High Performance Liquid Chromatography:Article Title: A New Renal Protective Strategy: Shenfu Decoction Targets Hypertensive Renal Disease through the AMPK/SIRT1/PGC-1α Pathway.
Article Snippet: This is a PDF of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability.. This version will undergo additional copyediting, typesetting and review before it is published in its final form.. As such, this version is no longer the Accepted Manuscript, but it is not yet the definitive Version of Record; we are providing this early version to give early visibility of the article.
Liquid Chromatography with Mass Spectroscopy:Article Title: A New Renal Protective Strategy: Shenfu Decoction Targets Hypertensive Renal Disease through the AMPK/SIRT1/PGC-1α Pathway.
Article Snippet: This is a PDF of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability.. This version will undergo additional copyediting, typesetting and review before it is published in its final form.. As such, this version is no longer the Accepted Manuscript, but it is not yet the definitive Version of Record; we are providing this early version to give early visibility of the article.
Article Title: Protocol for high-throughput, automated, solid-phase extraction of sphingolipids from human urine.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Acetonitrile (ACN, LC–MS grade) Fisher Chemical Cat# A955-4 Ammonium formate Sigma-Aldrich Cat# 70221 Formic acid (Optima LC–MS grade) Fisher Chemical Cat# A117-50 Isopropanol (IPA, LC–MS grade) Fisher Chemical Cat# A464-4 Methanol (MeOH, LC–MS grade) Fisher Chemical Cat# A456-4 Methyl tert-butyl ether (MTBE) Sigma-Aldrich Cat# 34875 PBS, pH 7.4 Thermo Fisher Cat# 10010023 1-Propanol (PrOH, LC–MS grade) Fisher Chemical Cat# A399-4 Sphingolipid internal standards Avanti Polar Lipids See recipe Water (H 2 O, LC-MS grade) Fisher Chemical Cat# W6-4 Critical commercial assays/Consumables Agilent Captiva EMR-Lipid 96-well plate Agilent Technologies Cat# 5191-4110 96-well deep-well plates (1 mL) Eppendorf or VWR e.g., VWR Cat# 82054-142 Captiva 96-deep well collection plate (1 mL) Agilent Cat# A696001000 Adhesive sealing foil Thermo Fisher Cat# AB0625 Positive-displacement pipette tips Gilson Depends on model Autosampler vials with inserts or polypropylene 96-well LC plate Agilent Cat# 5182-0554 and 5183-2086 or Cat# 5042-8502 Experimental models: Organisms/strains Human urine samples University of Utah IRB-approved protocol NCT03335865 Software and algorithms Agilent MassHunter Acquisition (for QQQ/QTOF) Agilent Technologies Version 10.1 Agilent MassHunter Quantitative Analysis Agilent Technologies Version B.07.00 Prism 10 Graphpad N/A Excel Microsoft N/A Other Tecan Resolvex A200 positive-pressure manifold Tecan N/A Agilent 6490 Triple Quadrupole LC–MS Agilent Technologies G6490A Agilent 1290 Bin Pump Agilent Technologies G4220A Agilent 1290 Sampler Agilent Technologies G4226A Agilent Column Compartment Agilent Technologies G1316A Waters Acquity UPLC CSH C18 column (2.1 3 100 mm, 1.7 μm) Waters Cat# 186005297 Nitrogen evaporator (e.g., Biotage, Organomation) Various N/A Sonicator VWR or Branson N/A Benchtop centrifuge Eppendorf N/A − 80 ◦ C freezer Thermo Fisher N/A 2 STAR Protocols 7, 104644, September 18, 2026 ..
Purification:Article Title: A New Renal Protective Strategy: Shenfu Decoction Targets Hypertensive Renal Disease through the AMPK/SIRT1/PGC-1α Pathway.
Article Snippet: This is a PDF of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability.. This version will undergo additional copyediting, typesetting and review before it is published in its final form.. As such, this version is no longer the Accepted Manuscript, but it is not yet the definitive Version of Record; we are providing this early version to give early visibility of the article.
