Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hb Oxidation in stored RBCs and Vesicles

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Erythrocyte, Blood

DISEASE(S): Disease Free

SUBMITTER: Matthew Wither

LAB HEAD: Angelo D'Alessandro

PROVIDER: PXD002798 | Pride | 2015-10-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20150212_Angelo_RBCs_day21_control_01.raw	Raw
	20150212_Angelo_RBCs_day21_control_02.raw	Raw
	20150212_Angelo_RBCs_day21_control_03.raw	Raw
	20150212_Angelo_RBCs_day21_control_04.raw	Raw
	20150212_Angelo_RBCs_day21_control_05.raw	Raw

Items per page:

1 - 5 of 73

Publications

Hemoglobin oxidation at functional amino acid residues during routine storage of red blood cells.

Wither Matthew M Dzieciatkowska Monika M Nemkov Travis T Strop Pavel P D'Alessandro Angelo A Hansen Kirk C KC

Transfusion 20151001 2

<h4>Background</h4>Routine storage of red blood cells (RBCs) results in the progressive accumulation of storage lesions. While the clinical relevance of these lesions is still a matter of debate, alterations to RBC morphology and biochemistry, especially in terms of energy and redox homeostasis, are likely to affect RBC physiology and functionality at a minimum. Identification of oxidative modifications that accumulate on key RBC proteins will help bridge the gap between storage induced alterati ...[more]

PMID: 26426339

Similar Datasets

Hb Oxidation in stored RBCs and Vesicles

Project 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.

2016-10-04 | MSV000080222 | MassIVE

Influenza A virus- integrated glycomics, proteomics and glycoproteomics

Project description:This study describes how site-specific glycosylation of Influenza A virus changes in response to pressures from the host immune system, thereby allowing the virus to evolve and escape neutralization. We compared the glycosylation patterns of different virus strains as they evolve and correlated this information with changes in biological activity. Furthermore, modelling and molecular dynamics studies were performed to understand the basis for glycan microheterogeneity and interactions of the virions with host-immune molecules.

2016-04-26 | PXD003498 | Pride

Systematic Evaluation of Protein Reduction and Alkylation reveals Massive Unspecific Side Effects by Iodine-containing Reagents

Project description:In this study, we systematically evaluated reduction and alkylation of proteins using three reducing agents (DTT, TCEP, and BME) in combination with four alkylation agents (IAA, IAC, AA, and CAA). We tested these conditions using strong anion exchange (SAX) fractionated in-solution digests and in-gel digested fractions of samples enriched for cytosolic proteins of HeLa cells. We analyzed the data using Proteome Discoverer 2 in combination with the MASCOT search engine with different combinations of variable and fixed modifications as well as error tolerant and mass tolerant searches. Furthermore, we compared IAA and AA alkylated samples by dimethyl labeling and performed multi stage activation triggered by the neutral loss of alkylated methionine side chains. This led to the identification of prominent offside alkylation due to iodine containing reagents at tyrosine, serine, threonine, histidine, lysine, methionine, aspartic and glutamic acid as well as the peptide N-terminus with varying abundances based on the reduction and alkylation reagents used.

2017-05-30 | PXD005183 | Pride

Project description:Vesiculation in Gut Bacteroidota

| PRJNA1298834 | ENA

Glycopeptide identification by LC-MS/MS

Project description:Automatic and rapid identification of glycopeptides by nano-uplc-ltq-ft-ms and proteomic search engine

2016-12-23 | PXD003578 | Pride

miRNA* loading on Ago2

Project description:In flies, microRNAs (miRNAs) are synthesized as a short imperfect duplex, where the miRNA is paired to another small RNA, dubbed the "miRNA*". Usually, miRNA*s are degraded in the last steps of miRNA maturation, but we found evidence that some of them can be loaded on the Ago2 protein. Small RNAs (18-29 nt) from fly heads (WT, ago2 mutants, dcr-2 homozygous and heterozygous mutants) were sequenced using a Solexa Genome Analyzer instrument. The ago2 cDNA library was loaded twice on the instrument, yielding two technical replicates.

