PXD002798

PXD002798 is an original dataset announced via ProteomeXchange.

Title	Hb Oxidation in stored RBCs and Vesicles
Description	We used a state of the art proteomics workflow, based upon nano-UPLC-MS\MS and advanced database searching to identify oxidative modifications to functional residues of hemoglobin subunit beta . Progressive accumulation of oxidized residues in stored erythrocytes and selective removal in vesicles was observed, further substantiating the hypothesis about vesiculation as a self-protecting mechanism in aging erthrocytes.
HostingRepository	PRIDE
AnnounceDate	2015-10-05
AnnouncementXML	Submission_2015-10-05_08:56:28.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002798
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Matthew Wither
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Octanoyl; LG-anhyropyrrole; DHP; His->Trp; Met->Trp; QTGG; Ser->Gly; NHS-LC-Biotin; Biotin; Ethylphosphate; Label:15N(1); Methylamine; Gly->Cys; Tyr->Met; Phe->Arg; BITC; Trp->Hydroxykynurenin; SecCarbamidomethyl; Delta:H(1)O(-1)18O(1); Label:2H(4)+Acetyl; Pro->Asn; AEC-MAEC; Asp->Asn; Delta:H(4)C(2); Succinyl:2H(4); Pro->Asp; EQAT:2H(5); Asp->Thr; Cys->Ala; Val->Asn; O-pinacolylmethylphosphonate; Lys->Met; Hex1HexNAc1; iTRAQ8plex:13C(6)15N(2); Asp->Tyr; Arg->Val; Glu->Asn; Pro->Thr; Xle->Glu; iTRAQ4plex115; SPITC; Deoxyhypusine; Gly->Trp; Ala->Ser; Gln->Xle; Amidino; Trp->Oxolactone; Xle->Lys; HMVK; SulfoGMBS; Gly->Ala; Thr->Xle; NDA; Thr->Ala; Arg->Tyr; Met->Tyr; Val->Glu; CresylSaligeninPhosphate; Phenylisocyanate; Hydroxytrimethyl; Iodo; OxArgBiotin; AhaEthynylUridine; Glu->Pro; GlycerylPE; Label:15N(3); CLIP_TRAQ_3; Amidine; Ser->Val; Met->His; NeuGc; Val->Thr; Dimethyl:2H(4)13C(2); Cys->His; Bipyridine; Carbamyl; IED-Biotin; SulfanilicAcid; DNPS; Ser->Lys; Cation:Na; Asn->Trp; Arg->Glu; Deamidated; Lys->His; CAMthiopropanoyl; 4-ONE+Delta:H(-2)O(-1); Met->Ser; Met-loss; Label:13C(4)15N(2)+GlyGly; Val->Ala; Phe->Ser; 2-monomethylsuccinyl; Val->Met; Pro->Glu; Phe->Ala; Delta:S(-1)Se(1); Phe->Asp; Pro->Ala; Delta:H(6)C(6)O(1); Glu->Met; Met->Asp; Guanidinyl; Difuran; Asn->Asp; EQIGG; PhosphoHex; 4AcAllylGal; SPITC:13C(6); Asn->Ser; Label:13C(6)+Dimethyl; GeranylGeranyl; Label:18O(1); Arg2PG; PropylNAGthiazoline; Delta:H(2)C(3); Arg->Cys; Met->Lys; Decanoyl; HexNAc; Propargylamine; FMN; CAF; Phe->Gln; LG-lactam-R; Quinone; Cys->Asn; Propiophenone; Phe->Lys; Gly->Xle; Arg->His; Thr->Val; Argbiotinhydrazide; Ser->Pro; Diethylphosphate; Xle->Gln; HNE; Ala->Val; Label:2H(4)13C(1); Label:13C(6); Label:13C(5); Met->Gln; Ser->LacticAcid; Gln->Thr; Cysteinyl; Cyano; Nitro; SulfanilicAcid:13C(6); Myristoyl; Ethanolyl; Met->Arg; Gln->Pro; Label:13C(9); Gly->Pro; Phosphopropargyl; AMTzHexNAc2; Tyr->Asp; Nethylmaleimide+water; Phe->Xle; Glu->Gln; Delta:H(4)C(3)O(1); Formyl; ICPL:13C(6)2H(4); Gly; Cys->Xle; Gly->Asp; Arg-loss; Ala->Arg; GIST-Quat:2H(6); Met->Val; Cation:Zn[II]; His->Met; BHTOH; O-Methylphosphate; Pro->Xle; His->Cys; Phe->Asn; Gln->Ala; Pro->Ser; Trp->Kynurenin; Thr->Met; Dihydroxyimidazolidine; Pro->Tyr; AEBS; Didehydroretinylidene; His->Gly; Ala->Cys; Label:13C(6)15N(2)+Dimethyl; SMA; Label:2H(9)13C(6)15N(2); Label:2H(4)+GlyGly; Tyr->Pro; Hep; Gln->His; Phe->Thr; NBS; Succinyl; Gly->Thr; Succinyl:13C(4); Glu->Ser; Ethyl+Deamidated; Xlink:EGScleaved; Cys->Gln; Ub-VME; Xle->Asn; Leu->MetOx; Gln->Glu; Label:15N(4); Lys->Ala; Ala->Pro; Thrbiotinhydrazide; Tyr->Lys; LeuArgGlyGly; Arg->Gly; Glu->Arg; Glu->Val; His->Tyr; Dimethyl; AHA-SS_CAM; Delta:H(4)C(6); Gly->Met; Label:15N(2); Trp->Gln; Asp->Trp; Cresylphosphate; ICDID:2H(6); Saligenin; His->Phe; mTRAQ; Label:15N(2)2H(9); IMID:2H(4); iTRAQ4plex114; Val->Gly; Tyr->Xle; Tyr->Ala; Label:2H(4); Deamidated:18O(1); Butyryl; Xle->Arg; ICDID; Pro->Lys; Asn->Val; Propionamide:2H(3); Gln->Val; Ala->Gly; Asn->Glu; Hydroxymethyl; PyridoxalPhosphate; TMT; ESP; Pro->Trp; Asp->Gln; HexN; Cytopiloyne+water; 2HPG; Gly->Arg; O-Dimethylphosphate; Ser->Gln; sulfo+amino; Met->Asn; Ala->Tyr; Gly->Glu; Bromo; Phe->Val; Trp->Val; Carboxymethyl:13C(2); Ala->Xle; Label:2H(10); Tyr->Asn; 3sulfo; Gln->Gly; Gln->Cys; Phe->Cys; Trp->Cys; Pyridylacetyl; ICAT-C; Sulfo; TMT2plex; Ala->Phe; Asn->Ala; PhosphoHexNAc; Dansyl; Acetyldeoxyhypusine; mTRAQ:13C(3)15N(1); Amidated; IBTP; Cys->Glu; Gly->Phe; Gln->pyro-Glu; Cation:Li; Propyl:2H(6); Asn->Gly; Ser->Thr; Arg->Pro; Label:13C(1)2H(3); Val->Cys; Xle->Val; Menadione-HQ; Arg->Xle; Piperidine; Asn->Pro; Thr->Tyr; Delta:H(2)C(3)O(1); Asn->Arg; Lys->Gly; Xle->Asp; Thr->Phe; CLIP_TRAQ_2; Pyridylethyl; dHex; Xlink:DTSSP; glucosone; Ser->Asp; Gly->Gln; EQAT; Propionyl; Cys->Pro; Methylthio; Lys->Val; Asp->Arg; Gln->Tyr; DTT_ST:2H(6); Xle->Cys; Hex(2); Ser->Asn; GlyGly; BHAc; ISD_z+2_ion; Trp->His; Biotin:Thermo-88310; Ser->Met; Met->Cys; Gln->Asn; Tyr->Phe; Gln->Ser; Xlink:DMP; Asp->Lys; Glycerophospho; Sulfide; Cys->Ser; FP-Biotin; Diiodo; 2-dimethylsuccinyl; Ala->Asp; Label:13C(6)15N(4)+Dimethyl; Propionyl:13C(3); Val->Trp; Hex(1)HexNAc(1)dHex(1); Asp->Ser; Val->His; ICPL:2H(4); Thioacyl; Carboxyethyl; IMID; TMPP-Ac; Isopropylphospho; Glu->Thr; NEIAA:2H(5); Glu->pyro-Glu; Palmitoyl; Pro->Gln; mTRAQ:13C(6)15N(2); Lys->Glu; NIPCAM; Ala->His; His->Lys; Trp->Ala; Amino; Myristoleyl; Phe->CamCys; HPG; Acetylhypusine; Malonyl; Asp->Met; Lys->Asp; Nmethylmaleimide; Trp->Gly; Asp->Phe; His->Val; Glu->Xle; GluGlu; NEIAA; Asp->Val; Label:13C(4)15N(1); TNBS; Cytopiloyne; PEITC; Asp->Ala; Delta:H(8)C(6)O(2); Phe->Pro; ICPL:13C(6); Lys->Ser; Glu->Cys; Label:13