Fusion lumos

Manufactured by Thermo Fisher Scientific

Sourced in Germany, United States

The Fusion Lumos is a high-performance mass spectrometry system designed for advanced proteomics and metabolomics research. It offers high-resolution, high-sensitivity detection and accurate mass measurement capabilities.

Automatically generated - may contain errors

Lab products found in correlation

Spelling variants of this product

Orbitrap Fusion Lumos mass spectrometer (236 citations) Orbitrap Fusion Lumos MS (18 citations) Fusion Lumos Tribrid mass spectrometer (10 citations) Thermo Fusion Lumos (5 citations) Thermo Orbitrap Fusion Lumos Tribrid Mass Spectrometer (4 citations) Orbitrap Fusion Lumos Tribid mass spectrometer (3 citations) Thermo Orbitrap Fusion Lumos mass spectrometer (3 citations) OrbiTrap Fusion LUMOS Tribrid Mass Spectrometer (LC–MS) (3 citations) Orbitrap Fusion Lumos LC–MS (2 citations) Fusion Lumos Tribrid MS (2 citations)

74 protocols using fusion lumos

Tryptic Peptide Analysis by DIA-MS

Check if the same lab product or an alternative is used in the 5 most similar protocols

The tryptic peptides were analysed using a Fusion Lumos mass spectrometer connected to an Ultimate Ultra3000 chromatography system (both Thermo Scientific) incorporating an autosampler. In brief, 2 μg of de-salted peptides were loaded onto a 50 cm emitter packed with 1.9 μm ReproSil-Pur 200 C18-AQ (Dr Maisch) using a RSLC-nano uHPLC system connected to a Fusion Lumos mass spectrometer (both Thermo). Peptides were separated using a 140 min linear gradient from 5% to 30% acetonitrile, 0.5% acetic acid. The mass spectrometer was operated in DIA mode, acquiring a MS 350–1,650 Da at 120 k resolution followed by MS/MS on 45 windows with 0.5 Da overlap (200–2,000 Da) at 30 k with a NCE setting of 27.

Hooftman A., Peace C.G., Ryan D.G., Day E.A., Yang M., McGettrick A.F., Yin M., Montano E.N., Huo L., Toller-Kawahisa J.E., Zecchini V., Ryan T.A., Bolado-Carrancio A., Casey A.M., Prag H.A., Costa A.S., De Los Santos G., Ishimori M., Wallace D.J., Venuturupalli S., Nikitopoulou E., Frizzell N., Johansson C., Von Kriegsheim A., Murphy M.P., Jefferies C., Frezza C, & O’Neill L.A. (2023). Macrophage fumarate hydratase restrains mtRNA-mediated interferon production. Nature, 615(7952), 490-498.

+ Open protocol

+ Expand

Mass spectrometry-based phosphopeptide analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

TiO₂ and Fe-NTA phosphopeptide enriched samples were each resuspended in 10 µl of 1% formic acid, 0.05% heptafluorobutyric acid and 2% acetonitrile. The samples (2.5 - 5 µl) were then loaded onto the Fusion Lumos (ThermoFisher) connected to an UltiMate nanoRSLC UPLC and autosampler system (Dionex).
The peptides were initially concentrated and desalted with H2O:CH3CN (98:2, 0.2% TFA) at 15 µl/min on a micro C18 precolumn (300 µm x 5 mm, Dionex). After a 4 min wash, the micro C18 precolumn was switched (Valco 10 port UPLC valve, Valco) into line to a fritless nano column (75µ x ~15cm), which contained C18AQ media (1.9µ, 120 Å Dr Maisch). Peptides were then separated on a linear gradient of H2O:CH3CN (98:2, 0.1% formic acid) to H2O:CH3CN (64:36, 0.1% formic acid) at 0.2 µl/min over 30 min. Positive ions were generated with electrospray ionization at 2000V. Data dependent acquisition (DDA) was performed with survey scan from m/z of 350 to 1750, resolution of 120,000 at m/z 200, accumulation target value of 400,000 ions and lockmass enabled (m/z 445.12003). A top-speed approach with a cycle time of 2s was used for data-dependent tandem MS analysis. Ions were fragmented by higher-energy collisional dissociation (HCD) with intensity threshold at 25,000. A mass tolerance of 10 ppm and dynamic exclusion of 20s was set.

