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Orbitrap fusion lumos system

Manufactured by Thermo Fisher Scientific
Sourced in United States

The Orbitrap Fusion Lumos system is a high-performance mass spectrometer designed for advanced proteomics and metabolomics research. It combines the Orbitrap mass analyzer with a linear ion trap, enabling high-resolution, high-mass accuracy, and high-sensitivity analysis of complex biological samples.

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4 protocols using orbitrap fusion lumos system

1

Metabolomics Analysis with UHPLC-Orbitrap

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Metabolites were analyzed using a Dionex UltiMate 3000 UHPLC system coupled with an Orbitrap Fusion Lumos system (Thermo Fisher Scientific, Milford, MA, USA). Each sample was run twice with technical repetitions. Metabolite samples were injected into an Agilent Poroshell 120 SB-C18 column (2.1 × 100 mm, 2.7 μm) using an autosampler. Chromatographic separation was achieved with two mobile phases: mobile phase A [5 % (v/v) acetonitrile and 0.1 % (v/v) formic acid] and mobile phase B [0.1 % (v/v) formic acid in acetonitrile]. The flow rate was set at 0.2 mL/minutes. The elution program was structured as follows: 0–2 mL/minutes with 100 % mobile phase A, followed by a gradient from 100 % to 0 % A over the next 10 minutes, and then a 4 mL/minutes maintenance period.
The mass spectrometer parameters for this experiment were as follows: electrospray voltage in positive mode was 3.5 kV; the temperature of the electrospray ionization source was 350 °C; the resolution of the initial full scan was 70,000; the scan range extended from 100 to 1,000 m/z; the resolution of the secondary data dependency scan was 35,000; and the automated gain control target was set to 1e6. To ensure the stability of the analysis, the QC was conducted by injecting a sample once every 14 samples throughout the analysis to monitor the consistency of sample preparation and instrument performance.
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2

Label-free Quantitative Proteomics Workflow

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A label-free proteomics approach was carried out in this research, which allows accurate relative quantification only between samples rather than within samples. Protein samples were precipitated with a solution of chloroform-methanol (2:1) and digested with trypsin. Afterwards, the samples were separated by C18 reversed-phase liquid chromatography using a Waters NanoAcquity system and analyzed by mass spectrometry (MS) using a Thermo Orbitrap Fusion Lumos system. MS data were searched against the corresponding fungal databases from the Joint Genome Institute (JGI), and gene function was determined by Gene Ontology (GO) enrichment analysis with GOATOOLS (44 (link)) and manual curation. Protein quantification results were obtained with the MaxQuant software (version 1.6.1.0) with a mass error tolerance of 4.5 ppm. On the other hand, peptide quantitation and oxidative modifications were analyzed as dynamic modifications (45 (link)) with PEAKS Studio (version 10.0, build 20190129). A list of all the included PTMs is given in Table S1 in the supplemental material. Additional details are provided in Text S1.
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3

Identification and Localization of Asp/Glu-ADPr Peptides

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For the identification and localization of Asp/Glu-ADPr peptides, three different data acquisition methodologies were used in this study. Briefly, two methodologies rely on ultra-fast MS/MS with HCD to detect the intense adenine diagnostic peak (mass = 136.061) and trigger the subsequent acquisition of high-quality HCD or ETD spectra, respectively, while the third method is exclusively high quality ETD on all precursors. In practive, Data-Dependent Acquisition (DDA) data were collected by a TopN (N = 20) method on the Orbitrap Fusion LUMOS system (Thermo Scientific) equipped with a FAIMS-Pro interface and coupled to an Easy-LC 1200 with a 75 micron x 40 cm fused silica capillary (CoAnn Technologies) packed with Poroshell 120 EC-C18 2.7 micron medium (Agilent). MS1 spectra were acquired at 60 k resolution, 300% normalized AGC, 50 ms maximum injection time, alternating between three FAIMS CVs (−40, −50, −60).
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4

Quantitative Proteomic Analysis of Samples

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An aliquot of each tryptic digest was analyzed by liquid chromatography–tandem mass spectrometry on an Orbitrap Fusion Lumos system (Thermo Scientific) coupled to a Dionex UltiMate 3000 RSLC nano HPL. The raw files were searched against the Human UniProt Database using MaxQuant software v1.5.5.1 (http://www.maxquant.org) (67 (link)) and the following criteria: peptide tolerance = 10 ppm, trypsin as the enzyme (2 missed cleavages allowed), and carboxyamidomethylation of cysteine as a fixed modification. Variable modifications are oxidation of methionine and N-terminal acetylation. Heavy SILAC labels were Arg10 (R10) and Lys8 (K8). Quantitation of SILAC ratios was based on razor and unique peptides, and the minimum ratio count was 2. The peptide and protein FDR was 0.01. The AP/MS and BioID datasets (minus common environmental contaminants as per http://maxquant.org and proteins identified via the decoy database) are provided in the Supplemental Data Files.
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