C(3)15N(1); Lys->MetOx; Ethanedithiol; Cys->Asp; Tyr->Arg; PyruvicAcidIminyl; DTT_C:2H(6); Label:13C(6)15N(1); VinylPMS; DiLeu4plex115; Tyr->Trp; Trp->Asn; Ethyl; Phe->Glu; His->Thr; Trp->Arg; Gly->Lys; Xle->Ala; Ala->Gln; Pentylamine; Label:13C(6)15N(2)+Acetyl; TMT6plex; OxProBiotinRed; Nethylmaleimide; thioacylPA; DTT_C; Ala->Glu; Methyl:2H(3); cGMP; G-H1; MDCC; Val->Arg; AHA-Alkyne; Acetyl:2H(3); Trp->Met; Xle->Thr; NEMsulfur; Label:13C(9)+Phospho; GIST-Quat:2H(3); BDMAPP; HNE+Delta:H(2); Trp->Xle; Hex; GIST-Quat:2H(9); Thr->Asn; Trp->Thr; Glucuronyl; Benzoyl; Methylphosphonate; GluGluGlu; Diisopropylphosphate; Cys->ethylaminoAla; Ethoxyformyl; Pro->Phe; His->Arg; LG-lactam-K; Trp->Tyr; 2-succinyl; Ser->Xle; DeStreak; Asp->Pro; Label:18O(2); Nitrosyl; Tyr->Thr; Dicarbamidomethyl; Met->Thr; PyMIC; Oxidation; Ser->Arg; Trp->Lys; Lys->CamCys; 2-nitrobenzyl; Pyro-carbamidomethyl; Methyl+Deamidated; Thr->His; Asn->Met; Xle->Met; DiLeu4plex117; Methylmalonylation; Xle->Tyr; DiLeu4plex118; Lys-loss; Arg->Trp; Tyr->Gly; Thr->Lys; Ser->Cys; Glu->His; Gly->Asn; Gln->Met; Asn->Xle; Ub-amide; Didehydro; Tyr->Glu; probiotinhydrazide; Thr->Arg; OxLysBiotin; Glu->Gly; Label:13C(6)+GlyGly; Ser->Ala; maleimide; Asn->Cys; Ser->Phe; Xlink:SSD; Lys->Gln; Pro->Gly; Met->Ala; EDT-maleimide-PEO-biotin; Ser->Tyr; GIST-Quat; Gly->Ser; Met->Gly; DAET; MG-H1; Label:13C(6)15N(4); Phe->Trp; Lysbiotinhydrazide; Cation:Ni[II]; dNIC; CarboxymethylDTT; Cys->Gly; Trp->Ser; OxArgBiotinRed; NeuAc; Xle->Gly; Cation:Ca[II]; Dioxidation; Cys->Lys; Delta:H(4)C(2)O(-1)S(1); iTRAQ4plex; trifluoro; Gln->Phe; biotinAcrolein298; Lys->Tyr; Thr->Glu; Val->Lys; Gly->His; Gln->Lys; 4-ONE; DTBP; Thiadiazole; Phe->Tyr; Arg->Asn; Methyl:2H(3)13C(1); Met->Phe; Iminobiotin; Label:13C(6)15N(2)+GlyGly; Ub-Br2; Ammonium; EGCG2; Label:13C(1)2H(3)+Oxidation; Label:13C(6)15N(4)+Methyl; Ala->Asn; Val->Asp; Xlink:DSS; NIC; Phe->Gly; Chlorpyrifos; Lys->Pro; Methylpyrroline; Val->Tyr; Glu->Trp; Arg->Ala; Label:2H(3); Cation:Ag; Menadione; Met-loss+Acetyl; Thr->Gly; Trp->Asp; Biotin:Thermo-21345; Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2); Lys->AminoadipicAcid; Delta:H(2)C(2); Lys->Asn; Cation:K; lapachenole; Fluoro; GGQ; His->Glu; Ahx2+Hsl; HydroxymethylOP; Val->Phe; Gln->Arg; Arg->Asp; Xlink:SMCC; BHT; HCysteinyl; SulfurDioxide; Ser->Glu; Thr->Cys; Label:13C(3); Pro->His; Glu->Phe; Glu; Delta:H(4)C(3); Tyr->Cys; Trp->Pro; Asn->Tyr; ICPL; Label:13C(6)15N(4)+Methyl:2H(3)13C(1); HCysThiolactone; Arg->Ser; DiLeu4plex; UgiJoullieProGly; Tyr->Ser; Biotin:Thermo-33033-H; HexNAc(1)dHex(1); Phe->Met; Ala->Trp; BisANS; Thr->Gln; Asp->Glu; Arg; AccQTag; His->Ala; His->Asn; Ala->Met; Can-FP-biotin; Glutathione; Bacillosamine; His->Pro; Chlorination; OxLysBiotinRed; DTT_ST; Trioxidation; Val->Pro; NO_SMX_SMCT; Asp->Cys; MTSL; Cation:Mg[II]; Methyl:2H(2); cysTMT; Tyr->Gln; Glycosyl; Glu->Tyr; Asp->Gly; Delta:H(6)C(3)O(1); Methyl; Xlink:EGS; Cys->Thr; Lys->Trp; Xlink:DMP-de; Label:13C(4)+Oxidation; Lys->Arg; Thr->Ser; a-type-ion; Lys->Phe; cGMP+RMP-loss; Label:13C(9)15N(1); PET; Gln->Trp; Xle->Trp; CLIP_TRAQ_4; Ala->Thr; Lys->Thr; Pro->Val; Thiophospho; Arg->Met; Delta:H(5)C(2); DimethylpyrroleAdduct; iTRAQ8plex; Biotin-phenacyl; Gln->Asp; Crotonaldehyde; His->Gln; His->Ser; Propionamide; HNE-Delta:H(2)O; Trp->Phe; Phosphoadenosine; Pro->pyro-Glu; Methyl+Acetyl:2H(3); AHA-SS; LG-Hlactam-K; Thr->Pro; Arg->Lys; 3-deoxyglucosone; Asp->Xle; DFDNB; Glu->Asp; ESP:2H(10); Pro->Arg; glycidamide; Cys->Phe; Asn->Thr; Delta:H(8)C(6)O(1); Trimethyl; Dimethyl:2H(6)13C(2); Phosphoguanosine; Carbofuran; Xle->Pro; Glu->Ala; Arg->Gln; Gly->Val; Val->Xle; DMPO; Cation:Fe[II]; ethylamino; Label:13C(5)15N(1); Phospho; Carboxy; Thr->Asp; Furan; Xlink:DMP-s; CarbamidomethylDTT; Asp->His; Lys->Xle; Phe->His; Xlink:DST; NEMsulfurWater; Hydroxycinnamyl; TMAB; Cation:Cu[I]; Palmitoleyl; Val->Ser; Ser->Trp; Lys->Cys; Thr->Trp; Xle->Phe; Cys->Met; Diethyl; Xle->Ser; Ethanolamine; Asn->Phe; Dimethyl:2H(4); Hypusine; Tyr->His; NEM:2H(5); Met->Glu; PhosphoUridine; Ala->Lys; Asn->His; Dimethyl:2H(6); pupylation; Cys->Val; Pro->Met; Arg->Thr; Asn->Gln; Met->Pro; Arg->Npo; Label:13C(8)15N(2); Gly->Tyr; BMP-piperidinol; Pro->Cys; QAT:2H(3); Label:13C(6)+Acetyl; Nmethylmaleimide+water; Trp->Glu; Carboxymethyl; AEC-MAEC:2H(4); Met->Xle; Val->Gln; Biotin:Thermo-33033; Xle->His; Acetyl; Arg->Phe; Cys->Trp; LG-pyrrole; ADP-Ribosyl; Biotin-PEO-Amine; Phenylisocyanate:2H(5); His->Xle; Propyl; UgiJoullieProGlyProGly; Tyr->Val; Label:13C(4); Glu->Lys; Cys->Tyr; Ser->His; O-Isopropylmethylphosphonate; QEQTGG; LG-anhydrolactam; Delta:H(2)C(5); Asn->Lys
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-08-26 06:36:10	ID requested
⏵ 1	2015-10-05 08:56:30	announced

Wither M, Dzieciatkowska M, Nemkov T, Strop P, D'Alessandro A, Hansen KC, Hemoglobin oxidation at functional amino acid residues during routine storage of red blood cells. Transfusion, 56(2):421-6(2016) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: RBC Transfusion, LC-MS\MS, Hemoglobin, Oxidation

Angelo D'Alessandro
contact affiliation	University of Colorado Denver - Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
contact email	angelo.dalessandro@ucdenver.edu
lab head
Matthew Wither
contact affiliation	University of Colorado Denver
contact email	matthew.wither@ucdenver.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/10/PXD002798

PRIDE project URI

• PRIDE
  1. PXD002798
     1. Label: PRIDE project
     2. Name: Hb Oxidation in stored RBCs and Vesicles