Luu L.D., Zhong L., Kaur S., Raftery M.J, & Lan R. (2021). Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence. Frontiers in Cellular and Infection Microbiology, 11, 660280.

+ Open protocol

+ Expand

LC-MS/MS Analysis of Kyse450 Proteome

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

LC-MS/MS analysis and label-free based MS quantification of proteins in Kyse450 cells were performed as previously described^{23 (link)}. A Firmiana proteomics workstation was used to process the raw MS data. Kyse450 lysates were digested into peptides with trypsin, then subjected to MS analysis on a Fusion Lumos instrument (Thermo Fisher Scientific). Raw MS data were used to interrogate the NCBI human Refseq protein database (released on 04-07-2013, 32,015 entries) with the Mascot search engine (version 2.3, Matrix Science Inc.) with a false discovery rate < 1% at the peptide and protein level. The intensity-based label-free quantification (iBAQ) algorithm was used for protein quantification. The iBAQ value was transferred into a fraction of total protein iBAQ amount per experiment (FOT). Then the FOT values were multiplied by 10⁶ and log₁₀ transformed to obtain the FOT values for low abundance proteins.

Xian J., Wang S., Jiang Y., Li L., Cai L., Chen P., Liu Y., Zeng X., Chen G., Ding C., Hoffman R.M., Jia L., Zhao H, & Zhang Y. (2021). Overexpressed NEDD8 as a potential therapeutic target in esophageal squamous cell carcinoma. Cancer Biology & Medicine, 19(4), 504-517.

+ Open protocol

+ Expand

Unbiased Proteomics of Ethanol-Treated Myotubes

Check if the same lab product or an alternative is used in the 5 most similar protocols

Untreated and 100 mM ethanol-treated myotubes were processed for unbiased proteomics on a Thermo Scientific Fusion Lumos mass spectrometry system (Thermo Scientific, San Jose, CA) as previously described. Quantifications were performed with the label-free quantitation method available in the MaxQuant program. The data were uploaded on the Qiagen IPA system for core analysis for signaling and metabolic pathways knowledge database and heatmap and canonical pathway overlays were generated as previously described[61 ]. To determine the relation between transcriptomics and proteomics, a Pearson’s correlation analysis of the expression data was performed for each time point. The RNA expression data were generated from the log ratios calculated using FPKM normalized data.

Kumar A., Davuluri G., Welch N., Kim A., Gangadhariah M., Allawy A., Priyadarshini A., McMullen M.R., Sandlers Y., Willard B., Hoppel C.L., Nagy L.E, & Dasarathy S. (2019). Oxidative stress mediates ethanol-induced skeletal muscle mitochondrial dysfunction and dysregulated protein synthesis and autophagy. Free radical biology & medicine, 145, 284-299.

+ Open protocol

+ Expand

HLA Immunoprecipitation and Mass Spectrometry

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Soluble lysates from up to 50 million single HLA expressing B721.221 cells and up to 0.2 g from tumor samples were immunoprecipitated with W6/32 antibody (sc-32235, Santa Cruz) as described previously^{4 (link)}. 10 mM iodoacetamide was added to the lysis buffer to alkylate cysteines for 71 alleles (Supplementary Table 1c; Supplementary Data 2). Peptides of up to three IPs for single HLA expressing samples and up to four IPs for tumor samples were combined, acid eluted either on StageTips or SepPak cartridges^{34 (link)}, and analyzed in technical duplicates using high resolution LC-MS/MS on a QExactive Plus (QE+), QExactive HF (QE-HF) or Fusion Lumos (Thermo Scientific). For acquisition parameters see Supplementary Note 2.

Sarkizova S., Klaeger S., Le P.M., Li L.W., Oliveira G., Keshishian H., Hartigan C.R., Zhang W., Braun D.A., Ligon K.L., Bachireddy P., Zervantonakis I.K., Rosenbluth J.M., Ouspenskaia T., Law T., Justesen S., Stevens J., Lane W.J., Eisenhaure T., Zhang G.L., Clauser K.R., Hacohen N., Carr S.A., Wu C.J, & Keskin D.B. (2019). A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nature biotechnology, 38(2), 199-209.

