Accucore 150 resin

Manufactured by Thermo Fisher Scientific

The Accucore 150 resin is a high-performance liquid chromatography (HPLC) stationary phase material. It is designed to provide efficient chromatographic separations with a particle size of 2.6 μm and a porous structure with a nominal pore size of 150 Å.

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19 protocols using accucore 150 resin

Proteomic Analysis by Orbitrap Lumos MS

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Mass spectrometric data were collected on an Orbitrap Lumos mass spectrometer coupled to a Proxeon NanoLC-1200 UHPLC. The 100-µm capillary column was packed with 35 cm of Accucore 150 resin (2.6 μm, 150 Å; Thermo Fisher Scientific). The scan sequence began with an MS1 spectrum (Orbitrap analysis, resolution 60,000, 400–1600 Th, automatic gain control (AGC) target 4 × 10⁵, maximum injection time 50 ms). Data were acquired for 90 min per fraction. Analysis at the MS2 stage consisted of higher energy collision-induced dissociation (HCD), Orbitrap analysis with the resolution of 50,000, automatic gain control (AGC) 1.25 ×105, NCE (normalized collision energy) 37, maximum injection time 120 ms, and an isolation window at 0.5 Th. For data acquisition including FAIMS, the dispersion voltage (DV) was set at 5000 V, the compensation voltages (CVs) were set at −40 V, −60 V, and −80 V, and TopSpeed parameter was set at 1.5 s per CV.

Senabouth A., Daniszewski M., Lidgerwood G.E., Liang H.H., Hernández D., Mirzaei M., Keenan S.N., Zhang R., Han X., Neavin D., Rooney L., Lopez Sanchez M.I., Gulluyan L., Paulo J.A., Clarke L., Kearns L.S., Gnanasambandapillai V., Chan C.L., Nguyen U., Steinmann A.M., McCloy R.A., Farbehi N., Gupta V.K., Mackey D.A., Bylsma G., Verma N., MacGregor S., Watt M.J., Guymer R.H., Powell J.E., Hewitt A.W, & Pébay A. (2022). Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration. Nature Communications, 13, 4233.

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Orbitrap-based Proteomics Workflow

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Mass spectrometric data were collected on an Orbitrap Eclipse mass spectrometer coupled to a Proxeon NanoLC-1200 UHPLC. The 100 μm capillary column was packed with 35 cm of Accucore 150 resin (2.6 μm, 150Å; ThermoFisher Scientific). The scan sequence began with an MS1 spectrum (Orbitrap analysis, resolution 120,000, 350–1400 Th, automatic gain control (AGC) target 5 x10⁵, maximum injection time 100 ms). Data were acquired ~120 minutes per fraction. MS2 analysis consisted of collision-induced dissociation (CID), quadrupole ion trap analysis, automatic gain control (AGC) 2 x10⁴, NCE (normalized collision energy) 35, q-value 0.25, maximum injection time 120 ms), isolation window at 0.5 Th, and TopSpeed set at 3 sec. For FAIMS, the dispersion voltage (DV) was set at 5000V, the compensation voltages (CVs) used were −40V, −60V, and −80V, and the TopSpeed parameter was set at 1 sec.

Liu X., Gygi S.P, & Paulo J.A. (2020). Isobaric tag-based protein profiling across eight human cell lines using high-Field Asymmetric Ion Mobility Spectrometry (FAIMS) and Real-Time database Searching (RTS). Proteomics, 21(1), e2000218.

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Orbitrap-based Mass Spectrometry Proteomics

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Mass spectrometric data were collected on an Orbitrap Eclipse mass spectrometer coupled to a Proxeon NanoLC-1200 UHPLC. The 100 μm capillary column was packed with 35 cm of Accucore 150 resin (2.6 μm, 150 Å; ThermoFisher Scientific). Data were acquired for 75 min per fraction for the whole proteome samples and 90 min for the phosphopeptide fractions. The scan sequence began with an MS1 spectrum: Orbitrap analysis, resolution 120 000, 350–1400 Th, automatic gain control (AGC) target 5 × 10⁵, maximum injection time 100 ms. MS2 analysis consisted of CID with multistage activation (MSA), quadrupole ion trap analysis, AGC 1 × 10⁴, NCE (normalized collision energy) 35, q-value 0.25, isolation window 0.4 Th, maximum injection time set to “auto” and TopSpeed set at 3 s. Advanced peak detection (APD) was turned on. For data acquisition that included FAIMS, the dispersion voltage (DV) was held constant at 5000 V, the compensation voltages (CVs) were set at −40, −60, and −80 V, and TopSpeed parameter was set to 1 s. No MS3 scans were acquired for these data sets.

Popow O., Liu X., Haigis K.M., Gygi S.P, & Paulo J.A. (2021). A Compendium of Murine (Phospho)Peptides Encompassing Different Isobaric Labeling and Data Acquisition Strategies. Journal of proteome research, 20(7), 3678-3688.

