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7 protocols using ammonium bicarbonate lc ms grade

1

Metabolite Extraction Reagents Purchase

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Methanol, acetonitrile, isopropanol, formic acid, and ammonium acetate were purchased from Thermo Fisher Scientific (Fair Lawn, NJ). Ammonium bicarbonate (LC-MS grade) and methyl tert-butyl ether (MTBE) were purchased from Sigma-Aldrich (St. Louis, MO). Ultra-pure water (18.2 m ω cm) was prepared in house by a Milli-Q purified water system (Merck KGaA, Darmstadt, Germany).
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2

Glycopeptide Enrichment and Purification

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Peptide N-glycosidase (PNGase F) was purchased from New England Biolabs (Ipswich, MA, USA). Dithiothreitol (DTT) was purchased from GE Healthcare (Uppsala, Sweden), HyperSep Hypercarb PGC was from Thermo Scientific (Runcorn WA7 1TA, UK). Sep-Pak Vac (1cc) was obtained from Waters (Milford, MA, USA). Centrifuge filters for ultrafiltration were a product of Millipore (Carrigtowohill, Ireland). Acetonitrile (LC/MS grade) and water were from Avantor (Center Valley, PA, USA), formic acid and ammonium bicarbonate (LC/MS grade) were products of Sigma-Aldrich (St. Louis, MO, USA). Reagent grade ammonia and acetone were obtained from Scharlab S. L (Sentmenat, Spain).
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3

Quantitative Analysis of Phytochemicals

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Standards for AOH, AME, TeA, and TEN (purity > 98%) were purchased from Qingdao Pribolab Biotech Co., Ltd. (Qingdao, China). Methanol and acetonitrile (LC-MS grade) were obtained from Fisher Scientific (Fair Lawn, NJ, USA). Ammonium bicarbonate (LC-MS grade) was purchased from Sigma-Aldrich (St. Louis, MO, USA). Phosphoric acid and sodium dihydrogen phosphate were both analytical-grade (Sinopharm Chemical Reagent Co., Ltd., Shanghai, China). Water was prepared using a Millipore Milli-Q System (Millipore, Bedford, MA, USA) with a conductivity ≥18.2 MΩ.cm at 25 °C.
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4

LC-MS Quantification of CDK4/6 Inhibitors

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Abemaciclib, palbociclib, and ribociclib, as well as their internal standards (IS) 2H8-Abemaciclib, 2H8-palbociclib, and 2H6-ribociclib (100.0% purity for all compounds), were purchased from Alsachim (Illkirch-Graffenstaden, France). The isotopic enrichment of the internal standards was 98.0%, 98.3%, and 99.9% for 2H8-Abemaciclib, 2H8-palbociclib, and 2H6-ribociclib, respectively. Methanol (MeOH), acetonitrile (ACN), formic acid, and water (all supragradient grade) were supplied by Biosolve Ltd (Valkenswaard, The Netherlands). Dimethylsulfoxide (DMSO, SeccoSolv ≥ 99.9% purity) was obtained from Merck (Darmstadt, Germany), and ammonium bicarbonate (LC-MS grade) was from Sigma-Aldrich (Darmstadt, Germany).
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5

Optimized Proteomics Sample Preparation

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All the chemicals used in the preparation of the background electrolyte (BGE) and the rest of solutions were of analytical reagent grade or better. Water (LC-MS grade), ammonium acetate (NH4Ac, ≥99.9%), ammonium bicarbonate (LC-MS grade), DLdithiothreitol (DTT, ≥99.0%) and iodoacetamide (IAA, ≥98.0%) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Acetic acid (HAc, glacial), formic acid (HFor, 99.0%), ammonia (25%) and sodium hydroxide (≥99.0%) were supplied by Merck (Darmstadt, Germany). iodoacetamide (IAA, ≥98.0%) was provided by Fluka (Buchs, Switzerland). Acetonitrile (≥99.9%) was purchased from Panreac (Castellar del Vallès, Spain). 2-propanol (≥99.9%) was supplied by Scharlau (Sentmenat, Spain).
Free trypsin (sequencing grade modified trypsin) and particles with immobilized trypsin (immobilized trypsin) were provided by Promega (Madison, Wisconsin, USA). β-LG (~90%, PAGE), α-CSN (>70%), β-CSN (>90%) and κ-CSN (≥80%) were purchased from Sigma-Aldrich. An Escherichia coli cell lysate (E. coli positive control whole cell lysateexpressing 6X His tag protein) was supplied by Abcam (Cambridge, UK).
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6

Metabolite Extraction and Quantification

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LC/MS-grade acetonitrile, water, isopropanol, and methanol (Burdick & Jackson) were purchased from Honeywell. LC/MS-grade ammonium bicarbonate, ammonium hydroxide, and methylenediphosphonic (medronic) acid were purchased from Sigma-Aldrich. Dried-down metabolic extracts of E. coli were purchased from Cambridge Isotope Laboratories (MSK-CRED-DD-KIT). Spike-in compounds (Supplementary Table 2) were purchased from Sigma-Aldrich, LGC Standards, and Toronto Research Chemicals.
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7

Lipidomics Mass Spectrometry Protocol

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LC/MS-grade methanol, acetonitrile, isopropanol, formic acid, ammonium acetate and ammonium hydroxide were purchased from Fisher Scientific (Fair Lawn, USA). LC/MS-grade ammonium bicarbonate and LC-grade methyl-tert-butyl-ether (MTBE) were purchased from Sigma-Aldrich Co. (St. Louis, USA). Isotopic internal standards were purchased from Cambridge Isotope Laboratories Inc. (Tewksbury, USA) and Toronto Research Chemicals (Toronto, Canada). A lipid mixture of SPLASH LIPI-DOMIX isotopic internal standard was purchased from Avanti Polar Lipids (Alabama, USA). Ultrapure water (18.2 MO cm) was prepared with an in-house Milli-Q Purified Water system (Merck KGaA, Darmstadt, Germany).
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