Ltq orbitrap elite

Manufactured by Thermo Fisher Scientific

Sourced in United States, Germany, Denmark, United Kingdom

The LTQ Orbitrap Elite is a high-performance mass spectrometer that combines a linear ion trap (LTQ) with an Orbitrap mass analyzer. The instrument provides high-resolution, accurate-mass (HR/AM) measurements with enhanced sensitivity and scan speed for a wide range of applications in proteomics, metabolomics, and other analytical fields.

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Close spelling variants of this product

Orbitrap Elite (368 citations) LTQ-Orbitrap (191 citations) LTQ-Orbitrap Elite mass spectrometer (85 citations) LTQ Orbitrap Elite MS (10 citations) LTQ-Velos Orbitrap Elite (8 citations) LTQ Orbitrap ELITE apparatus (6 citations) LTQ Orbitrap ELITE ETD mass spectrometer (5 citations) Finnigan LTQ-Orbitrap Elite (4 citations) LTQ-Orbitrap Elite mass (4 citations) LTQ Orbitrap Elite system (4 citations)

217 protocols using ltq orbitrap elite

Peptide Analysis via LC-MS/MS

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Peptide samples
from in-gel digestion
and bRPLC fractionation were analyzed on LTQ-Orbitrap Velos and LTQ-Orbitrap
Elite mass spectrometers (Thermo Electron, Bremen, Germany) interfaced
with an Easy-nLC II nanoflow liquid chromatography system (Thermo
Scientific, Odense, Southern Denmark). The peptide digests were reconstituted
in 0.1% formic acid and loaded onto a trap column (75 μm ×
2 cm) packed in-house with Magic C₁₈ AQ (Michrom Bioresources,
Inc., Auburn, CA) at a flow rate of 5 μL/min with solvent A.
Peptides were resolved on an analytical column (75 μm ×
10 cm) at a flow rate of 350 nL/min using a linear gradient of 7–30%
solvent B (0.1% formic acid in 95% acetonitrile) over 60 min. Data-dependent
acquisition with full scans in the 350–1800 m/z range were carried out using an Orbitrap mass
analyzer at a mass resolution of 60 000 in Velos and 120 000
in Elite at 400 m/z, respectively.
Twenty of the most intense precursor ions from a survey scan were
selected for MS/MS and were fragmented using higher-energy collision dissociation
(HCD) with 35% normalized collision energy and detected at a mass
resolution of 15 000 and 30 000 at 400 m/z in Velos and Elite, respectively. Dynamic exclusion
was set for 30 s with a 10 ppm mass window.

Pinto S.M., Manda S.S., Kim M.S., Taylor K., Selvan L.D., Balakrishnan L., Subbannayya T., Yan F., Prasad T.S., Gowda H., Lee C., Hancock W.S, & Pandey A. (2014). Functional Annotation of Proteome Encoded by Human Chromosome 22. Journal of Proteome Research, 13(6), 2749-2760.

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Proteomic Peptide Fractionation and Analysis

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Peptide fractions were analyzed on an LTQ-Orbitrap Elite mass spectrometer (Thermo Electron, Bremen, Germany) interfaced with Easy-nLC II nanoflow LC system (Thermo Scientific, Odense, Denmark). The pooled TMT-labeled peptides were reconstituted in 0.1% formic acid and loaded onto a trap column (75 μm x 2 cm) packed in-house with Magic C18 AQ (Michrom Bioresources, Inc., Auburn, CA, USA). Peptides were resolved on an analytical column (75 μm x 50 cm) at a flow rate of 300 nL/min using a linear gradient of 10–35% solvent B (0.1% formic acid in 95% acetonitrile) over 90 min. The total run time, including sample loading and column reconditioning, was 120 min. Data-dependent acquisition with full scans in 350–1700 m/z range was carried out using an Orbitrap mass analyzer at a mass resolution of 120,000 at 400 m/z. The fifteen most intense precursor ions from a survey scan were selected for MS/MS fragmentation using higher-energy collisional dissociation (HCD) fragmentation with 32% normalized collision energy and detected at a mass resolution of 30,000 at 400 m/z. Automatic gain control for full MS was set to 1 × 10⁶ for MS and 5 × 10⁴ ions for MS/MS with a maximum ion injection time of 100 ms. Dynamic exclusion was set to 30 sec. and singly charged ions were rejected. Internal calibration was carried out using the lock mass option (m/z 445.1200025) in ambient air.

