The LC/MS portion of the platform was based on Waters ACQUITY ultra‐performance liquid chromatography and a Thermo‐Finnigan linear trap quadrupole mass spectrometer, which consisted of an electrospray ionization source and a linear ion‐trap mass analyzer (Evans et al., 2009 ). The sample extract was dried and then reconstituted in acidic or basic LC‐compatible solvents, each of which contained 11 or more injection standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion optimized conditions and the other using basic negative ion optimized conditions in two independent injections using separate dedicated columns. Extracts reconstituted in acidic conditions were gradient‐eluted using water and methanol containing 0.1% formic acid, and the basic extracts, which also used water/methanol, contained 6.5 mm ammonium bicarbonate. The MS analysis alternated between MS and data‐dependent MS2 scans using dynamic exclusion. Raw data files are archived and extracted as described below.
Linear trap quadrupole mass spectrometer
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Linear trap quadrupole (LTQ) mass spectrometer is a type of mass spectrometry instrument. It utilizes a linear ion trap and a quadrupole mass analyzer to detect and analyze various molecular compounds.
Automatically generated - may contain errors
Lab products found in correlation
Acquity ultra performance liquid chromatography, by Thermo Fisher Scientific (7 mentions)
Acquity ultra performance liquid chroma tography uplc, by Thermo Fisher Scientific (3 mentions)
Trace dsq, by Thermo Fisher Scientific (2 mentions)
Nano electrospray source, by Thermo Fisher Scientific (2 mentions)
Acquity uplc, by Thermo Fisher Scientific (1 mentions)
Thermo finnigan trace dsq, by Thermo Fisher Scientific (1 mentions)
Waters acquity uhplc, by Waters Corporation (1 mentions)
Xcalibur software 1, by Thermo Fisher Scientific (1 mentions)
19 protocols using linear trap quadrupole mass spectrometer
1
LC-MS-Based Metabolomic Profiling Protocol
2
Multiomics profiling of fresh tumor samples
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Metabolomics and gene expression data from 67 fresh tumor tissue samples originally analyzed by Terunuma et al. were included in this study. Untargeted metabolomic quantification was performed by Metabolon Inc. Samples were prepared using the automated MicroLab STAR system from Hamilton company and mass-spectrometry experiments were done in a Waters ACQUITY UPLC and a Thermo-Finnigan linear trap quadrupole mass spectrometer and in a Thermo-Finnigan Trace DSQ fast-scanning quadrupole mass spectrometer [18 (link)].
3
Proteomic Profiling of Enriched Neostriatal Rafts
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Enriched neostriatal raft proteins were run briefly into a polyacrylamide gel (50 μg/lane). The gel was cut into 6 equally spaced pieces to reduce sample complexity, and subjected to in-gel trypsin digestion. Tryptic peptides were separated by HPLC (reversed phase chromatography, C18 column) and mass spectra were obtained by electrospray ionization with a linear trap quadrupole mass spectrometer (Thermo Scientific, San Jose, CA, USA). Collision-induced dissociation and the instrument’s dynamic exclusion software were used to produce MS/MS spectra from the 3 most intense ions in each survey scan.
Peptides were identified from MS/MS scans using SEQUEST (Thermo Scientific) and an in-house processing pipeline [14 (link)] The protein database was constructed from NCBI RefSeq rat sequences (25,322 entries downloaded December 2010). The relative abundance of identified proteins between groups was measured by spectral counting. A detailed description of the proteomics methods is included inS1 File .
Peptides were identified from MS/MS scans using SEQUEST (Thermo Scientific) and an in-house processing pipeline [14 (link)] The protein database was constructed from NCBI RefSeq rat sequences (25,322 entries downloaded December 2010). The relative abundance of identified proteins between groups was measured by spectral counting. A detailed description of the proteomics methods is included in
4
Histone H3 Immunoprecipitation and Mass Spectrometry
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Murine bone marrow cells were harvested and solubilized in lysis buffer prior to incubation with H3 Ab for 2–4 h in a cold room. Lysates were then incubated with 50 μL of Protein G Sepharose beads (Pierce, Rockford, IL, USA) and eluted into a linear trap quadrupole mass spectrometer (Thermo Scientific, Waltham, MA, USA) with a 2-kV electrospray voltage source. From a full MS scan (400–2000 m/z), the three most intense ions were then chosen for additional MS/MS analysis. Raw data from the full MS scan were analyzed using the MASCOT (http://www.matrixscience.com/ ) search engine.
