Ltq orbitrap

Manufactured by Thermo Fisher Scientific

Sourced in United States, Germany

The LTQ-Orbitrap is a high-resolution mass spectrometry system that combines a linear ion trap (LTQ) and an Orbitrap mass analyzer. It provides high mass accuracy, high-resolution, and sensitive detection of a wide range of molecular species.

Automatically generated - may contain errors

Lab products found in correlation

Trypsin, by Promega (8 mentions) Ltq orbitrap velos, by Thermo Fisher Scientific (4 mentions) Zorbax 300sb c18, by Agilent Technologies (3 mentions) Orbitrap fusion, by Thermo Fisher Scientific (3 mentions) 343 polarimeter, by PerkinElmer (3 mentions) Mascot software, by Matrix Science (3 mentions) Avance 3 hd 400 nmr spectrometer, by Bruker (3 mentions) Ltq orbitrap mass spectrometer, by Thermo Fisher Scientific (3 mentions) Nanoacquity uplc system, by Waters Corporation (3 mentions) High performance liquid chromatography (hplc), by Thermo Fisher Scientific (2 mentions) Ha peptide, by Merck Group (2 mentions) Tc c18 column, by Agilent Technologies (2 mentions) Streptavidin sepharose, by GE Healthcare (2 mentions) Dtssp, by Thermo Fisher Scientific (2 mentions) 3d7 sequence database version 3, by Matrix Science (2 mentions) Bira biotin protein ligase, by Avidity (2 mentions) Mascot, by Matrix Science (2 mentions) Nanoflow ultra high, by Thermo Fisher Scientific (2 mentions) Acquity uplc, by Waters Corporation (2 mentions) Symmetry c18 180 μm 20 mm trap column, by Waters Corporation (2 mentions)

Close spelling variants of this product

LTQ Orbitrap XL (774 citations) LTQ-Orbitrap hybrid mass spectrometer (21 citations) LTQ Orbitrap Velos instrument (17 citations) LTQ-Orbitrap Velos ETD (12 citations) LTQ-Orbitrap Fusion Lumos (8 citations) LTQ Orbitrap ELITE apparatus (6 citations) Thermo Finnigan LTQ-Orbitrap (5 citations) LTQ Orbitrap Elite system (4 citations) LTQ-Orbitrap Fusion mass spectrometer (4 citations) Finnigan LTQ-Orbitrap Elite (4 citations)

191 protocols using ltq orbitrap

Analytical Characterization of Compounds

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

All reagents were of commercial
grade and used as received unless indicated otherwise. The purity
of all tested compounds is >95% on the basis of liquid chromatography–mass
spectrometry (LC-MS) and nuclear magnetic resonance (NMR). ¹H- and ¹³C NMR spectra were recorded on a Bruker AV-400
(400 MHz), AV-600 (600 MHz), or AV-850 (850 MHz) spectrometer. Chemical
shifts are given in ppm (δ) relative to CD₃OD or
CDCl₃ as an internal standard. Coupling constants are given
in Hz, and peak assignments are based on 2D ¹H correlation
spectroscopy and ¹³C heteronuclear single quantum coherence
NMR experiments. All ¹³C attached proton test spectra are
proton-decoupled. LC-MS analysis was performed on a Finnigan Surveyor
high-performance liquid chromatography (HPLC) system with a Gemini
C18 50 × 4.60 mm column (detection at 200–600 nm) coupled
to a Finnigan LCQ Advantage Max mass spectrometer with electrospray
ionization (ESI). Methods used are: 15 min (0–0.5 min: 10%
MeCN; 0.5–10.5 min: 10–90% MeCN; 10.5–12.5 min:
90% MeCN; 12.5–15 min: 90–10% MeCN) or 12.5 min (0–0.5
min: 10% MeCN; 0.5–8.5 min: 10–90% MeCN; 8.5–10.5
min: 90% MeCN; 10.5–12.5 min: 90––10% MeCN).
HRMS was recorded on an LTQ Orbitrap (ThermoFinnigan). For reverse-phase
HPLC purification, an automated Gilson HPLC system equipped with a
C18 semiprep column (Phenomenex Gemini C18, 5 μm 250 ×
10 mm) and a GX281 fraction collector was used.