Agarwal A., Park S., Ha S., Kwon J.S., Khan M.R., Kang B.G., Dawson T.M., Dawson V.L., Andrabi S.A, & Kang S.U. (2020). Quantitative mass spectrometric analysis of the mouse cerebral cortex after ischemic stroke. PLoS ONE, 15(4), e0231978.

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Cross-linking and Mass Spectrometry Analysis of PirA and PirB

Cited 3 times

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Before being subjected to a cross-linking reaction, the recombinant PirA^vp and PirB^vp were dialyzed against 1X PBS to remove Tris, the presence of which can inhibit the activity of bissulfosuccinimidyl suberate (BS3). PirA^vp was then mixed with PirB^vp in PBS at a concentration of 13.2 μM each. To serve as a control, PirA^vp and PirB^vp were also diluted with PBS separately. After incubating for 15 min at 25 °C, BS3 was added to the mixtures to a final concentration of 1 mM. The mixtures were then incubated at 25 °C for an additional 60 min and separated in SDS-PAGE. As loading controls, the PirA^vp, PirB^vp and PirA^vp + PirB^vp were incubated without BS3 and separated with the same SDS-PAGE.
For mass spectrometry analysis, the shifted bands of the crosslinked PirA^vp and PirB^vp were excised from the SDS-PAGE and digested with trypsin coupled with chymotrypsin in accordance with standard in-gel digestion procedures. The digested peptides were then analyzed with a NanoLC-nanoESI-MS/MS (LTQ-Orbitrap Elite, Thermo Fisher Scientific, Waltham, MA, USA) using the standard protocol of the Common Mass Spectrometry Facilities of the Institute of Biological Chemistry at Academia Sinica [31 (link),32 (link)] and subjected to data analysis using the Massmatrix software [33 (link)].

Lin S.J., Chen Y.F., Hsu K.C., Chen Y.L., Ko T.P., Lo C.F., Wang H.C, & Wang H.C. (2019). Structural Insights to the Heterotetrameric Interaction between the Vibrio parahaemolyticus PirAvp and PirBvp Toxins and Activation of the Cry-Like Pore-Forming Domain. Toxins, 11(4), 233.

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Quantitative Proteomics using Mass Spectrometry

Cited 1 time

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Protein samples were run on a short gel as described in a previously published protocol (Xu et al., 2009 (link)). Proteins in the gel bands were reduced with DTT (Sigma) and alkylated by iodoacetamide (Sigma). The gel bands were then washed, dried, and rehydrated with a buffer containing trypsin (Promega). Samples were digested overnight, acidified, and the resulting peptides were extracted. The extracts were dried and reconstituted in 5% formic acid. The peptide samples were loaded on a nanoscale capillary reverse phase C18 column by an HPLC system (Thermo EASY-nLC 1000) and eluted by a gradient. The eluted peptides were ionized and detected by a mass spectrometer (Thermo LTQ Orbitrap Elite). The MS and MS/MS spectra were collected over a 90 min liquid chromatography gradient. Database searches were performed using Sequest (v28, revision 13) search engine against a composite target/decoy Uniprot human protein database. All matched MS/MS spectra were filtered by mass accuracy and matching scores to reduce protein false discovery rate to <1%. Spectral counts matching to individual proteins reflect their relative abundance in one sample after the protein size is normalized. The spectral counts between samples for a given protein were used to calculate the p-value based on G-test (Bai et al., 2013 (link)).

