Human hemolysate glycated proteome
Ontology highlight
ABSTRACT:
INSTRUMENT(S): instrument model, LTQ Orbitrap XL
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Erythrocyte
SUBMITTER: 
MARIA RAMIREZ
PROVIDER: PRD000401 | Pride | 2011-11-11
REPOSITORIES: Pride
Similar Datasets
Project description:Glycated proteins identified in human plasma by HCD-MS2 and CID-MS3 analysis with the experiment for predictive analysis
2010-12-03 | PRD000346 | Pride
Project description:Human serum albumin is the most abundant plasma protein with a large number of lysine and arginine residues. Hence, it is highly susceptible to glycation in vivo. In hyperglycemic conditions, such as diabetes, the level of HSA glycation increases. Here we quantified glycated HSA peptides in a subject population of healthy and type 2 diabetes with and without nephropathy to assess its performance for the diagnosis of diabetic nephropathy compared to HbA1c.
2023-07-20 | PXD040028 | Pride
Project description:Quantitative proteomic analysis of human post-mortem substantia nigra from patients with Parkinson’s disease (n=3) versus controls (n=3) based on sixplex TMT (TMT6) isobaric labeling which allowed protein simultaneous identification and quantification. Samples were digested and pooled after TMT6 labeling. Peptides were fractionated by OFFGEL electrophoresis (24 fractions). Each peptidic fraction was analyzed in two technical replicates by LC−MS/MS analysis on a LTQ Orbitrap XL mass spectrometer equipped with a NanoAcquity HPLC system. MS data were processed using EasyProtConv (v. 1.21). Peak lists were generated from raw data combining CID and HCD spectra, and submitted to Easyprot (v2.2) which uses Phenyx (GeneBio, Geneva, Switzerland) for protein identification [1]. Searches were conducted against UniProt Swiss-Prot database (08-Feb-2011, 525’207 entries) specifying Homo sapiens taxonomy. Trypsin was selected as the proteolytic enzyme, one missed cleavage was allowed, cysteines carbamidomethylation, TMT6 amino terminus and TMT6 lysine were set as a fixed modification whereas oxidized methionine as variable. The minimum peptide length was five amino acids and precursor error tolerance was 10 ppm. False positive ratios were estimated using a reverse decoy database [3]. Peptide z-scores were set to maintain a false positive peptide ratio below 1%. Proteins with at least two unique distinct peptide sequences were selected and clustered based on shared peptides indistinguishable by MS [4] using Isobar (v 1.3.1) package. The protein entry containing the most peptides was selected as the group reporter. For protein quantification, TMT6 reporter ion intensities were extracted, corrected for isotopic impurities as provided by the manufacturer and each channel was normalized imposing equal median intensity. Only spectra from protein specific peptides not eliminated after outlier filtering were used for quantification. Isobar R package (v 1.3.1.) was used to calculate protein ratios and select statistically significant differentially regulated proteins between the two states.
2014-01-28 | PXD000427 | Pride
Project description:The submitted dataset contains raw files from 96 synthetic peptide libraries, using either HCD or ETD as fragmentation technique. The synthesized 96 tryptic peptide libraries containing >100,000 unmodified peptides plus their corresponding >100,000 phosphorylated counterparts with precisely known sequences and modification sites. All these libraries were subjected to LC-MS/MS on an Orbitrap mass spectrometer using HCD and ETD fragmentation. The generated mass spectrometric data deposited in this database can be used in numerous ways to develop, evaluate and improve experimental and computational proteomic strategies. Raw MS data files were converted into Mascot generic format files (MGF) using Mascot Distiller (2.4.2.0, www.matrixscience.com). Important parameters included: i) signal to noise ratio of 20 for MS/MS and ii) time domain off (no merging of spectra of the same precursor). The MGF files were searched against human IPI v3.72 including the sequences of all 96 libraries,using the Mascot search engine (2.3.1, 24). Search settings: Decoy search using a randomized version of the human IPI v3.72 including the sequences of all 96 libraries was enabled; monoisotopic peptide mass (considering up to two 13C isotopes); trypsin/P as protease; a maximum of four missed cleavages; peptide charge +2 and +3; peptide tol. +/- 5 ppm; MS/MS tol. +/- 0.02 Da; instrument type ESI-Trap (for HCD data) or ETD-Trap (for ETD data) respectively; variable modifications: oxidation (M), phospho (ST), phospho (Y). The result files were exported to pepXML and Mascot XML with default options provided by Mascot.