Xin B.T., Huber E.M., de Bruin G., Heinemeyer W., Maurits E., Espinal C., Du Y., Janssens M., Weyburne E.S., Kisselev A.F., Florea B.I., Driessen C., van der Marel G.A., Groll M, & Overkleeft H.S. (2019). Structure-Based Design of Inhibitors Selective for Human Proteasome β2c or β2i Subunits. Journal of Medicinal Chemistry, 62(3), 1626-1642.

+ Open protocol

+ Expand

Mass Spectrometry-Based Protein Identification

Cited 1 time

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

After SDS-PAGE, colloidal Coomassie-stained bands were excised, digested with trypsin, and analyzed by LC-MS on an LTQ-Orbitrap (Thermo Finnigan) mass spectrometer coupled to a Dionex 3000 nano liquid chromatography system as described previously (25 (link)). For peptide and protein identification, raw files were converted to peak lists in Mascot generic format (MGF) files using raw2msm v1.7 software (Matthias Mann), and MGF files were then searched using a Mascot 2.2 in-house server against the Swiss-Prot database. Only peptides with Mascot ion score over 25 were considered, and only proteins with at least two unique peptides were considered. For phosphopeptide analysis, only phosphopeptides with ion scores over 18 were considered. The individual MS/MS spectra for the phosphopeptide ions were quantified using Xcalibur 2.2 software.

Li M., Quan C., Toth R., Campbell D.G., MacKintosh C., Wang H.Y, & Chen S. (2015). Fasting and Systemic Insulin Signaling Regulate Phosphorylation of Brain Proteins That Modulate Cell Morphology and Link to Neurological Disorders. The Journal of Biological Chemistry, 290(50), 30030-30041.

+ Open protocol

+ Expand

Proteomic Profiling of Nanoparticle Corona

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

For proteomic assays, the protein corona was isolated and purified using the gel permeation chromatography as described in the above section. Then the protein pellets were denatured using 8 M urea at 65 °C for 15 min and digested using trypsin (Promega, Inc.) according to the method developed by Shevchenko et al.^{42 (link)}. The resulting peptide mixtures were re-suspended in 0.1% formic acid and analyzed by electrospray liquid chromatography mass spectrometry (LC-MS/MS) using an HPLC (Surveyor, ThermoFinnigan, CA) interfaced with an LTQ Orbitrap (ThermoFinnigan). The data have been analyzed against mouse protein databases in order to identify the mouse proteins in the corona on the nanoparticles. The identified proteins have been ordered according to their abundance and are shown in (Supplementary Table 1)^{43 (link)}.

Miao L., Lin J., Huang Y., Li L., Delcassian D., Ge Y., Shi Y, & Anderson D.G. (2020). Synergistic lipid compositions for albumin receptor mediated delivery of mRNA to the liver. Nature Communications, 11, 2424.

+ Open protocol

+ Expand

Protein Identification using SDS-PAGE and LC-MS

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

Protein immunoprecipitates were electrophoretically separated via SDS-PAGE and stained with Coommassie dye. After excised from gels, protein bands were digested with trypsin. Resultant peptides were further separated via a Dionex 3000 nano liquid chromatography system and analysed by LC-MS on an LTQ-Orbitrap (Thermo Finnigan) mass spectrometer. Mascot generic format (MGF) files were obtained from raw files using raw2msm v1.7 software (Matthias Mann), and searched using a Mascot 2.2 in-house server against the Swiss-Prot database to identify peptides and proteins.

Quan C., Du Q., Li M., Wang R., Ouyang Q., Su S., Zhu S., Chen Q., Sheng Y., Chen L., Wang H., Campbell D.G., MacKintosh C., Yang Z., Ouyang K., Wang H.Y, & Chen S. (2020). A PKB-SPEG signaling nexus links insulin resistance with diabetic cardiomyopathy by regulating calcium homeostasis. Nature Communications, 11, 2186.