Jablonowski C.M., Quarni W., Singh S., Tan H., Bostanthirige D.H., Jin H., Fang J., Chang T.C., Finkelstein D., Cho J.H., Hu D., Pagala V., Sakurada S.M., Pruett-Miller S.M., Wang R., Murphy A., Freeman K., Peng J., Davidoff A.M., Wu G, & Yang J. (2024). Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing associated with therapeutic response to splicing inhibitor. eLife, 12, RP90993.

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Metaproteomic Analysis of Preterm Infant Gut

Cited 3 times

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Sample collection, processing, and metaproteomic measurements by LC–MS/MS were already described (Xiong et al., 2017 (link); Brown et al., 2018 (link)). Briefly, using necrotizing enterocolitis (NEC) as a representative dysbiotic condition, 91 metaproteomic measurements were taken from 17 preterm infant fecal samples over the first 90 days of life. Six infants developed NEC during the study (Supplemental Table 3). 0.3 g of raw fecal stool was processed using an indirect enrichment strategy (Xiong et al., 2015 (link))^, and 50ug of digested peptides were analyzed in technical duplicate via two-dimensional nanospray liquid chromatography–tandem mass spectrometry (LC–MS/MS) on an LTQ-Orbitrap Elite mass spectrometer (Thermo Scientific).

Peters S.L., Morowitz M.J, & Hettich R.L. (2022). Antibiotic resistance and host immune system-induced metal bactericidal control are key factors for microbial persistence in the developing human preterm infant gut microbiome. Frontiers in Microbiology, 13, 958638.

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Nanoflow LC-MS/MS peptide identification

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The peptide mixture was separated with a linear gradient of 5–43% buffer B (80% ACN and 0.1% FA) in 180 min at a flow rate of 250 nl/min on a C₁₈-reversed phase column (75 μm ID, 15 cm length) packed in-house with ReproSil-Pur C18-AQ μm resin (Dr. Maisch GmbH) in buffer A (0.1% FA). A nanoflow Easy-nLC system (Thermo Scientific) was on-line coupled to a Thermo Finnigan LTQ-Orbitrap Elite fitted with a nanospray flex Ion source (Thermo Fisher, San Jose, CA).
A “top 15” data-dependent tandem mass spectrometry approach was utilized to identify peptides in the samples. In a top 15 scan protocol, a full scan spectrum (survey scan, 300–1650 Th) is acquired followed by collision-induced dissociation (CID) mass spectra of the 15 most abundant ions in the survey scan. The survey scan was acquired using the Orbitrap mass analyzer to obtain high mass accuracy and high mass resolution data (240,000 resolution), and up to 15 of the most intense peptides were selected and subjected to fragmentation in the linear ion trap (LTQ). Dynamic exclusion was set at 30 seconds. The charge state rejection function was enabled with “unassigned” and “single” charge states rejected. By knowing the accurate mass and fragmentation pattern of the peptide, the peptide’s amino acid sequence can be reliably inferred.

Zhang X., Ma D., Caruso M., Lewis M., Qi Y, & Yi Z. (2014). Quantitative Phosphoproteomics Reveals Novel Phosphorylation Events in Insulin Signaling Regulated by Protein Phosphatase 1 Regulatory Subunit 12A. Journal of proteomics, 109, 63-75.

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Metaproteomics Protein Extraction and Analysis

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Protein extraction, digestion and mass spectrometry analysis followed previously reported protocols (Bryson et al., 2016 ; Supplementary Methods). This procedure utilized SDS lysis and trichloroacetic acid precipitation of proteins, followed by cleanup and trypsin digestion on centrifugal filters, and finally Multidimensional Protein Identification Technology was used for the liquid chromatography tandem mass spectrometry measurements using an LTQ Orbitrap Elite mass spectrometer (Thermo Scientific, Waltham, MA, USA) (Washburn et al., 2001 (link)). Peptide identifications are available under the PRIDE archive PXD002641.
The final database used for SIP searches (60 006 CDS) was constructed from all CDS with at least one peptide identification in regular (that is, unlabeled search mode) Sipros searches of each metaproteome against the 391 847 CDS from the full metagenome assembly and a reduced database consisting of 181 704 CDS from only high metagenome coverage contigs. To ensure support for our reduced database selection approach, test Sipros searches in labeled mode were performed comparing subsets of the spectra data against the non-reduced metagenome database. Under these conditions all labeled proteins identified were also identified in unlabeled searches, suggesting a low rate of missed protein detections by using a reduced database (data not shown).