2013-05-05 | PXD000138 | Pride
Project description:We investigated the differential phosphoproteome of the mouse heart after isoproterenol stimulus of the AC3-I and AC3-C mice. The former is a model of specific in vivo CaMKII inhibition by a transgenically expressed peptide, whereas the latter is a transgenic mouse expressing a control peptide. Data processing: all raw data files of the individual SCX fractions of each of the 2 mouse experiments were imported into Proteome Discoverer v1.3.0.339 and the combined peak list was split into CID and HCD data (where applicable) before database searching. Subsequently, CID and HCD peak lists were searched individually against an International Protein Index (IPI; http://www.ebi.ac.uk/ipi) database containing mouse sequences and common contaminants such as bovine serum albumin and human keratins (IPI-Mouse v3.84; 60 248 sequences) through a direct connection to our in-house Mascot server (Mascot v2.3.2, Matrix Science, London, UK). The following settings were used: carbamidomethylation on cysteines as static modification; light, intermediate, and heavy dimethylation of peptide N-termini and lysine side chains, as well as oxidation on methionine and phosphorylation on serine, threonine, or tyrosine as variable modifications; and precursor mass tolerance of 20 ppm and 0.8 Da on the fragment masses (for CID) but 20 ppm and 0.02 Da for HCD searching. The enzyme was specified as trypsin, and 2 missed cleavages were allowed.
2013-08-02 | PXD000174 | Pride
Project description:Protein extraction and proteolytic digestion were performed using a Filter-Assisted Sample Preparation (FASP) protocol. In case of phosphopeptide enrichment immobilized Fe(III) affinity chromatography (Fe-IMAC) was performed. The peptides were fractionated using an HPLC system fitted with an SCX column. 10 sample datasets were used: 1. CRC_N: Normal tissue samples were obtained from 20 colorectal cancer patients, no quantification.Phosphopeptide enrichment was performed. 2. CRC_T: Human colorectal cancer tissue samples were obtained from 20 patients, no quantification. Phosphopeptide enrichment was performed. 3. CRC_iTRAQ: Human colorectal cancer tissue samples were obtained from 24 patients, iTRAQ quantification. 4. CRC_phospho_iTRAQ:Human colorectal cancer tissue samples were obtained from 24 patients, iTRAQ quantification.Phosphopeptide enrichment was performed. 5. HCT116_iTRAQ: Human colon cancer cell HCT116, iTRAQ quantification. 6. HCT116_phospho_iTRAQ: Human colon cancer cell HCT116, phosphopeptide enrichment, iTRAQ quantification. 7. SW_SILAC_HL: Human colon cancer cell SW480 and SW620, SW480 and SW620 were grown in SILAC media, containing l-arginine (Arg0) and l-lysine (Lys0) (SW480; light), or 13C615N4-l-arginine (Arg10) and 13C6-l-Lysine (Lys6) (SW620; heavy). 8. SW_SILAC_LH: SW480 and SW620 were grown in SILAC media, containing l-arginine (Arg0) and l-lysine (Lys0) (SW620; light), or 13C615N4-l-arginine (Arg10) and 13C6-l-Lysine (Lys6) (SW480; heavy). 9. SW_phospho_SILAC_HL: SW480 and SW620 were grown in SILAC media, containing l-arginine (Arg0) and l-lysine (Lys0) (SW480; light), or 13C615N4-l-arginine (Arg10) and 13C6-l-Lysine (Lys6) (SW620; heavy). Phosphopeptide enrichment was performed. 10. SW_phospho_SILAC_LH: SW480 and SW620 were grown in SILAC media, containing l-arginine (Arg0) and l-lysine (Lys0) (SW620; light), or 13C615N4-l-arginine (Arg10) and 13C6-l-Lysine (Lys6) (SW480; heavy). Phosphopeptide enrichment was performed. For creation of xml and mgf files, Proteome Discoverer 1.3 and Mascot v2.3 software were used.