Recombinant:Article Title: Protocol for high-throughput, automated, solid-phase extraction of sphingolipids from human urine.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Acetonitrile (ACN, LC–MS grade) Fisher Chemical Cat# A955-4 Ammonium formate Sigma-Aldrich Cat# 70221 Formic acid (Optima LC–MS grade) Fisher Chemical Cat# A117-50 Isopropanol (IPA, LC–MS grade) Fisher Chemical Cat# A464-4 Methanol (MeOH, LC–MS grade) Fisher Chemical Cat# A456-4 Methyl tert-butyl ether (MTBE) Sigma-Aldrich Cat# 34875 PBS, pH 7.4 Thermo Fisher Cat# 10010023 1-Propanol (PrOH, LC–MS grade) Fisher Chemical Cat# A399-4 Sphingolipid internal standards Avanti Polar Lipids See recipe Water (H 2 O, LC-MS grade) Fisher Chemical Cat# W6-4 Critical commercial assays/Consumables Agilent Captiva EMR-Lipid 96-well plate Agilent Technologies Cat# 5191-4110 96-well deep-well plates (1 mL) Eppendorf or VWR e.g., VWR Cat# 82054-142 Captiva 96-deep well collection plate (1 mL) Agilent Cat# A696001000 Adhesive sealing foil Thermo Fisher Cat# AB0625 Positive-displacement pipette tips Gilson Depends on model Autosampler vials with inserts or polypropylene 96-well LC plate Agilent Cat# 5182-0554 and 5183-2086 or Cat# 5042-8502 Experimental models: Organisms/strains Human urine samples University of Utah IRB-approved protocol NCT03335865 Software and algorithms Agilent MassHunter Acquisition (for QQQ/QTOF) Agilent Technologies Version 10.1 Agilent MassHunter Quantitative Analysis Agilent Technologies Version B.07.00 Prism 10 Graphpad N/A Excel Microsoft N/A Other Tecan Resolvex A200 positive-pressure manifold Tecan N/A Agilent 6490 Triple Quadrupole LC–MS Agilent Technologies G6490A Agilent 1290 Bin Pump Agilent Technologies G4220A Agilent 1290 Sampler Agilent Technologies G4226A Agilent Column Compartment Agilent Technologies G1316A Waters Acquity UPLC CSH C18 column (2.1 3 100 mm, 1.7 μm) Waters Cat# 186005297 Nitrogen evaporator (e.g., Biotage, Organomation) Various N/A Sonicator VWR or Branson N/A Benchtop centrifuge Eppendorf N/A − 80 ◦ C freezer Thermo Fisher N/A 2 STAR Protocols 7, 104644, September 18, 2026 ..
Article Title: A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Mouse - Brain Caltech, Pasadena N/A Mouse - Liver Caltech, Pasadena N/A Mouse - Serum Caltech, Pasadena N/A Mouse - Cecal content Caltech, Pasadena N/A Mouse - Feces Caltech, Pasadena N/A Human - Serum/Plasma Alzheimer Gut Microbiome Project N/A Chemicals, peptides, and recombinant proteins Water, OptimaTM LC/MS Grade Fisher Chemical W6-4 Methanol, OptimaTM LC/MS Grade Fisher Chemical A456-500 L-Carnitine hydrochloride MilliporeSigma 6645-46-1 Phenylpropionyl chloride MilliporeSigma 645-45-4 Phenylacetyl chloride MilliporeSigma 103-80-0 Benzoyl chloride MilliporeSigma 98-88-4 Pyridine MilliporeSigma 110-86-1 Critical commercial assays Phree Phospholipid Removal Phenomenex 8E-S133-TGB MagMAX Microbiome Ultra Total Nucleic Acid Isolation Kit Thermo Fisher Scientific Cat#A42357 Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Scientific Cat#P11496 KAPA HyperPlus Roche Cat#KK8514 NovaSeq 6000 S4 flowcell v1.5 (300-cycle) Illumina Cat#20028312 Deposited data LC-MS/MS - Mouse Brain This paper MassIVE: MSV000096035 LC-MS/MS - Mouse Liver This paper MassIVE: MSV000096037 LC-MS/MS - Mouse Serum This paper MassIVE: MSV000096036 LC-MS/MS - Mouse Cecal Content This paper MassIVE: MSV000096038 LC-MS/MS - GF Mouse Feces This paper MassIVE: MSV000096039 LC-MS/MS - 3xTg Mouse Feces This paper MassIVE: MSV000093230 LC-MS/MS - 5xFAD Mouse Feces This paper MassIVE: MSV000093168 Metagenomics - 3xTg Mouse Feces This paper ENA: ERP165389 Metagenomics - 5xFAD Mouse Feces This paper ENA; ERP165388 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax The Jackson Laboratory Cat#004807 Mouse: B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax The Jackson Laboratory Cat#034848 Software and algorithms R version 4.5.2 The R Foundation https://www.r-project.org/ MZmine version 3.9 mzio https://mzio.io/mzmine-news/ GNPS2 GNPS2 https://gnps2.org/homepage PanReDU El Abiead et al.59 https://redu.gnps2.org/selection/ (Continued on next page) 18 Cell Reports 45, 117499, June 23, 2026 .. As previously described,55 8-weeks-old wild-type C57BL/6J mice (The Jackson Laboratory, Cat#000664), homozygous 3xTg22 [B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax] (The Jackson Laboratory, Cat#004807) and hemizygous 5xFAD23 [B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax] (The Jackson Laboratory, Cat#034848) mice were obtained from the Jackson Laboratory and maintained in the laboratory of S.K.M at the California Institute of Technology (Caltech).
