Quantitative proteomic analysis of human erythropoiesis
Ontology highlight
ABSTRACT:
INSTRUMENT(S): TripleTOF 5600
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Feng Zhou
PROVIDER: MSV000080681 | MassIVE | Sat Mar 25 19:14:00 GMT 2017
SECONDARY ACCESSION(S): PXD006170
REPOSITORIES: MassIVE
Similar Datasets
Project description:Untargeted metabolomics profiling of mice urine after 5 Gy and 7.5 Gy total body radiation exposure at 24 hours. Metabolic profiling of urine samples were performed by TripleTOF 5600+ (AB Sciex) in both ionization mode
2021-11-24 | ST002165 | MetabolomicsWorkbench
Project description:This study investigates the proteomic alterations in striatal synaptic mitochondria isolated from 3-month-old wild-type and Pink1 KO rats using the SWATH-MS strategy. This dataset consists of 32 raw MS files, comprising 8 DIA (SWATH) and 24 DDA runs on a TripleTOF 5600 (SCIEX). Our findings revealed synaptic mitochondrial proteomic changes due to loss of Pink1.
2016-09-28 | PXD004558 | Pride
Project description:Liquid chromatography -mass spectrometry was performed on an AB Sciex TripleTOF 5600TM mass spectrometry system (AB SCIEX, USA) for nontargeted metabolomics analysis
2022-04-24 | PXD033405 | iProX
Project description:A Multiple Affinity Removal System (MARS) Human 14 spin cartridge was used to deplete a dolphin serum which was then digested with trypsin and analyzed without prior fractionation by nanoLC-MS/MS. These files are associated with "2011-9-25_Neely-DolphinSerum." Data analysis: raw data generated by the AB Sciex 5600 were converted to a peak list using the AB Sciex MS Data Converter (v. 1.1 beta, July 2011). Protein identifications were made using Mascot (v. 2.3.02) searching against the Ensembl (release 64) turTru1 dolphin genome assembly protein database [16,598 sequences] and the common Repository of Adventitious Proteins database (cRAP; 2012.01.01; the Global Proteome Machine) using the following parameters: trypsin was selected as the enzyme and three missed cleavages were allowed; carbamidomethylation (Cys) was specified as a fixed modification; glucosylgalactosyl (Lys), oxidation (Met, Pro), and 2-succinyl (Cys) were specified as variable modifications; a precursor tolerance of 10 ppm and fragment ion tolerance of 0.5 Da; instrument type was ESI-QUAD-TOF. Additionally, a non-depleted dolphin sera that had been digested followed by quasi-fractionation using SPE, was analyzed by nano-LC-MS/MS which lead to an additional peptide identification, KGEPGESAYVYR, and these files are associated with "2012-12-12 Dolphin IDA".
2013-09-23 | PXD000431 | Pride
Project description:To discover ESCC related proteins, we used SWATH to quantify the protein abundance between ESCC and adjacent tissues. Briefly, we pooled 10 ESCCtissues and their corresponding adjacent tissues for SWATH acquisition with three replicates.Three DDA repeats were also acquired with the pooled 10-paired ESCC tissue.The trypsin digested peptide mixture was analyzed by AB SCIEX 5600 (AB SCIEX).The database searching procedure was achieved using ProteinPilot v4.5 (AB Sciex). The database is IPI_homo_sapiens_V3.87.
2015-09-22 | PXD001764 | Pride
Project description:This study investigates the proteomic alterations in bone marrow neutrophils isolated from 5-8 week old Gfi1+/-, Gfi1K403R/-, Gfi1R412X/-, and Gfi1R412X/R412X mice using the SWATH-MS technique. This dataset consists of 26 raw MS files, comprising 13 DDA (for spectral library generation)and 13 DIA (for SWATH) runs on a TripleTOF 5600 plus (SCIEX). Our findings revealed significant changes in the expression of neutrophil granule proteins and NADPH-oxidase complex components in Gfi1-mutant neutrophils.