2013-01-11 | PXD000089 | Pride
Project description:The platelet releasate defined by quantitative reversed protein profiling. Dimethyl labeled proteins of platelets in resting (light label) and activated state (collagen and thrombin activation, intermediate label) from three healthy volunteers fractionated by SCX, analyzed on a LTQ Obitrap Velos using a data dependent decision tree method (HCD/ETD).Peak lists were generated from the raw data files using the Proteome Discoverer software package version 1.3.339. Peptide identification was performed by searching the individual peak lists (HCD, ETD-IT and ETD-FT) against a concatenated target-decoy database containing the human sequences in the Uniprot database (release 2012_06) supplemented with a common contaminants database using the Mascot search engine version 2.3 (Matrix Science, London, United Kingdom) via the Proteome Discoverer interface (version 1.3). The search parameters included the use of semitrypsin as proteolytic enzyme allowing up to a maximum of 2 missed cleavages. Carbamidomethylation of cysteines was set as a fixed modification whereas oxidation of methionines and the dimethyl light and intermediate labels on N-termini and lysine residues were set as variable modifications. Precursor mass tolerance was initially set at 50 ppm, while fragment mass tolerance was set at 0.6 Da for ETD-IT fragmentation and 0.05 Da for HCD and ETD-FT fragmentation. Subsequently, the peptide identifications were filtered for true mass accuracy <4 ppm and an ion score of 40 until an FDR <1% at peptide level was achieved.
2014-02-03 | PXD000072 | Pride
Project description:We performed nanoLC-MS/MS analysis of an in vitro generated, trypsin-digested brominated human serum albumin standard, spiked into a complex trypsin-digested proteomic background, in an LTQ-Orbitrap instrument. We found that brominated peptides spiked in at a 1-10% ratio (mass:mass) were easily identified by manual inspection when higher-energy collisional dissociation (HCD) and collision induced dissociation (CID) were employed as the dissociation mode; however, confident assignment of brominated peptides from protein database searches required a novel approach. By addition of a custom modification, corresponding to the substitution of a single bromine with 81Br rather than 79Br for dibromotyrosine (79Br81BrY), the number of validated assignments for peptides containing dibromotyrosine increased significantly when analyzing both high resolution and low resolution MS/MS data.
2013-08-28 | PXD000430 | Pride
Project description:This dataset derives from experiments testing quantitation using label-free methods. We used the Sigma-Aldrich UPS1 and UPS2 protein standard sets, containing proteins of 6-83 kD; the UPS1 set includes 49 human proteins at a single molar concentration, while the UPS2 set includes six groups of eight human proteins spanning a six orders of magnitude in concentration. In both cases, dilutions of UPS1 or UPS2 proteins were made into an E. coli extract, which allows these experiments to mimic detection of low abundance proteins in a complex protein mixture. The UPS1/E. coli and UPS2/E. coli mixtures were run on three mass spectrometers, an Orbitrap Velos Elite and two ion-trap instruments (Velos and LTQ). Proteins were quantified using MS1 peak volume (Orbitrap) or MS2 intensities and spectral counts (Orbitrap, Velos, LTQ). The analyzed results show that the ion-trap instruments perform nearly as well for label-free quantitation as does the Orbitrap. In addition, the \"Top 3\" method for quantitation—measuring only the three most abundant peptides—performed no better than the \"iBAQ\" quantitation method. Data analysis: MS1 data were analyzed using MaxQuant. MaxQuant version 1.2.2.5 software was used for protein identification and quantitation. Using the search engine Andromeda, mass spectrometry data were searched against the database containing UPS and E. coli proteins. MaxQuant reports summed intensity for each protein, as well as its iBAQ value. In the iBAQ algorithm, the intensities of the precursor peptides