+ Open protocol

+ Expand

Proteomic Analysis of Brain Tissue

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Brain tissue was lysed using a GentleMACS dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) in 50 mM Tris HCl containing 5% sodium dodecyl sulfate (SDS) and supplemented with a protease inhibitor cocktail (1:200, Sigma-Aldrich, Missouri, USA). Homogenates were incubated with 5 mM dithiothreitol for 1 h at 56 °C followed by 10 mM iodoacetamide in the dark at room temperature for 45 min. Samples were loaded onto S-Trap microcolumns (Protifi, New-York, USA) and subjected to tryptic digestion [11 (link), 12 (link)]. Samples were vacuum dried and stored at -80 °C. The resulting peptides were analyzed by nanoflow liquid chromatography (NanoAcquity, Waters, Milford, MA, USA) coupled to high resolution, high mass accuracy mass spectrometry (Fusion Lumos, Thermo Scientific, Waltham, MA, USA) and sequentially analyzed in discovery mode. Raw data was processed with MaxQuant v1.6.0.16 [13 ]. Data was analyzed with the Andromeda search engine against the human proteome database (www.uniprot.com) and appended with common laboratory protein contaminants. Quantitative comparisons were calculated using Perseus v1.6.0.7. Pathway analysis was performed using Gene Analytics [14 (link)]. Proteins were categorized based on the Human Protein Atlas [15 (link)] (http://www.proteinatlas.org).

Vardi A., Pri-Or A., Wigoda N., Grishchuk Y, & Futerman A.H. (2021). Proteomics analysis of a human brain sample from a mucolipidosis type IV patient reveals pathophysiological pathways. Orphanet Journal of Rare Diseases, 16, 39.

+ Open protocol

+ Expand

Mass Spectrometry-based Proteomics Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

The tryptic peptides were analyzed on a Fusion Lumos mass spectrometer connected to an Ultimate Ultra3000 chromatography system (both Thermo Scientific, Germany) incorporating an autosampler. Five μL of the tryptic peptides, for each sample, was loaded on an Aurora column (Ionoptiks, Melbourne Australia) and separated by an increasing acetonitrile gradient, using a 150-min reverse-phase gradient (from 3%–40% Acetonitrile) at a flow rate of 400 nL/min. The mass spectrometer was operated in positive ion mode with a capillary temperature of 220 °C, with a potential of 1500 V applied to the column. Data were acquired with the mass spectrometer operating in automatic data-dependent switching mode, with MS resolution of 240 k, with a cycle time of 1 s and MS/MS HCD fragmentation/analysis performed in the ion trap. Mass spectra were analyzed using the MaxQuant Software package in biological triplicate. Label-free quantitation was performed using MaxQuant. All the samples were analyzed as biological triplicates.

Ryan D.G., Yang M., Prag H.A., Blanco G.R., Nikitopoulou E., Segarra-Mondejar M., Powell C.A., Young T., Burger N., Miljkovic J.L., Minczuk M., Murphy M.P., von Kriegsheim A, & Frezza C. (2021). Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism. eLife, 10, e72593.

+ Open protocol

+ Expand

High-Sensitivity LC-MS/MS Proteome Analysis

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

LC-MS/MS analysis was performed using a Dionex Ultimate 3000 nano-ultra high-pressure reverse-phase chromatography coupled on-line to a Q Exactive HF (GlyGly), Fusion Lumos (ISG15 interactome)³⁹ or a Q Exactive (Matching proteome)⁴⁰ mass spectrometer (Thermo Scientific) as described previously.^{38 (link)} In brief, samples were separated on an EASY-Spray PepMap RSLC C18 column (500 mm × 75 μm, 2 μm particle size, Thermo Scientific) over a 60 min (120 min in the case of the matching proteome) gradient of 2–35% acetonitrile in 5% dimethyl sulfoxide (DMSO), 0.1% formic acid at 250 nL/min. MS1 scans were acquired at a resolution of 60,000 at 200 m/z and the top 12 most abundant precursor ions were selected for high collision dissociation (HCD) fragmentation.

