGF-I, serum form, membrane, data, dTAF[[II]]230, TAF[[II]]250, p90, steel factor, hematopoietic growth factor KL, TAF200, integral to membrane, somatomedin, l(3)84Ab, BG:DS00004.13, sTfR, IBP1, TAFII-250, membranous organ component, Procedure, TAF250/230, Cell, Peptide, results, CSA2, HMG-CoAR, sKITLG, dTAF230, AI195355, polypeptide, TAFII250, Phenobarbituric Acid, p230, mechano growth factor, whole membrane, TAF[[II]]250/230, TFIID, Phenobarbital, Igf-1, Mtvr1, Phenylaethylbarbitursaeure, Intervention, Taf[[II]]250, SHEP7, transmembrane, Luminal, membrane of organ, TAF[[II]]230, Col4a-1, mast cell growth factor, Trfr, Stem cell factor, 5-Ethyl-5-phenylbarbituric acid, 5-Ethyl-5-phenyl-pyrimidine-2, Tripcellim, 5H)-trione, TAF[II]250, MASCOT, STAT5, CG17603, TAF[[II]], beta Trypsin, REDK, Trypure, stem cell factor, Kitlg, CD71, 5-ethyl-5-phenylpyrimidine-2, DmelCG17603, KL-1, Taf250, SR3-5, TRFR, MGF, Mgf, c-Kit ligand, KITLG, Peptid, Polypeptide, SCF, Phenylethylmalonylurea, Gb, TAF230, Phenobarbitone, TAF1Comparative Studies, RBC, Reticulocyte, red blood cell., red blood corpuscleprojections, Voltage-gated calcium channel subunit alpha Cav1.2, Forms, TfR, alpha-Alb, TFRC, Globulin, RBC, alpha-Spe, TfR1, Integral, alpha-Spc, TFR, alpha-Tubulin, Glycoprotein, Phenylethylbarbituric Acid, Talin, glycoproteins, tendrils, Calcium channel, BEST:LD32507, 6-trione, 4, TFR1, Analysis, glycoproteine, C-Glycosylated Proteins, integumentum commune, average, beta 2 Transferrin, beta1tub, ALPHA 84C, Analyses, CG9277, red blood corpuscle, Surface, DmelCG1913, alphaTub1, T, CT21159, proteins, Hand-Held Microscopy, SURGICAL AND MEDICAL PROCEDURES, beta1Tub, RED, Red, 6(1H, Surface Protein, Glycosylated Protein, alpha-Tub, Neoglycoproteins, DTA1, cord blood, alphat-1, anatomical protrusion, external covering of organism, tau Transferrin, Light, Band 2 Protein, Normalcy, Procedure, alpha-tubulin, fetal blood, Spectrum Analysis, CSA2, HMG-CoAR, Isotransferrin, epsilon Tubulin, shelf, Corpuscles, red blood cell count, Cell Membrane Protein, Membrane-Associated, alpha84B, Talpha1, Spectrometry, 5H)-trione, alpha1tub84B, Cell Membrane Proteins, Tln, alpha, alphatub84B, projection, ridge, human, beta1-tub, Hand Held Microscopy, DTB2, Corpuscle, 5-ethyl-5-phenylpyrimidine-2, Cells, Platelet, beta-Tub56D, Ankyrin, anon-EST:fe2E2, transferrin, C-Glycosylated, anon-EST:Liang-2.30, Peptidomics, lamellae, delta-Tubulin, alpha-Spect, number, anon-EST:Liang-1.59, PHENYLETHYLMALONYLUREA, alphaT, process of organ, lamella, surface, L type, relational shape quality, E430033M20Rik, Membrane-Associated Protein, Reticulocyte., Gene Products, 2610028K12Rik, Phenylethylbarbitursaeure, Blood Corpuscle, globular, alpha1, Normalities, Cell Membrane, beta Tubulin, interventionDescription, Erythropoieses, Siderophilin, glycoproteines, beta Spectrin, CG6831, beta1t, dre3, Rhea, man, O-Glycosylated Proteins, Phenobarbitol, laminae, Transferrin receptor protein 1, Alf, l(3)dre3, beta-tubulin56D, Dmbeta1, alpha-Spectrin, Trf, epsilon-Tubulin, anatomical process, Proteins, Cell Surface, Cell Surface Protein, alphatub, erythropoiesis, Cell, alpha-tub, Beta-1 metal-binding globulin, alpha1t, Simple Microscopy, Glycosylated Proteins, stab cell, beta 2-Transferrin, alphaSp, alphaTUB, alphaTub, Cell Surface Proteins, Mass Spectrum Analyses, organ process, Mtvr1, Membrane Associated Protein, Intervention, Phenylaethylbarbitursaeure, band form, alpha Tubulin, underdeveloped, gamma-Tubulin, N-Glycosylated Proteins, beta[[1]]-tubulin, Compound Microscopy, increased number, ankyrin, Magnetic, rod neutrophil, beta1, Rat brain class C, REDK, beta, Tub, processes, Gene Proteins, DmelCG6831, Compound, quantitative, glicoproteinas, tub, AI426448, Integral Membrane Proteins, Phenylethylbarbiturate, alpha1tub, O-Glycosylated, Blood, Surface Proteins, Imaging, Membrane-Associated Proteins, Organelle, neurotubule, betaTub1, band, delta Tubulin, alpha-tubulin 84B, l(3)04276, B1t, Light Microscopy, Liver regeneration-related protein LRRG03, Triton, AU015758, l(3)g3, MRB17.11, Reticulocyte, Nereid, microtubulus, beta-1 metal-binding globulin, alpha-spec, Mass Spectrum Analysis, glicoproteina, Glykoprotein, increased, N-Glycosylated, Simple, force amplitude, beta-Tubulin, 5-ethyl-5-phenyl-2, Mtvr-1, MRB17_11, alpha-spectrin, alpha-tub84B, 1t, T9, band cell, Protein p235, papilla, Hand-Held, TF, Membrane Associated Proteins, microtubuli, 3H, associated, Membrane Protein, TR, Transferrin, a1t, BETA 56D, wide/broad, lamina, flanges, beta-1, organism surface, sTfR, Optical Microscopy, Spectroscopy, AI195355, shortened, alphaSpec, Spectrins, tau-Transferrin, spectrin, Microtubule, beta-Spectrin, Blood Cell, beta-tub, beta-1 Metal-Binding Globulin, erythrocyte number, shelves, Glycosylated, red blood cell, Transferrins, 5-Ethyl-5-phenyl-pyrimidine-2, beta 1 Metal Binding Globulin, Transferrin C, Transferrin B, beta56D, DmelCG9277, umbilical cord blood, Metal-Binding Globulin, RBC differentiation, Tuba84B, beta-Tub, wide, CD71, alphaTub84, Health, nc33, tubulin, spine, integumentary system, Microscopy, Blood Corpuscles, Serotransferrin, isoform 1, Phenylethylmalonylurea, short, dermal system, CG1913, Proteomes, betaTub, accessory, Integral Membrane, beta1-Tubulin, human being, l(3)alpha-Spec, Band 2, alpha Spectrin, Gene, broad, Spectrum Analyses, Monoferric Transferrins, tubA84B, presence, supernumerary, protrusion, PRO1400, Intervention or Procedure, ms(3)nc33, klo, Mass, phenobarbital, alpha-Sp, CG1977, siderophilin, Mass Spectroscopy, hYAK3-2, betatub(56D), a-tub84B, beta[[1]] tubulin, 5-Phenyl-5-ethylbarbituric acid, stubby, Interventional, ridges, Optical, 5H)-pyrimidinetrione, gamma Tubulin, clone 1.59, tubalpha1, rotund, clone 2.30, Monoferric, Glykoproteine, DYRK5, Intervention Strategies, serum form, p90, 3A9, DmelCG1977, total expressed protein, Tubulin, talin, Tubalpha1, cardiac muscle, DM1alpha, count in organism, Phenobarbituric Acid, l(3)84Bd, erythrocyte cell differentiation, Protein, Acute Flaccid Myelitis, Membrane Proteins, Phenobarbital, flange, Mass Spectrum, Luminal, red blood cell differentiation, Normality, body surface, Trfr, 5-Ethyl-5-phenylbarbituric acid, FCP-B, aTub84B, Membrane, alpha-1 polypeptide, beta-1 Metal-Binding, Protein Gene Products, process, present in greater numbers in organism, Integral Membrane Protein, l(3)62Bd, TRFR, alpha-Tub84B, processus, alfa-Spec, Spec, Phenobarbitone, Platelet Protein p235, presence or absence in organismRBC, Reticulocyte, red blood cell., red blood corpuscle258trueReticulocytes vs mature red blood cellcomparative study reticulocytes vs mature red blood 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