that map to each protein are summed together and divided by the number of theoretically observable peptides, which is considered to be all tryptic peptides between 6 and 30 amino acids in length. This operation converts a measure that is expected to be proportional to mass (intensity) into one that is proportional to molar amount (iBAQ). To determine relative molar abundances for each E. coli and human protein using MS1 data, two methods were used. In the first, we determined each proteins relative iBAQ (riBAQ), a normalized measure of molar abundance. We removed from the analysis all contaminant proteins that entered our sample-preparation workflow, for example keratins and trypsin, and then divided each remaining proteins iBAQ value by the sum of all non-contaminant iBAQ values. We also measured the average intensity of the three (or fewer, if fewer peptides were detected) peptides with the highest intensity, Top3, for each protein detected9. Peptides were chosen separately for each experiment, so the same peptides were not necessarily used across the four experiments. We generated a normalized \"top three\" abundance factor by dividing the average intensity for the three most abundant peptides of an individual protein and by the sum of all Top3 values in an experiment. Peptide intensities were summed for all charge states and variable modifications. For MS2 label-free analysis with MS2 spectra, MS2 data were searched against the database described above using SEQUEST. Setting to 1% the peptide false-discovery rate, estimated using a decoy (reversed) database, proteins were identified using the PAW pipeline. Normalized molar intensity (im) was calculated by dividing i, the summed intensity for an individual protein, by its molecular mass; the i/mr value for each protein was divided by the sum of all i/mr values. Normalized molar counts (cm) were calculated similarly, except the summed spectral counts for a protein (c) was used instead.
2013-12-05 | PXD000602 | Pride
Project description:Many protein activities are driven by ATP binding and hydrolysis. Here, we explore the ATP binding proteome of the model plant Arabidopsis thaliana using Acyl-ATP (AcATP) probes. These probes target ATP binding sites and covalently label lysine residues in the ATP binding pocket. Protein extracts were labelled with NHS-LC-Biotin, purified over neutravidin and eluted with formic acid. Eluted proteins were separated by 1-D SDS Gel and digested with Trypsin. Peptide mixtures were analysed by LC-MS/MS on an LTQ Velos. Spectra were searched using Mascot 2.3 using a fixed modification of cysteine (57.02 Da for carbamidomethyl), and variable modifications of methionine (15.99 Da for oxidation) and lysine (339.16 and 355.16 Da for BHAc and OBHAc labeling, respectively). A mass tolerance was set to 0.3 Da for the precursor ions and 0.4 Da for fragment ions. Up to two mis-cleavages for trypsin were permitted since the labeling would prevent cleavage at the labeled lysine. The MS2 spectra were searched against the TAIR10_pep_2012 (version November 2012) containing 35386 proteins of Arabidopsis thaliana, supplemented with a small database with 1095 artefact proteins and a reversed decoy database of the same proteins (totals 72962 entries). An oxidized version of the modifier was observed. Alternatively Arabidopsis leaf proteome was labeled with desthiobiotin-acyl ATP and digested with trypsin. Labeled peptides were purified on streptavidin matrix and sequenced by LC-MS/MS on an LTQ linear ion trap. Here the MS2 spectra were searched using SEQUEST against the TAIR9_pep_20090619 database (version June 2009) containing 32,769 proteins of Arabidopsis thaliana. MS2 searches included fixed iodoacetamide modification of cysteine (57 Da for alkylation), and variable modifications of methionine (16 Da for oxidation) and lysine (196 Da for DBAcATP labeling). Up to three mis-cleavages with trypsin were allowed and non-tryptic or half-tryptic peptides were excluded. A mass tolerance was set to 3 Da for the precursor ions and 1 Da for fragment ions.
2013-06-19 | PXD000188 | Pride