2010-08-02 | E-GEOD-12462 | biostudies-arrayexpress

Flagellin (FliC) phosphorylation affects Type 2 protease secretion and biofilm dispersal in Pseudomonas aeruginosa PAO1

Project description:Protein phosphorylation has a major role in controlling the life-cycle and infection stages of bacteria. Proteome-wide occurrence of S/T/Y phosphorylation has been reported for many prokaryotic systems. Previously, we reported the phosphoproteome of Pseudomonas aeruginosa and Pseudomonas putida. In this study, we show the role of S/T phosphorylation of one motility protein, FliC, in regulating multiple surface-associated phenomena of Pseudomonas aeruginosa PAO1. The absence of phosphorylation in the conserved T27 and S28 residues of flagellin FliC, interestingly, did not affect swimming motility, but affected the secretome of type 2 secretion system (T2SS) and biofilm formation of PAO1. Flagellin phosphomutants had increased levels and activities of type 2 secretome proteins. This occurs by a possible mechanism affecting the secretion efficiency of T2SS machinery. Flagellin phosphomutants also formed reduced biofilm at 24h and had delayed biofilm dispersal under static and dynamic flow conditions, respectively. The levels of type 2 secretome and biofilm formation under static conditions had an inverse correlation. Hence, increase in the levels of type 2 secretome was accompanied by reduced biofilm formation in the flagellin phosphomutants. Altogether, we found a system of phosphorylation that co-ordinately regulates surface related processes such as proteases secretion by T2SS, biofilm formation and dispersal.

2022-03-02 | PXD003645 | Pride

A disulfide redox switch mechanism regulates glycoside hydrolase function

Project description:Disulfide bond is a key post-translational modification involved in protein folding, stability, and functional regulation. While the structural role of disulfide bonds has been extensively studied in protein chemistry, their potential involvement in regulating catalytic activity of carbohydrate-active enzymes through redox switch mechanisms remains an untapped realm. In this work, we demonstrate that a glycoside hydrolase from the large family GH2 has its catalytic activity regulated via an intramolecular disulfide bond, adapting dynamically to redox fluctuations in its environment. The enzyme is inactive in its oxidized state, becoming active when reduced through a fully reversible process. Under oxidative conditions, multiple crystallographic structures showed that the disulfide bond formation induces a massive structural disorder in the active site, disrupting the substrate binding site and remarkably the acidic catalytic residues configuration. Conversely, high-resolution cryo-EM structure of the active (reduced) state revealed a notable well-structured active site with catalytic residues properly positioned for a classical Koshland retaining mechanism. This reversible order-disorder mechanism based on disulfide switch to regulate catalytic activity broadens our understanding regarding redox systems involved in carbohydrate breakdown and metabolism, which have implications for biotechnology and microbial biology.

2025-10-30 | PXD070002 | Pride

Proteomic insights into novel food insects: Homology-based proteome characterization and allergenicity considerations for EU-regulated insect species

Project description:Insects have emerged as a sustainable alternative protein source and recently gained regulatory approval in the European Union as novel foods and animal feed ingredients. However, the limited availability of species-specific proteomic databases presents a significant challenge for the accurate identification of proteins in insect-based food products, relevant for food authenticity, safety and allergenicity concerns. In this study, we developed a homology-based proteomic workflow to address the lack of comprehensive sequence data for edible insect species and to explore their allergenic potential. This nanoflow tandem mass spectrometry method (nano-HPLC HR-MS) aims to be generally applicable to underexplored species. We identified between 1079 and 1893 proteins for each of the six investigated insect species Acheta domesticus, Locusta migratoria, Tenebrio molitor, Alphitobius diaperinus, Gryllodes sigillatus and Hermetia illucens, increasing their numbers of known proteins up to 24-fold. Furthermore, we assessed the influence of error-tolerant peptide-spectra matching searches and database composition on protein identification and confirmed on average 90% of selected peptides using targeted methods. We consistently detected known and putative allergens across all tested species, providing further evidence on their allergenic potential. Data from this study may provide the general basis for the development of targeted parallel reaction monitoring mass spectrometry-based assays for so far unsequenced species authentication and quantification of their proteins e.g. in novel foods.

2025-06-03 | PXD061237 | Pride

Acetylated proteomic identification of stored platelets

Project description:In this project, the protein acetylation levels in human platelets and in WT and SIRT3-/- mouse platelets during storage were examined.

2022-06-09 | PXD026341 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data