Indirect Immunoperoxidase Assay:Article Title: Protocol for high-throughput, automated, solid-phase extraction of sphingolipids from human urine.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Acetonitrile (ACN, LC–MS grade) Fisher Chemical Cat# A955-4 Ammonium formate Sigma-Aldrich Cat# 70221 Formic acid (Optima LC–MS grade) Fisher Chemical Cat# A117-50 Isopropanol (IPA, LC–MS grade) Fisher Chemical Cat# A464-4 Methanol (MeOH, LC–MS grade) Fisher Chemical Cat# A456-4 Methyl tert-butyl ether (MTBE) Sigma-Aldrich Cat# 34875 PBS, pH 7.4 Thermo Fisher Cat# 10010023 1-Propanol (PrOH, LC–MS grade) Fisher Chemical Cat# A399-4 Sphingolipid internal standards Avanti Polar Lipids See recipe Water (H 2 O, LC-MS grade) Fisher Chemical Cat# W6-4 Critical commercial assays/Consumables Agilent Captiva EMR-Lipid 96-well plate Agilent Technologies Cat# 5191-4110 96-well deep-well plates (1 mL) Eppendorf or VWR e.g., VWR Cat# 82054-142 Captiva 96-deep well collection plate (1 mL) Agilent Cat# A696001000 Adhesive sealing foil Thermo Fisher Cat# AB0625 Positive-displacement pipette tips Gilson Depends on model Autosampler vials with inserts or polypropylene 96-well LC plate Agilent Cat# 5182-0554 and 5183-2086 or Cat# 5042-8502 Experimental models: Organisms/strains Human urine samples University of Utah IRB-approved protocol NCT03335865 Software and algorithms Agilent MassHunter Acquisition (for QQQ/QTOF) Agilent Technologies Version 10.1 Agilent MassHunter Quantitative Analysis Agilent Technologies Version B.07.00 Prism 10 Graphpad N/A Excel Microsoft N/A Other Tecan Resolvex A200 positive-pressure manifold Tecan N/A Agilent 6490 Triple Quadrupole LC–MS Agilent Technologies G6490A Agilent 1290 Bin Pump Agilent Technologies G4220A Agilent 1290 Sampler Agilent Technologies G4226A Agilent Column Compartment Agilent Technologies G1316A Waters Acquity UPLC CSH C18 column (2.1 3 100 mm, 1.7 μm) Waters Cat# 186005297 Nitrogen evaporator (e.g., Biotage, Organomation) Various N/A Sonicator VWR or Branson N/A Benchtop centrifuge Eppendorf N/A − 80 ◦ C freezer Thermo Fisher N/A 2 STAR Protocols 7, 104644, September 18, 2026 ..
