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Accucore c18 resin

Manufactured by Thermo Fisher Scientific
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The Accucore C18 resin is a high-performance reversed-phase chromatography material. It is designed for use in liquid chromatography applications to separate and analyze a variety of chemical compounds.

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Lab products found in correlation

Proxeon easy nlc 1200 lc pump, by Thermo Fisher Scientific (6 mentions) Orbitrap fusion lumos mass spectrometer, by Thermo Fisher Scientific (5 mentions) Orbitrap fusion lumos, by Thermo Fisher Scientific (4 mentions) Proxeon easy nlc 1200, by Thermo Fisher Scientific (4 mentions) Orbitrap fusion mass spectrometer, by Thermo Fisher Scientific (4 mentions) Q exactive, by Thermo Fisher Scientific (1 mentions) Magic c4 resin, by Bruker (1 mentions) Ltq orbitrap elite, by Thermo Fisher Scientific (1 mentions) Accela 600 lc pump, by Thermo Fisher Scientific (1 mentions) Q exactive mass spectrometer, by Thermo Fisher Scientific (1 mentions) Proxeon easy nlc 1000, by Thermo Fisher Scientific (1 mentions) Proxeon easy nlc 1000 liquid, by Thermo Fisher Scientific (1 mentions) Easy nlc 1200 system, by Thermo Fisher Scientific (1 mentions)

15 protocols using accucore c18 resin

1

LC-MS/MS Analysis of Peptides

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Both unfractionated samples were each analyzed 20 times consecutively on an Orbitrap Fusion Lumos mass spectrometer operated in positive-mode with a Proxeon EASY-nLC 1200 liquid chromatograph (Thermo Fisher Scientific) as described previously.2 (link) Peptide fractionation was performed on a 100 μm inner diameter microcapillary column packed with 35 cm of Accucore C18 resin (2.6 μm, 150 Å, Thermo Fisher Scientific). Approximately 1 μg of peptide was loaded onto the column for LC–MS/MS analysis.
Separation occurred across a 90 min gradient from 4% to 35% acetonitrile in 0.125% formic acid. The flow rate was set to 525 nL/min over the gradient. To prevent carry over, the 20 analyses of the human only sample (H) were queued first followed by the 20 analyses of the human + 10% yeast spike-in sample (HY).
A data dependent Top Speed (3 s) method was used to collect spectra: high resolution MS1 spectra (Orbitrap resolution: 120 000; mass range: 350–1400 Th; and automatic gain control (AGC) target: 4 × 105; maximum injection time 50 ms) and high resolution MS2 spectra (Quadrupole isolation window: 1.6 Th; Orbitrap resolution: 7500; HCD energy: 30%; AGC target: 5 × 104; maximum injection time: 22 ms). Dynamic exclusion was enabled with a duration time of 120 s.
Lim M.Y., Paulo J.A, & Gygi S.P. (2019). Evaluating False Transfer Rates from the Match-between-Runs Algorithm with a Two-Proteome Model. Journal of proteome research, 18(11), 4020-4026.
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2

Orbitrap Fusion Lumos LC-MS/MS Protocol

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All LC-MS/MS experiments were performed on an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) coupled with a Proxeon EASY-nLC 1200 LC pump (Thermo Fisher Scientific). Peptides were separated on a 100µm inner diameter microcapillary column packed with 35cm of Accucore C18 resin (1.8µm, 100Å, Thermo Fisher Scientific). Peptides were separated using a 2 hour gradient of 6–33% acetonitrile in 0.125% formic acid with a flow rate of ~400nL/min. Each analysis used an MS3-based TMT method as described previously29. MS1 data was acquired at a mass range of m/z 350 – 1350, resolution 120,000, AGC target 5 × 105, maximum injection time 150ms, and with a dynamic exclusion of 120 seconds for the peptide measurements in the Orbitrap.
Data dependent MS2 spectra were acquired in the ion trap with a normalized collision energy (NCE) set at 35%, AGC target set to 2.2 × 104 and a maximum injection time of 120ms. MS3 scans were acquired in the Orbitrap with a HCD collision energy set to 55%, AGC target set to 5.5 × 105, maximum injection time of 200ms, resolution at 15,000 and with a maximum synchronous precursor selection (SPS) precursors set to 10.
Kim H., Wrann C.D., Jedrychowski M., Vidoni S., Kitase Y., Nagano K., Zhou C., Chou J., Parkman V.J., Novick S.J., Strutzenberg T.S., Pascal B.D., Le P.T., Brooks D.J., Roche A.M., Gerber K.K., Mattheis L., Chen W., Tu H., Bouxsein M.L., Griffin P.R., Baron R., Rosen C.J., Bonewald L.F, & Spiegelman B.M. (2018). Irisin Mediates Effects on Bone and Fat via αV Integrin Receptors. Cell, 175(7), 1756-1768.e17.
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3