+ Open protocol

+ Expand

Quantitative Heparan Sulfate Analysis

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

Purification of HS from BMDCs was carried out using HS preparation methods as previously described [18] (link). Cells were harvested from 10-day GM-CSF based DC differentiation cultures of marrow from the femurs of Ndst1f/f CD11cCre+ versus Cre− control mice as described for BMDC Primary Cell Preparations, above. Briefly, following glycan de-polymerization with heparin lyases overnight, disaccharide analysis was carried out using quantitative liquid chromatography/mass spectrometry (LC/MS) [19] (link): After drying samples down, aniline labeling of disaccharide reducing ends was carried out (in 15 μl of 1 M NaCNBH₃ and [¹²C₆]aniline freshly prepared in dimethyl sulfoxide/acetic acid (7:3, v/v) for 16 h at 37 °C) with products dried down. Using a C18 reversed phase column (0.21 × 15 cm; Thermo), derivatized disaccharides were separated with ion pairing agent (dibutylamine, Sigma) [20] (link), and eluted ions of interest were monitored in negative ion mode on a mass spectrometer (LTQ Orbitrap, Thermo-Finnigan; capillary temp 150 °C; spray voltage 4.0 kV). Extracted ion current data were analyzed with Qual Browser software (Thermo-Finnigan). Quantitative composition analysis of disaccharides was performed by comparison with known amounts of differentially labeled standard [¹³C₆]aniline added to the sample before LC/MS.

Gupta P., Johns S.C., Kim S.Y., El Ghazal R., Zuniga E.I, & Fuster M.M. (2019). Functional Cellular Anti-Tumor Mechanisms are Augmented by Genetic Proteoglycan Targeting. Neoplasia (New York, N.Y.), 22(2), 86-97.

+ Open protocol

+ Expand

Nanoflow HPLC-MS/MS Peptide Analysis

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

Resulting peptides were analyzed by RP-nano-HPLC-ESI-MS/MS using a nanoACQUITY HPLC system (Waters, Milford, MA, USA) coupled to an LTQ-Orbitrap Discovery Hybrid FTMS (Thermo Fisher Scientific, Bremen, Germany). For RP-nano-HPLC-ESI-MS/MS, a sample (2 μl) of the desired peptide digest was loaded into the reverse phase column (Symmetry C18, Waters Corporation, Milford, MA, USA, 5 μm, 180 μm × 20 mm) by an autosampler. After 3 min desalting, the precolumn was switched online with the analytical C18 column (BEH C18, 1.7 μm, 75 μm × 100 mm) equilibrated in 99% solvent A (100% D.I. water, 0.1% formic acid) and 1% solvent B (100% acetonitrile, 0.1% formic acid). Peptides were eluted using a linear acetonitrile gradient from 99% solvent A to 85% solvent B during 45 min at 400 nl min⁻¹ flow rate. The LTQ-Orbitrap (Thermo Finnigan, San Jose, CA, USA) was operated in the data-dependent acquisition mode with the XCalibur software. Survey scan MS was acquired in the Orbitrap in the 400–2000 m/z range with the resolution set to a value of 30 000 and collision energy set at 35%. The four most intense ions per survey scan were selected for CID fragmentation, and the resulting fragments were analyzed in the linear trap mass analyzer (Thermo Finnigan). Dynamic exclusion was employed within 60 s to prevent repetitive selection of the same peptide.

Ding D.C., Wen Y.T, & Tsai R.K. (2017). Pigment epithelium-derived factor from ARPE19 promotes proliferation and inhibits apoptosis of human umbilical mesenchymal stem cells in serum-free medium. Experimental & Molecular Medicine, 49(12), e411-.

+ Open protocol

+ Expand

Nanoflow LC-MS/MS proteomic workflow

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

Proteins were identified by nanoLC-MS/MS with LTQ-Orbitrap (Thermo Finnigan, San Jose, CA). Peptide samples were separated on a C₁₈ column (150 μm, 150 mm length, Column Technology Inc.) after being desalted on a trap column (Zorbax 300 SB C₁₈, Agilent Technologies, Palo Alto, CA). The mobile phase A was 0.1% formic acid in HPLC-grade water, and 0.1% formic acid in ACN for the mobile phase B. The peptide mixture was separated at 2 μl/min with a linear gradient of 4%–50% B for 110 min, following by 50%–100% B from 110 min to 115 min, then maintained at 100% B for 5 min. Data dependent MS/MS mode was acquired, in which each scan cycle consisted of one full MS scan in profile mode followed by seven MS/MS scans in centroid mode.

Wang X., He Y., Ye Y., Zhao X., Deng S., He G., Zhu H., Xu N, & Liang S. (2018). SILAC–based quantitative MS approach for real-time recording protein-mediated cell-cell interactions. Scientific Reports, 8, 8441.