5
Comprehensive Metabolite Profiling by UHPLC-MS/GC-MS
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UHPLC/MS was performed using a Waters Acquity UHPLC (Waters Corporation, Milford, MA) coupled to a linear trap quadrupole mass spectrometer (Thermo Fisher Scientific, Inc, Waltham, MA) equipped with an electrospray ionization source. Two separate UHPLC/MS injections were performed on each sample: 1 optimized for positive ions and 1 for negative ions. Samples for GC/MS were analyzed on a Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole MS (Thermo Fisher Scientific, Inc, Waltham, MA) operated at unit mass resolving power. Chromatographic separation followed by full-scan mass spectra were performed to record retention time, molecular weight (m/z), and MS/MS of all detectable ions presented in the samples.
6
Quantitative Mass Spectrometry of Peptides
7
Mass Spectrometry-based Proteomics Analysis
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MS was carried out as previously described[14 (link)]. Briefly, dried peptides were resuspended in trifluoroacetic acid (TFA) and 6μL was injected and loaded onto a C18 trap column. The sample was subsequently separated by a C18 reverse-phase column. The mobile phases consisted of water with 0.1% formic acid (A) and 90% acetonitrile with 0.1% formic acid (B). A 65-min linear gradient from 5 to 60% B was used. Eluted peptides were introduced into the mass spectrometer via a 10-μm silica tip (New Objective Inc., Ringoes, NJ) adapted to a nano-electrospray source (Thermo Fisher Scientific). The spray voltage was set at 1.2 kV and the heated capillary at 200°C. The linear trap quadrupole (LTQ) mass spectrometer (ThermoFisher Scientific) was operated in data-dependent mode with dynamic exclusion in which one cycle of experiments consisted of a full-MS (300–2000 m/z) survey scan and five subsequent MS/MS scans of the most intense peaks. Pathways enriched with the proteins were generated by Ingenuity Pathways Analysis (IPA, version 8.5, Ingenuity Systems, Redwood City, CA).
8
Targeted Metabolomics via LC-MS
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The LC/MS portion of the platform was based on a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo-Finnigan linear trap quadrupole (LTQ) mass spectrometer, which consisted of an electrospray ionization (ESI) source and linear ion-trap (LIT) mass analyzer. The sample extract was dried then reconstituted in acidic or basic LC-compatible solvents, each of which contained eight or more injection standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion optimized conditions and the other using basic negative ion optimized conditions in two independent injections using separate dedicated columns. Extracts reconstituted in acidic conditions were gradient eluted using water and methanol containing 0.1% formic acid, while the basic extracts, which also used water/methanol, contained 6.5 mM ammonium bicarbonate. The MS analysis alternated between MS and data-dependent MS2 scans using dynamic exclusion (Evans et al., 2009 (link)). Raw data files are archived and extracted as described below.
9
UPLC-LTQ Mass Spectrometry Protocol
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The LC/MS portion of the platform was based on a Waters ACQUITY ultra-performance liquid chroma-tography (UPLC) and a Thermo-Finnigan linear trap quadrupole (LTQ) mass spectrometer. Sample extracts were dried and then reconstituted in acidic or basic LC-compatible solvents, each of which contained 8 or more injection standards at fixed concentrations to ensure injection and chromatographic consistency.
10
Untargeted Metabolomics Analysis by LC-MS
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The LC/MS portion of the platform was based on a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo-Finnigan linear trap quadrupole (LTQ) mass spectrometer, which consisted of an electrospray ionization (ESI) source and linear ion-trap (LIT) mass analyzer. The sample extract was dried and then reconstituted in acidic or basic LC-compatible solvents, each of which contained 8 or more injection standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion optimized conditions and the other using basic negative ion optimized conditions in two independent injections using separate dedicated columns. Extracts reconstituted in acidic conditions were gradient eluted using water and methanol containing 0.1% formic acid, while the basic extracts, which also used water/methanol, contained 6.5 mM ammonium bicarbonate. The MS analysis alternated between MS and data-dependent MS2 (link) scans using dynamic exclusion. Raw data files were archived and extracted as described below.
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