Mass Spectrometry-based Proteomics Protocol

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Data were collected using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific, San Jose, CA) coupled with a Proxeon EASY-nLC 1200 LC pump (Thermo Fisher Scientific). Peptides were separated on a 100 μm inner diameter microcapillary column packed with 35 cm of Accucore C18 resin (2.6 μm, 100 Å, Thermo Fisher Scientific). Peptides were separated using a 3 hours gradient of 6–22% acetonitrile in 0.125% formic acid with a flow rate of ~400 nL/min. Each analysis used an MS3-based TMT method as described previously described 40 (link).The data were acquired using a mass range of m/z 400 – 1400, resolution at 120,000, AGC target of 1 × 106, a maximum injection time 100 ms, dynamic exclusion of 180 seconds for the peptide measurements in the Orbitrap. Data dependent MS2 spectra were acquired in the ion trap with a normalized collision energy (NCE) set at 35%, AGC target set to 2.0 × 105 and a maximum injection time of 120 ms. MS3 scans were acquired in the Orbitrap with an HCD collision energy set to 45%, AGC target set to 1.5 × 105, maximum injection time of 200 ms, resolution at 50,000 and with a maximum synchronous precursor selection (SPS) precursors set to 10.
Perry E.A., Bennett C.F., Luo C., Balsa E., Jedrychowski M., O’Malley K., Latorre-Muro P., Ladley R.P., Reda K., Wright P.M., Gygi S.P., Myers A.G, & Puigserver P. (2021). Tetracyclines promote survival and fitness in mitochondrial disease models. Nature metabolism, 3(1), 33-42.
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4

Orbitrap Fusion Mass Spectrometry-Based Proteomics

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Samples were analyzed on an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific, San Jose, CA) coupled to a Proxeon EASY-nLC 1200 liquid chromatography (LC) pump (Thermo Fisher Scientific). Peptides were separated on a 100 μm inner diameter microcapillary column packed with 35 cm of Accucore C18 resin (2.6 μm, 150 Å, ThermoFisher). For each analysis, approximately 2 μg of peptides were separated using a 150 min gradient of 8 to 28% acetonitrile in 0.125% formic acid at a flow rate of 450–500 nL/min. Each analysis used an MS3-based TMT method71 ,72 , which has been shown to reduce ion interference compared to MS2 quantification73 . The data were collected as described previously using an SPS-MS3 method74 .
Lee J.D., Paulo J.A., Posey R.R., Mugoni V., Kong N.R., Cheloni G., Lee Y.R., Slack F.J., Tenen D.G., Clohessy J.G., Gygi S.P, & Pandolfi P.P. (2021). Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. Nature methods, 18(3), 293-302.
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5

Proteomic Mass Spectrometry Workflow

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Mass spectrometry data was collected using a Q Exactive or LTQ Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) coupled with a Famos Autosampler (LC Packings) and an Accela 600 liquid chromatography (LC) pump (Thermo Fisher Scientific). Peptides were separated onto a 100 μm inner diameter microcapillary column packed with ~0.5 cm of Magic C4 resin (5 μm, 100 Å, Michrom Bioresources) followed by ~20 cm of Accucore C18 resin (1.6 μm, 150 Å, Thermo Fisher Scientific). For each analysis, we loaded ~2 μl onto the column. Peptides were separated using a 50-minute gradient of 8 to 30% acetonitrile in 0.125% formic acid with a flow rate of ~300 nL/min.
Jedrychowski M.P., Wrann C.D., Paulo J.A., Gerber K.K., Szpyt J., Robinson M.M., Nair K.S., Gygi S.P, & Spiegelman B.M. (2015). Detection and Quantitation of Circulating Human Irisin by Tandem Mass Spectrometry. Cell metabolism, 22(4), 734-740.
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6