Adhesive:Article Title: Protocol for high-throughput, automated, solid-phase extraction of sphingolipids from human urine.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Acetonitrile (ACN, LC–MS grade) Fisher Chemical Cat# A955-4 Ammonium formate Sigma-Aldrich Cat# 70221 Formic acid (Optima LC–MS grade) Fisher Chemical Cat# A117-50 Isopropanol (IPA, LC–MS grade) Fisher Chemical Cat# A464-4 Methanol (MeOH, LC–MS grade) Fisher Chemical Cat# A456-4 Methyl tert-butyl ether (MTBE) Sigma-Aldrich Cat# 34875 PBS, pH 7.4 Thermo Fisher Cat# 10010023 1-Propanol (PrOH, LC–MS grade) Fisher Chemical Cat# A399-4 Sphingolipid internal standards Avanti Polar Lipids See recipe Water (H 2 O, LC-MS grade) Fisher Chemical Cat# W6-4 Critical commercial assays/Consumables Agilent Captiva EMR-Lipid 96-well plate Agilent Technologies Cat# 5191-4110 96-well deep-well plates (1 mL) Eppendorf or VWR e.g., VWR Cat# 82054-142 Captiva 96-deep well collection plate (1 mL) Agilent Cat# A696001000 Adhesive sealing foil Thermo Fisher Cat# AB0625 Positive-displacement pipette tips Gilson Depends on model Autosampler vials with inserts or polypropylene 96-well LC plate Agilent Cat# 5182-0554 and 5183-2086 or Cat# 5042-8502 Experimental models: Organisms/strains Human urine samples University of Utah IRB-approved protocol NCT03335865 Software and algorithms Agilent MassHunter Acquisition (for QQQ/QTOF) Agilent Technologies Version 10.1 Agilent MassHunter Quantitative Analysis Agilent Technologies Version B.07.00 Prism 10 Graphpad N/A Excel Microsoft N/A Other Tecan Resolvex A200 positive-pressure manifold Tecan N/A Agilent 6490 Triple Quadrupole LC–MS Agilent Technologies G6490A Agilent 1290 Bin Pump Agilent Technologies G4220A Agilent 1290 Sampler Agilent Technologies G4226A Agilent Column Compartment Agilent Technologies G1316A Waters Acquity UPLC CSH C18 column (2.1 3 100 mm, 1.7 μm) Waters Cat# 186005297 Nitrogen evaporator (e.g., Biotage, Organomation) Various N/A Sonicator VWR or Branson N/A Benchtop centrifuge Eppendorf N/A − 80 ◦ C freezer Thermo Fisher N/A 2 STAR Protocols 7, 104644, September 18, 2026 ..
Transferring:Article Title: Protocol for high-throughput, automated, solid-phase extraction of sphingolipids from human urine.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Acetonitrile (ACN, LC–MS grade) Fisher Chemical Cat# A955-4 Ammonium formate Sigma-Aldrich Cat# 70221 Formic acid (Optima LC–MS grade) Fisher Chemical Cat# A117-50 Isopropanol (IPA, LC–MS grade) Fisher Chemical Cat# A464-4 Methanol (MeOH, LC–MS grade) Fisher Chemical Cat# A456-4 Methyl tert-butyl ether (MTBE) Sigma-Aldrich Cat# 34875 PBS, pH 7.4 Thermo Fisher Cat# 10010023 1-Propanol (PrOH, LC–MS grade) Fisher Chemical Cat# A399-4 Sphingolipid internal standards Avanti Polar Lipids See recipe Water (H 2 O, LC-MS grade) Fisher Chemical Cat# W6-4 Critical commercial assays/Consumables Agilent Captiva EMR-Lipid 96-well plate Agilent Technologies Cat# 5191-4110 96-well deep-well plates (1 mL) Eppendorf or VWR e.g., VWR Cat# 82054-142 Captiva 96-deep well collection plate (1 mL) Agilent Cat# A696001000 Adhesive sealing foil Thermo Fisher Cat# AB0625 Positive-displacement pipette tips Gilson Depends on model Autosampler vials with inserts or polypropylene 96-well LC plate Agilent Cat# 5182-0554 and 5183-2086 or Cat# 5042-8502 Experimental models: Organisms/strains Human urine samples University of Utah IRB-approved protocol NCT03335865 Software and algorithms Agilent MassHunter Acquisition (for QQQ/QTOF) Agilent Technologies Version 10.1 Agilent MassHunter Quantitative Analysis Agilent Technologies Version B.07.00 Prism 10 Graphpad N/A Excel Microsoft N/A Other Tecan Resolvex A200 positive-pressure manifold Tecan N/A Agilent 6490 Triple Quadrupole LC–MS Agilent Technologies G6490A Agilent 1290 Bin Pump Agilent Technologies G4220A Agilent 1290 Sampler Agilent Technologies G4226A Agilent Column Compartment Agilent Technologies G1316A Waters Acquity UPLC CSH C18 column (2.1 3 100 mm, 1.7 μm) Waters Cat# 186005297 Nitrogen evaporator (e.g., Biotage, Organomation) Various N/A Sonicator VWR or Branson N/A Benchtop centrifuge Eppendorf N/A − 80 ◦ C freezer Thermo Fisher N/A 2 STAR Protocols 7, 104644, September 18, 2026 ..
