Tsq altis

Manufactured by Thermo Fisher Scientific

Sourced in United States, Germany

The TSQ Altis is a triple quadrupole mass spectrometer designed for quantitative and qualitative analysis. It features high sensitivity, resolution, and mass accuracy to provide reliable results for a wide range of applications.

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32 protocols using tsq altis

LC-MS/MS Analysis of Peptides

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Samples were analyzed on a TSQ Altis (Thermo Fisher Scientific) coupled to an UltiMate 3000 (Thermo Fisher Scientific) and an easy spray analytical column (ES802A, 25 cm, 75 mm ID PepMap RLSC, C18, 100 Å, 2 mm particle size column (Thermo Fisher Scientific)). First, samples were reconstituted in 2% LC-MS grade FA. Samples were loaded on a trap column (Acclaim PepMap 100 C18 HPLC Column 0.3 × 5 mm with 5 μm particles (Thermo Fisher Scientific)) with 2.2% buffer A (0.1% FA) for 3 min and subsequently separated using 0 to 32% buffer B (99.9% ACN, 0.1% FA) in 35 min at 300 nl/min and followed by a 20 min column wash with 80% buffer B at 300 nl/min and 10-min column equilibration at 2.2% B. The TSQ Altis spray voltage was set at 1.9 kV and fragmented at 1.5 mTorr in the second quadrupole. The first quadrupole was set at 0.7 da FWHM, and the third quadrupole was set at 1.2 da FWHM. All transitions were measured with optimized collision energy without scheduling and a cycle time of 1.5 s.

Veth T.S., Francavilla C., Heck A.J, & Altelaar M. (2023). Elucidating Fibroblast Growth Factor–Induced Kinome Dynamics Using Targeted Mass Spectrometry and Dynamic Modeling. Molecular & Cellular Proteomics : MCP, 22(8), 100594.

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Quantitative Phosphoproteomics of T-Loop

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The QuantaKinome platform was applied to measure T-loop phosphopeptides by using a targeted LC-MS approach which is based on the method described in Schmidlin et al. Briefly, frozen biopsy were lysed in SDC lysis buffer, proteins were extracted and 200 μg of protein was digested with LysC for 2 h (1:50 enzyme to protein ratio) and trypsin overnight (1:50 enzyme to protein ratio) (method is described in more detail previously by Schmidlin et al.¹⁴ (link)). Peptides were desalted and phosphorylated peptides were enriched using an automated platform (Agilent Bravo) as described previously (Post et al.). Samples were dried and stored at −80°C until LC-MS analysis, performed on a TSQ Altis (Thermo Scientific) coupled to an Ultimate 3000 ((Thermo Scientific) equipped with a ES802 analytical LC column. Next, half of the processed samples were measured in randomized order using the targeted LC-MS assay. Samples were dissolved in 2% FA and loaded on an ES802 column on an Ultimate 3000 RSLC nano LC coupled to a TSQ Altis (Thermo Scientific).

Debets D.O., de Graaf E.L., Liefaard M.C., Sonke G.S., Lips E.H., Ressa A, & Altelaar M. (2024). Predicting treatment outcome using kinome activity profiling in HER2+ breast cancer biopsies. iScience, 27(6), 109858.

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Intracellular Glycine Isotopic Enrichment Analysis

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Intracellular glycine isotopic enrichment was measured in red blood cells (RBC) using liquid chromatography-tandem mass spectroscopy (LC-MS/MS). Briefly, RBC free glycine was converted into its DANS [5-(dimethylamino)-1-napthalene sulfonamide] derivative and analyzed using a Kinetex C18 2.6μ 100 × 2.1 mm column (Phenomenex, Torrance, CA) on a triple quadrupole mass spectrometer (TSQ Altis; Thermo Scientific, San Jose, CA). The ions were then analyzed by SRM (selected reaction monitoring) mode. The transitions observed were precursor ions m/z 309, and 311 to product ion m/z 170.
IEs of various acylglycines in urine were measured using liquid chromatography-tandem mass spectroscopy (LC-MS/MS). Acylglycine was butylated and analyzed using an Omega C18 2.6μ 100 × 2.1 mm column (Phenomenex, Torrance, CA) on a triple quadrupole mass spectrometer (TSQ Altis; Thermo Scientific, San Jose, CA). The ions were then analyzed by SRM mode. The transitions observed were: Acetylglycine m/z 174 to 76 & 176 to 78; Isobutyrylglycine m/z 202 to 76 & 204 to 78; Benzoylglycine m/z 236 to 105 & 238 to 105; Tigylglycine m/z 214 to 83 & 216 to 83; Isovalerylglycine m/z 216 to 76 & 218 to 78; and Hexanoylglycine m/z 230 to 76 & 232 to 78; Octanoylglycine m/z 258 to 76 & 260 to 78; and Benzoylglycine m/z 236 to 105 & 238 to 105.

Tan H.C., Hsu J.W., Tai E.S., Chacko S., Kovalik J.P, & Jahoor F. (2024). The impact of obesity-associated glycine deficiency on the elimination of endogenous and exogenous metabolites via the glycine conjugation pathway. Frontiers in Endocrinology, 15, 1343738.

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Pharmacokinetics of Levobupivacaine Plasma Concentrations

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All patients received a dedicated intravenous line contralateral to the fluid line for blood sampling. Venous blood samples of 2 mL each were obtained at 2.5, 5, 7.5, 10, 12.5, 15, 30, 60, and 120 min after completion of the blockade. Each blood sample was collected in a tube containing heparin and immediately placed on ice. Plasma was separated by centrifugation of blood samples at 1,500 × g for 10 min and stored at -20 °C until subsequent analyses. Plasma levobupivacaine concentrations were measured using high-performance liquid chromatography (Accela; Thermo Fisher Scientific Co., Ltd., Kanagawa, Japan) and liquid chromatography-mass spectrometry with a triple-stage quadrupole mass spectrometer (TSQ Quantum Ultra; Thermo Fisher Scientific Co., Ltd.) or high-performance liquid chromatography (Vanquish Flex; Thermo Fisher Scientific K.K., Tokyo, Japan) and liquid chromatography-mass spectrometry with a triple-stage quadrupole mass spectrometer (TSQ Altis; Thermo Fisher Scientific K.K.).

Shigeta H., Yasumura R, & Kotake Y. (2022). Comparison of plasma levobupivacaine concentrations with and without epinephrine following erector spinae plane block for breast cancer surgery: a randomized controlled trial. BMC Anesthesiology, 22, 86.

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Quantification of DNA Methylation States

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Genomic DNA was isolated by Phenol:chloroform method. 5 μg of genomic DNA was digested to nucleoside level by using Nucleoside digestion mix (M0649S; NEB). Mass spectrometry-based quantitation of cytosine, 5mC and 5hmC was performed as described (59 (link), 60 (link)). Briefly, Cytosine, 5mC, 5hmC were quantitated using a Thermo Vanquish UHPLC coupled to a Thermo TSQ-Altis tandem mass spectrometer through an electrospray ion source operating in positive ion mode at 3.5kV. Stock standard solutions were prepared in deionized water at a concentration of 1 mmol/L each. Calibration standard mixtures were prepared at concentrations between 1.0–250umol/L for dC, 0.04–10 umol/L for mdC, and 0.002–0.5 umol/L for hmdC. Linear calibration plots were prepared using concentration versus peak area integration (zero intercept) with a R² greater than 0.999. By comparing the internal standard normalized peak areas in the digest sample to the corresponding retention times from the calibration standards, the micromolar concentrations of the nucleosides were determined against the standard curve. The molar ratio as a percent was then calculated as follows:

\underline{Mol % hmdC} = ([hmdC] / ([dC] + [mdC] + [hmdC]) \times 100

Kharat S.S., Ding X., Swaminathan D., Suresh A., Singh M., Sengodan S.K., Burkett S., Marks H., Pamala C., He Y., Fox S.D., Buehler E.C., Muegge K., Martin S.E, & Sharan S.K. (2020). Degradation of 5hmC-marked stalled replication forks by APE1 causes genomic instability. Science signaling, 13(645), eaba8091.

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Quantification of Momilactone A and B

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Oryza sativa cv. Kitaake and Echinochloa crus-galli were grown in sand in the greenhouse for three weeks. Roots were harvested, weighed, snap-frozen in liquid nitrogen and homogenized. Metabolites were extracted in 10 times MeOH to sample weight, and momilactone A and B were measured on a Vanquish HPLC (Thermo Fisher Scientific) coupled via electrospray ionization to an TSQ Altis (Thermo Fisher Scientific) mass spectrometer, and quantified using authentic standards provided by Kazunori Okada, University of Tokyo [74 (link)].

Knoch E., Kovács J., Deiber S., Tomita K., Shanmuganathan R., Serra Serra N., Okada K., Becker C, & Schandry N. (2022). Transcriptional response of a target plant to benzoxazinoid and diterpene allelochemicals highlights commonalities in detoxification. BMC Plant Biology, 22, 402.

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Shotgun Lipidomics of HDL Lipid Composition

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Lipid composition of HDL was determined using multidimensional mass spectrometry-based shotgun lipidomics [24 ]. In brief, 1 ml of each HDL sample was accurately transferred to a disposable glass tube; a mixture of lipid internal standards was added, and then lipid extraction was performed using a modified Bligh and Dyer procedure [25 (link)]. The samples were diluted to 500 fmol total lipid per μL and analyzed on a triple quadrupole mass spectrometer (TSQ Altis, Thermo Fisher Scientific, San Jose, CA) and a Q Exactive mass spectrometer (Thermo Scientific, San Jose, CA), both equipped with an automated nanospray device (TriVersa NanoMate, Advion Bioscience Ltd., Ithaca, NY), as described [26 (link)]. Identification and quantification of lipid species were performed using an automated software program [27 (link), 28 (link)].