Liquid Chromatography-Mass Spectrometry Workflow

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Our MS data were collected similar to as described previously38 (link). In brief, we used a Q Exactive mass spectrometer (Thermo Fisher Scientific, San Jose, CA) coupled with a Famos Autosampler (LC Packings) and an Accela600 LC pump (Thermo Fisher Scientific). Peptides were separated on a 100 μm inner diameter microcapillary column packed with ∼25 cm of Accucore C18 resin (2.6 μm, 150 Å, Thermo Fisher Scientific). For each analysis, we loaded ~1 μg onto the column.
Peptides were separated using a 1 h gradient of 5–25% acetonitrile in 0.125% formic acid with a flow rate of ∼300 nl/min. The scan sequence began with an Orbitrap MS1 spectrum with the following parameters: resolution 70,000, scan range 300–1500 Th, automatic gain control (AGC) target 1 × 105, maximum injection time 250 ms, and centroid spectrum data type. We selected the top 20 precursors for MS2 analysis which consisted of HCD high-energy collision dissociation with the following parameters: resolution 17,500, AGC 1 × 105, maximum injection time 60 ms, isolation window 2 Th, normalized collision energy 30, and centroid spectrum data type. The underfill ratio was set at 1%, which corresponds to a 1.1 × 104 intensity threshold. In addition, unassigned and singly charged species were excluded from MS2 analysis and dynamic exclusion was set to automatic.
Iuchi S, & Paulo J.A. (2021). RNAmetasome network for macromolecule biogenesis in human cells. Communications Biology, 4, 1399.
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7

Mass Spectrometry-based Proteomics Protocol

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Data were collected using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific, San Jose, CA) coupled with a Proxeon EASY-nLC 1200 LC pump (Thermo Fisher Scientific). Peptides were separated on a 100 μm inner diameter microcapillary column packed with 35 cm of Accucore C18 resin (2.6 μm, 100 Å, Thermo Fisher Scientific). Peptides were separated using a 3 hours gradient of 6–22% acetonitrile in 0.125% formic acid with a flow rate of ~400 nL/min. Each analysis used an MS3-based TMT method as described previously described 40 (link).The data were acquired using a mass range of m/z 400 – 1400, resolution at 120,000, AGC target of 1 × 106, a maximum injection time 100 ms, dynamic exclusion of 180 seconds for the peptide measurements in the Orbitrap. Data dependent MS2 spectra were acquired in the ion trap with a normalized collision energy (NCE) set at 35%, AGC target set to 2.0 × 105 and a maximum injection time of 120 ms. MS3 scans were acquired in the Orbitrap with an HCD collision energy set to 45%, AGC target set to 1.5 × 105, maximum injection time of 200 ms, resolution at 50,000 and with a maximum synchronous precursor selection (SPS) precursors set to 10.
Perry E.A., Bennett C.F., Luo C., Balsa E., Jedrychowski M., O’Malley K., Latorre-Muro P., Ladley R.P., Reda K., Wright P.M., Gygi S.P., Myers A.G, & Puigserver P. (2021). Tetracyclines promote survival and fitness in mitochondrial disease models. Nature metabolism, 3(1), 33-42.
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8