2020-04-07 | PXD010943 | Pride
Project description:MicroRNA399-mediated regulation of the ubiquitin-conjugating enzyme UBC24/PHO2 is crucial for phosphate (Pi) acquisition and translocation in plants. Because of a potential role for PHO2 in protein degradation and its association with membranes, an iTRAQ-based quantitative membrane proteomic method was employed to search for components downstream of PHO2. A total of 7491 proteins were identified from Arabidopsis roots by mass spectrometry, 35.2 % of which were predicted to contain at least one transmembrane helix. Among the quantifiable proteins, 5 were significantly differentially expressed between the wild-type and pho2 mutant under 2 growth conditions. Using immunoblot analysis, we validated the upregulation of several PHT1 Pi transporters and PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 (PHF1) in pho2 and demonstrated that PHO2 mediates the degradation of PHT1 proteins. Genetic evidence that loss of PHF1 or PHT1;1 alleviated Pi toxicity in pho2 further suggests their roles as downstream components of PHO2. Moreover, we showed that PHO2 interacts with PHT1s in the post-endoplasmic reticulum compartments and mediates the ubiquitination of endomembrane-localized PHT1;1. This study not only uncovers a mechanism by which PHO2 modulates Pi acquisition by regulating the abundance of PHT1s in the secretory pathway destined for plasma membranes, but also provides a database of the membrane proteome that will be widely applicable in root biology research. Spectra Processing: The MS/MS raw spectra generated from the Waters Q-TOF Premier (the first replicate) and the AB SCIEX TripleTOF 5600 (the second and third replicates) instruments were processed to detect MS/MS peaks using UniQua (Chang et al., 2013). For the UniQua processing, the spectra were converted into mzXML format using massWolf (version 4.3.1) and ProteoWizard (version 3.0.4623) for the raw data generated from the Waters and AB SCIEX instruments, respectively. The UniQua parameters for Waters Q-TOF Premier were: smoothing = 9, centroiding high = 80%, maximum resolution = 16,000, baseline cutoff = 1.5 counts, reporter m/z range = 114-117, and reporter dynamic range = 5-1,000. The UniQua parameters for AB SCIEX TripleTOF 5600 were: smoothing = 11, centroiding high = 80%, maximum resolution = 25,000, baseline cutoff = 4 counts, reporter m/z range= 114-117 and reporter dynamic range = 5-100,000. The processed MS/MS spectra were then converted into Mascot generic format (.mgf) using mzXML2Search in Trans Proteomics Pipeline (TPP)1 (Deutsch et al., 2010) version 4.4 rev. 1. To obtain better quantification results, the MS/MS spectra with peak number less than 10, average intensity of the top 10 abundant peaks less than 15 counts and iTRAQ average intensity less than 30 counts were further removed from the peaklist file. Protein Qualification and Quantitation: The processed spectra were searched against the TAIR10 database (December 2011, 27,416 sequences) using the Mascot version 2.3 (Matrix Science, London, UK). For the MASCOT search, the mass tolerance for peptide precursor and MS/MS fragments was 0.1 Da. Only one missed cleavage was allowed for tryptic peptides. The methylthiolation (C), iTRAQ4plex (N-term) and iTRAQ4plex (K) were set as fixed modification. The Oxidation (M) and iTRAQ4plex (Y) were set as variable modification. The quantitation option was enabled and set to the iTRAQ4-plex approach. The peptide was considered to be identified if the MASCOT ion score greater than 27 (P less than 0.05). In addition, the protein was considered to be identified if the MASCOT protein score was greater than or equal to 27 with at least one unique and two different peptides identified. For the protein quantitation, only unique peptide was quantified in MASCOT and used to determine the protein ratio in MASCOT. To minimize the systematic ratio error due to sample preparation, the protein ratios were normalized by the mode of the overall protein ratios. For the data acquired by the Q-TOF Premier, 72,817 peptides and 3107 proteins were quantified. For the data acquired by the TripleTOF 5600, 41,885 peptides and 2893 proteins were quantified in the first replicate; 82,397 peptides and 4939 proteins were quantified in the second replicate.
2020-01-22 | PXD000398 | Pride
Project description:We analyzed total proteome of three methyltransferase gene knockouts strains of Escherichia coli: ΔrsmF (JW5301), ΔrlmC (JW2756), ΔrlmE (JW3146) from Keio collection and wild type (WT). Proteins were assessed using IDA approach (i.e. Information Dependent Acquisition) and SWATH (Data-Independent Acquisition) on Sciex TripleTof 5600+ mass‐spectrometer with a NanoSpray III ion source (ABSciex, Canada) coupled to a NanoLC Ultra 2D+ nano‐HPLC system (Eksigent). Dataset covers 16 samples.
2020-01-21 | PXD017171 | Pride
Project description:We have grown C6 glioma cells and rat astrocytes, as well as astrocyte cells co-cultured together with C6 glioma. We performed proteome-wide LC-MS analysis of this experimental groups. The data including LC-MS/MS raw files and exported MaxQuant report. For our co-cultivated in vitro model we used astrocytes and C6 glioma cells. Astrocytes cell lines isolated from rat brain tissue. We analyzed astrocytes in two conditions: beforeand after co-cultivation. Proteins were assessed in an untargeted label-free bottom-up proteomic experiment using IDA approach (i.e. InformationDependent Acquisition) on AB Sciex TripleTOF 6600 Q-TOF mass-spectrometer coupled with LFQ (label-free quantification) approach by MaxQuant software. Dataset covers 165 samples (11 biological rand 5 technical replicates)
2021-10-05 | PXD026776 | Pride
Project description:We performed an untargeted metabolomics analysis on plasma of three animal cohorts. 1) Control rats, 2) Toxins-treated rats (model of the Gulf War Syndrome), and 3) toxins-treated rats+(-)-epicatechin (Flavanol). Metabolites were extracted with ethanol:methanol (50:50) and data acquired by LC-MS/MS (Eksigent nanoLC 400 system -TripleTOF 5600, AB Sciex).
| MSV000086118 | GNPS