Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HeLa, Orbitrap Fusion Lumos, Parameter optimization

ABSTRACT: Here, we report the optimization result of Orbitrap Fusion Lumos acquistion parameters.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Yasushi Ishihama

PROVIDER: PXD008282 | JPOST Repository | Fri Nov 24 00:00:00 GMT 2017

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	170516check02HCDOT.raw	Raw
	170516check03HCDOT_AAPFOff.raw	Raw
	170516check04CIDOT.raw	Raw
	170516check05CIDOT_AAPFOff.raw	Raw
	F003458.mzid	Mzid

Items per page:

1 - 5 of 8

Similar Datasets

JPST000362 HeLa, Orbitrap Fusion Lumos, Parameter optimization [Reanalysis: JPST000362]

Project description:Here, we report the optimization result of Orbitrap Fusion Lumos acquistion parameters. [Original project description]

2023-03-25 | RPXD034321 | JPOST Repository

Evaluating cPILOT Performance on Orbitrap Instruments

Project description:A global cPILOT assay developed on an Orbitrap Velos instrument was transitioned to an Orbitrap Fusion Lumos instrument. Parameters such as the LC gradient, m/z isolation window, dynamic exclusion, targeted mass analyses, and SPS-N were optimized. The number of proteins identified on the Fusion Lumos (1848) without fractionation are close to those identified to the Orbitrap Velos (2199) with sample pre-fractionation. Additionally, including sample fractionation with the Fusion Lumos optimized parameters resulted in the identification of 4968 proteins, of which 1234 were quantified in each tissue type and genotype (N=5 or 6). Combined, the various experiments described herein informed of system-wide changes in brain, heart, and liver proteins from a late-stage amyloid precursor protein/presenilin-1 (APP/PS-1) human transgenic double knock – in mouse model of AD.

2021-09-08 | PXD012133 | Pride

"How to deal with internal fragment ions ?" (synthetic unmodified histone H3 Tail)

Project description:Synthetic histone H3.1were analyzed via MSMS on and Orbitrap Fusion Lumos. Various fragmentation parameters (e.g Reaction time, supplementary activation) were used in order to study the fragmentation efficiency and formation of internal fragment ions.

2025-02-24 | PXD050421 | Pride

Optimizing chromatographic conditions for orbitrap-based MS platforms

Project description:We compared the performance of multidimensional protein identification (MudPIT) on Velos Pro Orbitrap (VPO) and Velos Orbitrap Elite (VOE) mass spectrometers to single dimension reversed phase (RP) chromatography on a Q Exactive Plus (QE+) and an Orbitrap Fusion™ Lumos™ (OFL). Using a digested HeLa cell protein extract, we carried out 16 different chromatography conditions on four different instrumentation platforms with three replicates of each condition, for a total of 48 proteomics analyses. We first compared selected chromatography conditions of the QE+ and OFL by varying column lengths, inner diameters, and C18-RP particle sizes. We next selected one chromatography condition on each system and varied the effective RP gradients lengths

2019-03-04 | PXD009875 | Pride

Shotgun Proteomics of Tomato Fruits: Evaluation and Optimization of Sample Preparation Methods and Mass Spectrometric Parameters

Project description:Optimization of sample preparation protocols and mass spectrometric parameters is essential for adequate proteome coverage. Though several protocols are available for 2D electrophoresis-based proteome profiling, very few protocols exist for sample preparation for shotgun proteomics and optimization of mass spectrometric parameters using plant tissues. Here, we report an optimized protocol for shotgun proteomics of tomato fruit, which is a recalcitrant tissue comprising of low concentration of proteins and high percentage of sugars and secondary metabolites

2016-06-30 | PXD003920 | Pride

WGA protocol optimization

Project description:WGA protocol optimization

| PRJEB34940 | ENA

O-GlcNAc/O-phophate mapping of Sec24C LC-MS/MS, Boyce Lab Duke University

Project description:O-GlcNAc/O-phophate mapping of isolated Sec24C by LC-MS/MS on an Orbitrap Fusion Lumos.

2025-02-23 | PXD060692 | Pride

Improved data acquisition settings on Q Exactive HF-X Hybrid Quadrupole-Orbitrap and Orbitrap Fusion Lumos Tribrid mass spectrometers for proteomic analysis of limited samples

Project description:Deep proteomic profiling of complex biological and medical samples available at low nanogram and subnanogram levels is still challenging. To generate the most thorough and informative nanoflow liquid chromatography-tandem mass spectrometry-based proteomic profiling results for a limited sample analyzed on a Q Exactive HF-X Hybrid Quadrupole-Orbitrap and Orbitrap Fusion Lumos Tribrid mass spectrometers, it is imperative to know how much material is subjected to the analysis in order to tune the data acquisition settings. Many instrument vendors provide default data acquisition methods that are often a good starting point in method optimization. This study demonstrates that by adjusting selected instrument parameters, e.g., ion injection time, automated gain control as well as the number of data-dependent acquisition tandem MS scans per cycle in TopN data acquisition settings, and by minimally altering the conditions for resuspending or storing the sample in solvents of different compositions, up to 15-fold more thorough proteomic profiling can be achieved compared to conventionally used settings.

2023-02-07 | MSV000091218 | MassIVE

Composition of the marine exometabolome is more stable than the functionally redundant microbial community in the oligotrophic North Atlantic

Project description:<p>Untargeted features from the Bermuda Atlantic Time-series Study (BATS) site collected during the time period spanning 2016 to 2019. Metabolites were sampled from surface seawater to 1000 m deep and throughout the year. Dissolved organic matter extracts were analyzed in positive and negative ion mode with an ultra-high performance liquid chromatography system (Vanquish UHPLC, Thermo Scientific) coupled with an Orbitrap Fusion Lumos Tribid mass spectrometer.</p>

2024-02-28 | MTBLS5228 | MetaboLights

Performance of the Orbitrap Fusion Lumos Tribrid in single-shot analyses of human samples

Project description:One of the major additions in mass spectrometry technology has been the irruption of the Orbitrap mass analyzer, which has boosted the proteomics analyses of biological complex samples since its introduction. Here we assessed the performance of the new generation Orbitrap Fusion Lumos Tribrid mass spectrometer in the identification and quantitation of peptides and phosphopeptides in single-shot analyses of human whole cell lysates using robust data-dependent acquisition methods. Our study explored the capabilities of the instrument for (phospho-)peptide identification and quantitation using different gradient lengths, different sample amounts, and different combinations of peptide fragmentation and mass analysers acquisition methods. Moreover, the acquisition of the same complex sample with different acquisition methods resulted in the generation of a dataset to be used as a reference for further analyses, and a starting point for future optimizations in particular applications.

2017-03-09 | PXD004940 | 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