GNPS - 20230830_NIEHS_MCF_23MCF024_Orbi
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion
ORGANISM(S): Not Applicable
SUBMITTER: 
Alan K. Jarmusch
PROVIDER: MSV000092792 | GNPS | Wed Aug 30 10:53:00 BST 2023
REPOSITORIES: GNPS
Similar Datasets
Project description:chemical standards run on Orbitrap Tribrid Fusion via syringe infusion. MS1 and MS/MS data collected. MS/MS data collected using HCD and CID activation and at different normalized collision energies.
2023-08-30 | MSV000092792 | MassIVE
Project description:Syringe infusion HRMS/MS, UHPLC-HRMS, syringe infusion timsTOF Pro IMS data of derivatized spironolactone and metabolites. MS/MS collected using resonance and non-resonance collision excitation methods (CID and HCD) at different energy levels.
2024-04-26 | MSV000094621 | GNPS
Project description:In this study we compared three different fragmentation techniques and two combined fragmentation schemes available on a novel tribrid mass spectrometer (Orbitrap Fusion Lumos, Themro Fisher Scientific) CID, HCD, ETD, ETD with supplemental CID (ETciD) and ETD with supplemental HCD (EThcD) on cross-linked peptides obtained by tryptic cleavage of SDA-cross-linked Human Serum Albumin (HSA). The three-dimensional structure of HSA has been resolved by X-ray crystallography [35] and is used as ground-truth to evaluate the identification results. Right choice of the fragmentation method allows increasing the number of identified linkage sites, increasing the sequence coverage of both linked peptides thereby reducing the second peptide problem, and increasing the precision of cross-link site calling.
2016-08-02 | PXD003737 | Pride
Project description:Cross-linking mass spectrometry (XLMS) is becoming increasingly popular, and current advances are widening the applicability of the technique so that it can be utilized by non-specialist laboratories. Specifically, the use of novel mass spectrometry-cleavable (MS-cleavable) reagents dramatically reduces complexity of the data by providing i) characteristic reporter ions and ii) the mass of the individual peptides, rather than that of the cross-linked moiety. However, optimum acquisition strategies to obtain the best quality data for such cross-linkers with higher energy C-trap dissociation (HCD) alone is yet to be achieved. Therefore, we have carefully investigated and optimized MS parameters to facilitate the identification of disuccinimidyl sulfoxide (DSSO)-based cross-links on HCD-equipped mass spectrometers. From the comparison of 9 different fragmentation energies we chose several stepped- HCD fragmentation methods that were evaluated on a variety of cross-linked proteins. The optimal stepped-HCD method was then directly compared with previously described methods using an Orbitrap Fusion™ Lumos™ Tribrid™ instrument using a high-complexity sample. The final results indicate that our stepped-HCD method is able to identify more cross-links than other methods, mitigating the need for multistage MS (MSn) enabled instrumentation and alternative dissociation techniques.
2019-02-01 | PXD011861 | Pride
Project description:We compared the five different ways of fragmentation available on a tribrid mass spectrometer and optimized their collision energies with regard to optimal sequence coverage of cross-linked peptides. We created a library of bis(sulfosuccinimidyl)suberate (BS3/DSS) cross-linked precursors, derived from the tryptic digests of three model proteins (Human Serum Albumin, creatine kinase and myoglobin). This enabled in-depth targeted analysis of the fragmentation behavior of 1065 cross-linked precursors using the five fragmentation techniques: collision-induced dissociation (CID), beam-type CID (HCD), electron-transfer dissociation (ETD), and the combinations ETciD and EThcD. EThcD gave the best sequence coverage for cross-linked m/z species with high charge-density, while HCD was optimal for all others. We tested the resulting data-dependent decision tree against collision energy-optimized single methods on two samples of differing complexity (a mix of eight proteins and a highly complex ribosomal cellular fraction). For the high complexity sample the decision tree gave the highest number of identified cross-linked peptide pairs passing a 5% false discovery rate (on average ~21% more than the second best, HCD). For the medium complexity sample the higher speed of HCD proved decisive. Currently, acquisition speed plays an important role in allowing the detection of cross-linked peptides against the background of linear peptides. Enrichment of cross-linked peptides will reduce this role and favor methods that provide spectra of higher quality.
2017-04-19 | PXD006131 | Pride
Project description:Homodimerization of Mpl can also be accomplished in the absence of Tpo, by binding of a synthetic ligand (Chemical inducer of dimerization, CID) to a constitutively expressed fusion protein F36VMpl consisting of a ligand binding domain (F36V) and the intracellular signaling domain of Mpl. In contrast to Tpo stimulation, F36VMpl dimerization in human CD34+ progenitor cells generates robust erythropoiesis. Microarray gene expression profiling of progenitors demonstrated that F36VMpl dimerization, but not Tpo, results in upregulation of critical erythroid genes. CD34+ cord blood cells were transduced with F36VMpl-GFP (GFP reporter gene) and cultured on MS-5 stroma for 7 days in the presence of CID, Tpo, Epo or no factors (no CID, negative control). CD34+GFP+ cells were sorted on day 7 and subjected to microarray (n=3 independent experiments).
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Project description:Human cell line (HEK293T) replicate HCD and CID libraries collected at 3 different NCE values, collected on an Orbitrap Fusion Lumos
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Project description:GLP-1 induces an increase in heart rate, but its mechanism remains elusive. We used a phosphoproteomic approach to evaluate the effect of GLP-1 on the porcine sinus node. Tissue samples from the sinus node region and left ventricle were collected from eight animals following a 60-minute infusion with either GLP-1 or saline. We employed a tandem mass tag (TMT) labeling strategy to multiplex samples, enriched for phosphorylated peptides by titanium dioxide chromatography, and pre-fractionated the resulting peptide pool prior to LC-MS/MS measurements on an Orbitrap Ascend Tribrid mass spectrometer.
2024-06-10 | PXD042583 | Pride
Project description:Isobaric chemical tag labeling (e.g., iTRAQ and TMT) is a commonly used approach in quantitative proteomics research. Typically, peptides are covalently labeled with isobaric chemical tags, and quantification is enabled through detection of low-mass reporter ions generated after MS2 fragmentation. Recently, we have introduced and optimized a platform for intact protein-level TMT labeling that demonstrated >90% labeling efficiency in complex sample with top-down proteomics. Higher-energy collisional dissociation (HCD) is a commonly utilized fragmentation method for peptide-level isobaric chemical tag labeling because it produces accurate reporter ion intensities and avoids the loss of low mass ions. HCD energies have been optimized for peptide-level isobaric chemical tag labeling; however, fragmentation energies have not been systematically evaluated for TMT-labeled intact proteins for both protein identification and quantitation. In this study, we report a systematic evaluation of normalized HCD fragmentation energies on TMT-labeled HeLa lysate with top-down proteomics. Our results suggested that reporter ions often require higher collisional energy for higher ion intensities while most of intact proteins fragment when normalized HCD energies are between 30% and 50%. We further demonstrated that a stepped HCD fragmentation scheme with energies between 30 and 50% resulted in the optimized quantitation and identification for TMT-labeled intact HeLa protein lysate by providing average reporter ion intensity as > 3.60 E4 and average PrSM as > 1000 PrSM counts with high confidence.
2023-01-17 | PXD037491 | Pride
Project description:We developed TMMF strategy (Targeted MS strategy combined with Multi-Fragmentation) which provided plenty information of targeted glycopeptides based on complementary MS2 spectra from HCD, ETD and CID in a single MS run.
2021-03-12 | PXD024705 |