Bryson S., Li Z., Chavez F., Weber P.K., Pett-Ridge J., Hettich R.L., Pan C., Mayali X, & Mueller R.S. (2017). Phylogenetically conserved resource partitioning in the coastal microbial loop. The ISME Journal, 11(12), 2781-2792.

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Electron Transfer Dissociation Mass Spectrometry

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All samples were analyzed on an electron transfer dissociation (ETD)-enabled LTQ-Orbitrap Elite coupled to Proxeon EASY-nLC 1000 (Thermo Fisher Scientific) or on an Orbitrap Q-Exactive mass spectrometer (Thermo Fisher Scientific) coupled to an Agilent 1290 Infinity LC (Agilent Technologies). The full MS methods are available in the Supplemental Experimental Procedures.

Stucchi R., Plucińska G., Hummel J.J., Zahavi E.E., Guerra San Juan I., Klykov O., Scheltema R.A., Altelaar A.F, & Hoogenraad C.C. (2018). Regulation of KIF1A-Driven Dense Core Vesicle Transport: Ca2+/CaM Controls DCV Binding and Liprin-α/TANC2 Recruits DCVs to Postsynaptic Sites. Cell Reports, 24(3), 685-700.

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Peptide Separation and Identification

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The fractioned proteins were dissolved in 2% (v/v) ACN, 0.1% (v/v) FArandomized and 0.5 μg of each sample were loaded on a reverse phase C18 column (PepMap®RSLC, Thermo scientific, 2 μm particle size) and separated during a 90 min gradient with a flow rate of 300 nL min⁻¹ (Ulti-Mate 3000, Thermo Fisher Scientific, Austria). MS measurement was performed on an LTQ-Orbitrap Elite (Thermo Fisher Scientific, Bremen, Germany) with the following settings: Full scan range 350–1,800 m/z, max. 20 MS2 scans (activation type CID), repeat count 1, repeat duration 30 s, exclusion list size 500, exclusion duration 60 s, charge state screening enabled with rejection of unassigned and +1 charge states, minimum signal threshold 1,000.

Schneider S., Harant D., Bachmann G., Nägele T., Lang I, & Wienkoop S. (2019). Subcellular Phenotyping: Using Proteomics to Quantitatively Link Subcellular Leaf Protein and Organelle Distribution Analyses of Pisum sativum Cultivars. Frontiers in Plant Science, 10, 638.

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Synthetic Peptide Analysis by Mass Spectrometry

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Synthetic peptides corresponding to the idiotype peptides from MCL-41 (NMLFLQMNSLKTEDT, DDSKNMLFLQMNSLKTEDT, FLQMNSLKTEDT, IKNKIDGETTDYAAPV) were purchased from JPT (JPT Peptide Technologies, Berlin, Germany) with a purity of >70 %, dissolved and resuspended into 0.1 % FA. 250 fmol of each peptide was analyzed on an LTQ-Orbitrap Elite mass spectrometer (ThermoFisher, Bremen, Germany) using the same instrument settings as described above. Synthetic peptides were measured with two replicate LC-MS analyses, using either the CID or HCD fragmentation methods as defined above. Both included singly-charged species.

Khodadoust M.S., Olsson N., Wagar L.E., Haabeth O.A., Chen B., Swaminathan K., Rawson K., Liu C.L., Steiner D., Lund P., Rao S., Zhang L., Marceau C., Stehr H., Newman A.M., Czerwinski D.K., Carlton V.E., Moorhead M., Faham M., Kohrt H.E., Carette J., Green M.R., Davis M.M., Levy R., Elias J.E, & Alizadeh A.A. (2017). Antigen Presentation Profiling Reveals Recognition of Lymphoma Immunoglobulin Neoantigens. Nature, 543(7647), 723-727.

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