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Orbitrap Mass Spectrometry DIA Analysis

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Samples were analysed on an Orbitrap Exploris 480 Mass Spectrometer coupled to a Proxeon EASY-nLC pump 1000 (Thermo Fisher). Peptides were separated on a 15-cm column packed with Accucore150 resin (150 Å, 2.6-mm C18 beads Thermo Fisher) using an 80-min acetonitrile gradient. MS1 data were collected using the Orbitrap (60,000 resolution, 350–1,050 m/z, 100% normalized AGC, maxIT set to auto). DIA MS2 scans in the Orbitrap were carried out with overlapping 24-m/z windows for the first duty cycle (390–1,014 m/z) and for the second duty cycle (402–1,026 m/z) with 28% NCE, 30,000 resolution, for fixed 145–1,450 m/z range, 1,000% normalized AGC, and a 54-ms maxIT MS1 survey scan was carried out following each DIA MS/MS duty cycle.

Hickey K.L., Swarup S., Smith I.R., Paoli J.C., Miguel Whelan E., Paulo J.A, & Harper J.W. (2023). Proteome census upon nutrient stress reveals Golgiphagy membrane receptors. Nature, 623(7985), 167-174.

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High-Resolution Multidimensional Proteomics

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24 basic pH HPLC fractions were obtained by pooling a quarter of each of the corresponding fractions collected for the four founder-strain 16-plexes. Samples were loaded and separated on an in-house 100-µm capillary column packed with 30 cm of Accucore 150 resin (2.6 μm, 150 Å; Thermo Fisher Scientific). LC separation used a 105-min gradient (120 min method length). Data were collected using a high-resolution MS2 method with the mass spectrometer alternating between three compensatory FAIMS voltages (−80, −60 and −40 V). MS1 scans were collected in the Orbitrap with a resolution setting of 120 K, a 50% AGC target and a maximum injection time of 50 ms. MS2 scans were acquired in the Orbitrap (15 K resolution) in Top Speed mode with a cycle time of 1 s, a collision energy of 34, and an isolation width of 0.5. MS2 AGC was set at 100%, and a maximum injection time of 150 ms was allowed. Dynamic exclusion was enabled with an exclusion duration of 120 s and a mass tolerance of ±7 p.p.m., and only one charge state was allowed to trigger MS2 scans per precursor.

Yu Q., Liu X., Keller M.P., Navarrete-Perea J., Zhang T., Fu S., Vaites L.P., Shuken S.R., Schmid E., Keele G.R., Li J., Huttlin E.L., Rashan E.H., Simcox J., Churchill G.A., Schweppe D.K., Attie A.D., Paulo J.A, & Gygi S.P. (2023). Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression. Nature Communications, 14, 555.

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Comprehensive HPLC-MS Workflow for Biomolecular Analysis

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24 basic pH HPLC fractions (see “Basic pH reversed-phase fractionation”) were loaded and separated on an in-house 100-µm capillary column packed with 30 cm of Accucore 150 resin (2.6 μm, 150 Å; Thermo Fisher Scientific). LC separation used a 105-min gradient (120 min method length). Data were collected using a high-resolution MS2 method with the mass spectrometer alternating between three compensatory FAIMS voltages (−80, −60, and −40 V). MS1 scans were collected in the Orbitrap with a resolution setting of 120 K, a 50% AGC target, and a maximum injection time of 50 ms. MS2 scans were acquired in the Orbitrap (15 K resolution) Top Speed mode with a cycle time of 1 s, a collision energy of 34, and an isolation width of 0.5. MS2 AGC was set at 100%, and a maximum injection time of 150 ms was allowed. Dynamic exclusion was enabled with an exclusion duration of 120 s and a mass tolerance of ±7 p.p.m., and only one charge state was allowed to trigger MS2 scans per precursor.

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Orbitrap-based Proteomic Workflow

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Mass spectrometry data were collected using an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific, San Jose, Calif) coupled with a Proxeon EASY-nLC II liquid chromatography pump (Thermo Fisher Scientific). The general mass spectrometry workflow is shown in Figure 1. Peptides were separated on a 100-μm inner diameter microcapillary column packed with approximately 0.5 cm of Magic C4 resin (5 μm, 10 nm beads; Michrom Bioresources) followed by approximately 20 cm of Accucore 150 resin (2.6 μm, 150 Å; Thermo Fisher Scientific). For each analysis, we loaded approximately 1 μg onto the column.
Peptides were separated using a 1.5-hour gradient of 6% to 30% acetonitrile in 0.125% formic acid with a flow rate of approximately 300 nL/min. The scan sequence began with an MS¹ spectrum (Orbitrap analysis: resolution, 60,000; 300–1500 Thomson; automatic gain control target, 1 × 10⁶; maximum injection time, 150 milliseconds). The top 10 precursors were then selected for MS² analysis. MS² analysis consisted of collision-induced dissociation, quadrupole ion trap analysis, automatic gain control of 2 × 10³, normalized collision energy of 35, q value of 0.25, and maximum injection time of 100 milliseconds.