Picataggi A., Rodrigues A., Cromley D.A., Wang H., Wiener J.P., Garliyev V., Billheimer J.T., Grabiner B.C., Hurt J.A., Chen A.C., Han X., Rader D.J., Praticò D, & Lyssenko N.N. (2022). Specificity of ABCA7-mediated cell lipid efflux. Biochimica et biophysica acta. Molecular and cell biology of lipids, 1867(7), 159157.

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Quantitative Shotgun Lipidomics of Macrophages

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Multidimensional mass spectrometry-based shotgun lipidomics analysis of lipids for macrophages samples was performed as described (33 , 34 (link)). In brief, premixed internal standard was added to 10⁶ isolated macrophages for quantitation of lipid species and then normalized with the protein content (per mg protein), which was performed following the instruction of Pierce™ BCA protein assay kit (Cat #23225, Thermo Scientific). The lipids were extracted using a modified Bligh and Dyer procedure (35 ), and each lipid extract was reconstituted in chloroform/methanol (1:1, v/v) at a volume of 50 µL.
For shotgun lipidomics, lipid extracts were diluted to a final concentration of ~500 fmol total lipids µL^-1. Mass spectrometric analysis was performed on a triple quadrupole mass spectrometer (TSQ Altis, Thermo Fisher Scientific, San Jose, CA) and a Q Exactive mass spectrometer (Thermo Scientific, San Jose, CA), both of which were equipped with an automated nanospray device (TriVersa NanoMate, Advion Bioscience Ltd., Ithaca, NY) as described (36 (link)). Identification and quantification of lipid species were performed using an automated software program (37 (link), 38 (link)). Data processing (ion peak selection, baseline correction, data transfer, peak intensity comparison and quantitation) was performed as described (38 (link)).

Reeves A.R., Sansbury B.E., Pan M., Han X., Spite M, & Greenberg A.S. (2021). Myeloid-specific deficiency of long-chain acyl CoA synthetase 4 (Acsl4) reduces inflammation in vitro and in vivo by remodeling phospholipids and reducing production of arachidonic acid-derived proinflammatory lipid mediators. Journal of immunology (Baltimore, Md. : 1950), 207(11), 2744-2753.

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Multidimensional Lipid Profiling in Adipose

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Lipid species were analyzed using multidimensional mass spectrometry-based shotgun lipidomic analysis.⁸⁶ Briefly, adipose tissue homogenate containing 0.5 mg of protein (Pierce BCA assay) was accurately transferred to a disposable glass culture test tube. A premixture of lipid internal standards (IS) was added prior to conducting lipid extraction for quantification of the targeted lipid species. Lipid extraction was performed using a modified Bligh and Dyer procedure,^{87 (link)} and each lipid extract was reconstituted in chloroform:methanol (1:1, v:v) at a volume of 400 μL/mg protein. For shotgun lipidomics, lipid extract was further diluted to a final concentration of ~500 fmol total lipids per μL. Mass spectrometric analysis was performed on a triple quadrupole mass spectrometer (TSQ Altis, Thermo Fisher Scientific, San Jose, CA) which was equipped with an automated nanospray device (TriVersa NanoMate, Advion Bioscience Ltd., Ithaca, NY).^{88 (link)} Identification and quantification of lipid species were performed using an automated software program.^{89 (link),90 (link)} Data processing (e.g., ion peak selection, baseline correction, data transfer, peak intensity comparison and quantitation) was performed and result was normalized to the protein content (nmol lipid/mg protein) or wet tissue weight (nmol lipid/mg tissue).

Leach T.J., Chotkowski H.L., Wotring M.G., Dilwith R.L, & Glaser R.L. (2000). Replication of Heterochromatin and Structure of Polytene Chromosomes. Molecular and Cellular Biology, 20(17), 6308-6316.

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Quantitative LC-MRM Proteomics Analysis

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LC-MRM analysis was performed in triplicate on a nanoUHPLC interfaced with an electrospray triple quadrupole mass spectrometer (DionexRSLCnano and TSQ Altis, Thermo). For each sample, peptide mixture (5 μL) was loaded onto the trap column and the trapped peptides were eluted onto a C18 analytical column and separated using a 62.5-minute gradient. Collision energy (CE) values were optimized for this instrument in Skyline version 20.1.0.76 (24 (link)) using CE optimization equations empirically derived from data previously collected on the instrument. Skyline (v. 20.1.0.76) was used to evaluate the data (24 (link)).

Solanki H.S., Welsh E.A., Fang B., Izumi V., Darville L., Stone B., Franzese R., Chavan S., Kinose F., Imbody D., Koomen J.M., Rix U, & Haura E.B. (2021). Cell-type Specific Adaptive Signaling Responses to KRASG12C inhibition. Clinical cancer research : an official journal of the American Association for Cancer Research, 27(9), 2533-2548.

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