Pinto-Fernandez A., Salio M., Partridge T., Chen J., Vere G., Greenwood H., Olie C.S., Damianou A., Scott H.C., Pegg H.J., Chiarenza A., Díaz-Saez L., Smith P., Gonzalez-Lopez C., Patel B., Anderton E., Jones N., Hammonds T.R., Huber K., Muschel R., Borrow P., Cerundolo V, & Kessler B.M. (2020). Deletion of the deISGylating enzyme USP18 enhances tumour cell antigenicity and radiosensitivity. British Journal of Cancer, 124(4), 817-830.

+ Open protocol

+ Expand

Cross-linking Mass Spectrometry of Drosha

Check if the same lab product or an alternative is used in the 5 most similar protocols

RNA/protein complexes were prepared as described above. RNA/protein complexes were diluted to 1 μM by measuring absorbance at 450 nm. Samples without RNA were prepared similarly but in a buffer containing 20 mM HEPES (pH 7.1), 1 M NaCl, and 5 mM DTT. 1:1 mixtures of DSS and deuterated DSS (DSS-d4, Proteochem) were prepared in DMSO. Crosslinking reactions were performed at room temperature for 10 minutes, and quenched with 75 mM glycine. The crosslinked samples were concentrated, run on SDS PAGE, and stained with Coomassie Blue. Crosslinked bands were cut and submitted for mass spectrometry analysis by the UTSW Proteomics core facility. The samples were analyzed on a Fusion Lumos (Thermo Fisher Scientific) mass spectrometer coupled to a Dionex UltiMate 3000 RSLCNano LC system. The data were analyzed using the xQuest/xProphet pipeline (Rinner et al., 2008 (link)). The results were then sorted by ID-score and false discovery rate (FDR). Links shown in the crosslink maps consist of all inter-peptide Drosha-Drosha hits with an FDR ≤ 0.05, and Id-Score ≥ 20.

Partin A.C., Zhang K., Jeong B.C., Herrell E., Li S., Chiu W, & Nam Y. (2020). Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA. Molecular cell, 78(3), 411-422.e4.

+ Open protocol

+ Expand

Rodent Proteome Profiling by Nano LC-MS/MS

Check if the same lab product or an alternative is used in the 5 most similar protocols

A 2 μg aliquot was analyzed by nano LC/MS/MS with a Waters NanoAcquity HPLC system interfaced to a Thermo Fisher Fusion Lumos. Peptides were loaded on a trapping column and eluted over a 75 μm analytical column at 350 nL/min; both columns were packed with Luna C18 resin (Phenomenex). A 4-h gradient was employed. The mass spectrometer was operated in data-dependent mode, with MS and MS/MS performed in the Orbitrap at 60,000 FWHM resolution and 15,000 FWHM resolution, respectively. APD was turned on. The instrument was run with a 3-s cycle for MS and MS/MS. The acquisition order was randomized. Data Processing Data were processed through the MaxQuant software v1.6.2.3 (www.maxquant.org). Data were searched using Andromeda with the following parameters: Enzyme: Trypsin, Database: Uniprot Rat, Fixed modification: Carbamidomethyl (C), Variable modifications: Oxidation (M), Acetyl (Protein N-term), Fragment Mass Tolerance: 20 ppm Pertinent. MaxQuant settings were: Peptide FDR 0.01 Protein FDR 0.01 Min. peptide Length 7 Min. razor + unique peptides 1 Min. unique peptides 0 Min. ratio count for LFQ 1 Second Peptidesˆ TRUE Match Between Runs∗ TRUE.

Zlatic S.A., Duong D., Gadalla K.K., Murage B., Ping L., Shah R., Fink J.J., Khwaja O., Swanson L.C., Sahin M., Rayaprolu S., Kumar P., Rangaraju S., Bird A., Tarquinio D., Carpenter R., Cobb S, & Faundez V. (2022). Convergent cerebrospinal fluid proteomes and metabolic ontologies in humans and animal models of Rett syndrome. iScience, 25(9), 104966.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!