Marchegiani G., Paulo J.A., Sahora K, & Castillo C.F. (2015). The Proteome of Postsurgical Pancreatic Juice. Pancreas, 44(4), 574-582.

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High-Resolution Mass Spectrometry of Peptides

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Mass spectrometric data were collected on an Orbitrap Lumos mass spectrometer coupled to a Proxeon NanoLC-1200 UHPLC. The 100-µm capillary column was packed with 35 cm Accucore 150 resin (2.6 μm, 150 Å; Thermo Fisher Scientific). The scan sequence began with an MS1 spectrum (Orbitrap analysis, resolution 60,000, 400 − 1600 Th, automatic gain control (AGC) target 4 × 105, maximum injection time 50 ms). Data were acquired for 90 min per fraction. Analysis at the MS2 stage consisted of higher energy collision-induced dissociation (HCD), Orbitrap analysis with a resolution of 50,000, AGC of 1.25 × 10⁵, normalized collision energy (NCE) of 37, maximum injection time of 120 ms, and an isolation window at 0.5 Th. For data acquisition including field asymmetric ion mobility spectrometry (FAIMS), the dispersion voltage (DV) was set at 5000 V; the compensation voltages (CVs) were set at − 40 V, − 60 V, and − 80 V; and the TopSpeed parameter was set at 1.5 s per CV.

Shi H., Yin Z., Koronyo Y., Fuchs D.T., Sheyn J., Davis M.R., Wilson J.W., Margeta M.A., Pitts K.M., Herron S., Ikezu S., Ikezu T., Graham S.L., Gupta V.K., Black K.L., Mirzaei M., Butovsky O, & Koronyo-Hamaoui M. (2022). Regulating microglial miR-155 transcriptional phenotype alleviates Alzheimer’s-induced retinal vasculopathy by limiting Clec7a/Galectin-3+ neurodegenerative microglia. Acta Neuropathologica Communications, 10, 136.

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Proteome Analysis by Orbitrap Fusion Lumos

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Samples were desalted via C-18 Stagetips. Eleven, 3-h gradients were collected using an Orbitrap Fusion Lumos instrument coupled to a Proxeon EASY-nLC 1200 liquid chromatography (LC) pump (Thermo Fisher Scientific). Peptides were fractionated on a 100 μm inner diameter microcapillary column packed with ~35 cm of Accucore 150 resin (2.6 μm, 150 Å, ThermoFisher Scientific). For each analysis, we loaded 1 μg per sample onto the column. Peptides were separated using a 3 h gradient of 6 to 26% acetonitrile in 0.125% formic acid at a flow rate of ~400 nL/min. Each analysis used the multinotch MS3-based TMT method^{18 (link),19 (link)} on an Orbitrap Fusion Lumos.

O’Connell J.D., Paulo J.A., O’Brien J.J, & Gygi S.P. (2018). Proteome-Wide Evaluation of Two Common Protein Quantification Methods. Journal of proteome research, 17(5), 1934-1942.

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Orbitrap Eclipse Mass Spectrometry Workflow

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Mass spectrometric data were collected on an Orbitrap Eclipse mass spectrometer coupled to a Proxeon NanoLC-1200 ultra-high-performance liquid chromatography (UHPLC). The 100-μm capillary column was packed with 35 cm of Accucore 150 resin (2.6 μm, 150 Å; ThermoFisher Scientific). The scan sequence began with an MS1 spectrum (Orbitrap analysis, resolution 120,000, 350 to 1,400 Th, AGC target 5 × 10⁵, maximum injection time 100 ms). Data were acquired ∼120 min per fraction. MS2 analysis consisted of collision-induced dissociation, quadrupole ion trap analysis, AGC 2 × 10⁴, NCE 35, q value 0.25, maximum injection time 120 ms), isolation window at 0.5 Th, and TopSpeed set at 3 s. For field asymmetric ion mobility spectrometry, the dispersion voltage was set at 5,000 V; the compensation voltages used were −40, −60, and −80 V; and the TopSpeed parameter was set at 1 s.

Mena E.L., Donahue C.J., Vaites L.P., Li J., Rona G., O’Leary C., Lignitto L., Miwatani-Minter B., Paulo J.A., Dhabaria A., Ueberheide B., Gygi S.P., Pagano M., Harper J.W., Davey R.A, & Elledge S.J. (2021). ORF10–Cullin-2–ZYG11B complex is not required for SARS-CoV-2 infection. Proceedings of the National Academy of Sciences of the United States of America, 118(17), e2023157118.

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