Receptor Proteomics using Orbitrap Fusion LC-MS/MS

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All LC-MS/MS receptor proteomic experimental data was collected using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) coupled with a Proxeon EASY-nLC 1200 LC pump (Thermo Fisher Scientific). Peptides were separated on a 75µm inner diameter microcapillary column packed with 35 cm of Accucore C18 resin (2.6µm, 100Å, ThermoFisher Scientific). Peptides were separated using a 3hr gradient of 6–27% acetonitrile in 0.125% formic acid with a flow rate of 400nL/min. Each analysis used an MS3- based TMT method as described previously (McAlister et al., 2014 (link)). The data were acquired using a mass range of m/z 350 – 1350, resolution 120,000, AGC target 1 × 106, maximum injection time 100 ms, dynamic exclusion of 120 seconds for the peptide measurements in the Orbitrap.
Data dependent MS2 spectra were acquired in the ion trap with a normalized collision energy (NCE) set at 35%, AGC target set to 1.8 × 104 and a maximum injection time of 120ms. MS3 scans were acquired in the Orbitrap with a HCD collision energy set to 55%, AGC target set to 1.5 × 105, maximum injection time of 150ms, resolution at 15,000 and with a maximum synchronous precursor selection (SPS) precursors set to 10.
Kim H., Wrann C.D., Jedrychowski M., Vidoni S., Kitase Y., Nagano K., Zhou C., Chou J., Parkman V.J., Novick S.J., Strutzenberg T.S., Pascal B.D., Le P.T., Brooks D.J., Roche A.M., Gerber K.K., Mattheis L., Chen W., Tu H., Bouxsein M.L., Griffin P.R., Baron R., Rosen C.J., Bonewald L.F, & Spiegelman B.M. (2018). Irisin Mediates Effects on Bone and Fat via αV Integrin Receptors. Cell, 175(7), 1756-1768.e17.
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9

Quantitative Proteomics via TMT-MS3

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Mass spectrometry data were collected using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fischer Scientific) equipped with a Proxeon EASY-nLC 1000 liquid chromatography (LC) system (Thermo Fisher Scientific). Peptides were separated on a 100μm inner diameter microcapillary column packed with ~35 cm of Accucore C18 resin (2.6μm, 150 Å, Thermo Fisher Scientific). Approximately 2ug peptides were separated using a 2.5 h gradient of acidic acetonitrile. We used the multinotch MS3-based TMT method (McAlister et al., 2014 (link)). The scan sequence began with a MS1 spectrum (Orbitrap analysis; resolution 120,000; mass range 400−1400 Th). MS2 analysis followed collision-induced dissociation (CID, CE = 35) with a maximum ion injection time of 150 ms and an isolation window of 0.5 Da. The 10 most abundant MS1 ions of charge states 2-6 were selected for MS2/MS3 analysis. To obtain quantitative information, MS3 precursors were fragmented by high-energy collision-induced dissociation (HCD, CE = 55) and analyzed in the Orbitrap (resolution was 50,000 at 200 Th) with a maximum ion injection time of 150 ms and a charge state-dependent variable isolation window of 0.7 to 1.2 Da (Paulo et al., 2016 (link)).
Van Vranken J.G., Nowinski S.M., Clowers K.J., Jeong M.Y., Ouyang Y., Berg J.A., Gygi J.P., Gygi S.P., Winge D.R, & Rutter J. (2018). ACP acylation is an acetyl-CoA-dependent modification required for electron transport chain assembly. Molecular cell, 71(4), 567-580.e4.
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10

Quantitative Orbitrap mass spectrometry

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Samples were analyzed on an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific, San Jose, CA) coupled to a Proxeon EASY-nLC 1200 liquid chromatography (LC) pump (Thermo Fisher Scientific). Peptides were separated on a 100 μm inner diameter microcapillary column packed with 35 cm of Accucore C18 resin (2.6 μm, 150 Å, ThermoFisher). For each analysis, approximately 2 μg of peptides were separated using a 150 min gradient of 8–28% acetonitrile in 0.125% formic acid at a flow rate of 450–500 nL/min. Each analysis used an MS3-based TMT method,170 (link),171 (link) which has been shown to reduce ion interference compared to MS2 quantification.172 (link) The data were collected using the SPS-MS3 method.173 (link)
Lee J.D., Menasche B.L., Mavrikaki M., Uyemura M.M., Hong S.M., Kozlova N., Wei J., Alfajaro M.M., Filler R.B., Müller A., Saxena T., Posey R.R., Cheung P., Muranen T., Heng Y.J., Paulo J.A., Wilen C.B, & Slack F.J. (2023). Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. Cell reports, 42(12), 113478.
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