+ Open protocol

+ Expand

Comprehensive Biophysical Characterization Methods

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

Unless otherwise noted, all solvents and reagents were obtained from commercial suppliers and used without further purification. The peptide fragments analysis and purification were carried out on an Agilent Technologies 1200 HPLC system (Agilent, USA) equipped with UV-VIS and fluorescence detector using XBridge BEH C18 Column (10 μm, 150 mm × 4.6 mm, Waters Corp., USA) and XBridge BEH130 Prep C18 (10 μm, 250 mm × 10 mm, Waters Corp., USA). Mass spectra were acquired on a MALDI-TOF, Voyager-DETM STR Biospectrometry Workstation (Applied Biosystems Inc., USA) and a high-resolution electrospray ionization mass spectrometry (HR-ESI-MS, Thermo Finnigan, LTQ-Orbitrap). Fluroescence spectra were acquired by a fluorescence spectrophotometer (Hitachi F-7000, Japan). Cell images were collected using an Axioimager M1 microscope (Zeiss, Germany) and tumor spheroids were observed with FluoView FV10i confocal laser scanning microscope (Olympus, Japan). UV absorption for WST-1 assay was measured by SpectraMax M5 (Molecular Devices, USA). All in vivo data and images were taken on an IVIS Spectrum imaging system (Caliper, USA). The histological images were obtained from optical microscope (BX 51, Olympus, Japan).

Cho H.J., Lee S.J., Park S.J., Paik C.H., Lee S.M., Kim S, & Lee Y.S. (2016). Activatable iRGD-based peptide monolith: targeting, internalization, and fluorescence activation for precise tumor imaging. Journal of controlled release : official journal of the Controlled Release Society, 237, 177-184.

+ Open protocol

+ Expand

Proteomic Analysis of Acquired Premature Ejaculation

Cited 1 time

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

All semen specimens were collected by masturbation into sterile containers after 2–7 days of sexual abstinence. The semen was tested for C. trachomatis using immunochromatography and cultured for M. urealyticum and M. hominis. The samples were centrifuged at 1600 ×g for 5 min and supernatant seminal plasma was immediately stored at −80°C. Tandem mass tag (TMT) method followed by mass spectrometry analysis was used to compare the relative expression levels of seminal plasma proteins between the PE and control groups.27 (link)28 (link) Seminal plasma samples (six cases for acquired PE and six matched cases for control) were extracted and digested using trypsin. Later, the proteins were labeled with the TMT reagent. Peptide analysis was performed using the LTQ-Orbitrap instrument (Thermo Finnigan, San Jose, CA, USA) connecting to a Nano AUQUITY UPLC system via a nanospray source. Raw files of proteomics data were processed using MaxQuant (version 1.2.2.5). The false discovery rate (FDR) of the identification was estimated by searching against the databases with the reversed protein sequences. The site, peptide, and protein FDR were all set to 0.05. One-way analysis of variance was used to calculate significant differences in abundance among groups.

Hong Z.W., Feng Y.M., Ge Y.F., Jing J., Hu X.C., Shen J.M., Peng L.P., Yao B, & Xin Z.C. (2016). Relation of size of seminal vesicles on ultrasound to premature ejaculation. Asian Journal of Andrology, 19(5), 554-560.

+ Open protocol

+ Expand

Quantitative Protein Corona Profiling

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

To determine the protein corona composition, the gel lanes containing the protein corona associated with specific MBs were cut out from the gel following SDS-PAGE gel electrophoresis and in gel digestion with trypsin. The digested peptides were then re-suspended in 0.1%formic acid. Electrospray liquid chromatography mass spectrometry (LC-MS/MS) equipped with an HPLC (Surveyor, ThermoFinnigan, CA) interfaced with an LTQ Orbitrap (ThermoFinnigan, CA) was used to analyze the peptide mixtures. Spectra were searched with BioworksBrowser 3.3.1 SP1 (Ther-moFisher Scientific) using Sequest Uniprot/Swiss-Prot database (www.expasy.org). When the same protein identity was detected in multiple bands from the same samples, their SpCs were summed to get the total protein amount. The spectral count of each protein was then converted into a Normalized Spectral Count (NSpC), expressed as the spectral count in relation to its molecular weight and relative protein amount in percentage, using the following equation (Zybailov et al., 2006) :
where NpSpC k is the percentage of the normalised spectral count for protein k, SpC is the spectral count, and M w is the molecular weight in KDa for protein k.

Wan S., Egri G., Oddo L., Cerroni B., Dähne L., Paradossi G., Salvati A., Lynch I., Dawson K.A, & Monopoli M.P. (2016). Biological in situ characterization of polymeric microbubble contrast agents. The international journal of biochemistry & cell biology, 75.

+ 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!