Software:Article Title: Protocol for high-throughput, automated, solid-phase extraction of sphingolipids from human urine.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Acetonitrile (ACN, LC–MS grade) Fisher Chemical Cat# A955-4 Ammonium formate Sigma-Aldrich Cat# 70221 Formic acid (Optima LC–MS grade) Fisher Chemical Cat# A117-50 Isopropanol (IPA, LC–MS grade) Fisher Chemical Cat# A464-4 Methanol (MeOH, LC–MS grade) Fisher Chemical Cat# A456-4 Methyl tert-butyl ether (MTBE) Sigma-Aldrich Cat# 34875 PBS, pH 7.4 Thermo Fisher Cat# 10010023 1-Propanol (PrOH, LC–MS grade) Fisher Chemical Cat# A399-4 Sphingolipid internal standards Avanti Polar Lipids See recipe Water (H 2 O, LC-MS grade) Fisher Chemical Cat# W6-4 Critical commercial assays/Consumables Agilent Captiva EMR-Lipid 96-well plate Agilent Technologies Cat# 5191-4110 96-well deep-well plates (1 mL) Eppendorf or VWR e.g., VWR Cat# 82054-142 Captiva 96-deep well collection plate (1 mL) Agilent Cat# A696001000 Adhesive sealing foil Thermo Fisher Cat# AB0625 Positive-displacement pipette tips Gilson Depends on model Autosampler vials with inserts or polypropylene 96-well LC plate Agilent Cat# 5182-0554 and 5183-2086 or Cat# 5042-8502 Experimental models: Organisms/strains Human urine samples University of Utah IRB-approved protocol NCT03335865 Software and algorithms Agilent MassHunter Acquisition (for QQQ/QTOF) Agilent Technologies Version 10.1 Agilent MassHunter Quantitative Analysis Agilent Technologies Version B.07.00 Prism 10 Graphpad N/A Excel Microsoft N/A Other Tecan Resolvex A200 positive-pressure manifold Tecan N/A Agilent 6490 Triple Quadrupole LC–MS Agilent Technologies G6490A Agilent 1290 Bin Pump Agilent Technologies G4220A Agilent 1290 Sampler Agilent Technologies G4226A Agilent Column Compartment Agilent Technologies G1316A Waters Acquity UPLC CSH C18 column (2.1 3 100 mm, 1.7 μm) Waters Cat# 186005297 Nitrogen evaporator (e.g., Biotage, Organomation) Various N/A Sonicator VWR or Branson N/A Benchtop centrifuge Eppendorf N/A − 80 ◦ C freezer Thermo Fisher N/A 2 STAR Protocols 7, 104644, September 18, 2026 ..
Article Title: A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Mouse - Brain Caltech, Pasadena N/A Mouse - Liver Caltech, Pasadena N/A Mouse - Serum Caltech, Pasadena N/A Mouse - Cecal content Caltech, Pasadena N/A Mouse - Feces Caltech, Pasadena N/A Human - Serum/Plasma Alzheimer Gut Microbiome Project N/A Chemicals, peptides, and recombinant proteins Water, OptimaTM LC/MS Grade Fisher Chemical W6-4 Methanol, OptimaTM LC/MS Grade Fisher Chemical A456-500 L-Carnitine hydrochloride MilliporeSigma 6645-46-1 Phenylpropionyl chloride MilliporeSigma 645-45-4 Phenylacetyl chloride MilliporeSigma 103-80-0 Benzoyl chloride MilliporeSigma 98-88-4 Pyridine MilliporeSigma 110-86-1 Critical commercial assays Phree Phospholipid Removal Phenomenex 8E-S133-TGB MagMAX Microbiome Ultra Total Nucleic Acid Isolation Kit Thermo Fisher Scientific Cat#A42357 Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Scientific Cat#P11496 KAPA HyperPlus Roche Cat#KK8514 NovaSeq 6000 S4 flowcell v1.5 (300-cycle) Illumina Cat#20028312 Deposited data LC-MS/MS - Mouse Brain This paper MassIVE: MSV000096035 LC-MS/MS - Mouse Liver This paper MassIVE: MSV000096037 LC-MS/MS - Mouse Serum This paper MassIVE: MSV000096036 LC-MS/MS - Mouse Cecal Content This paper MassIVE: MSV000096038 LC-MS/MS - GF Mouse Feces This paper MassIVE: MSV000096039 LC-MS/MS - 3xTg Mouse Feces This paper MassIVE: MSV000093230 LC-MS/MS - 5xFAD Mouse Feces This paper MassIVE: MSV000093168 Metagenomics - 3xTg Mouse Feces This paper ENA: ERP165389 Metagenomics - 5xFAD Mouse Feces This paper ENA; ERP165388 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax The Jackson Laboratory Cat#004807 Mouse: B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax The Jackson Laboratory Cat#034848 Software and algorithms R version 4.5.2 The R Foundation https://www.r-project.org/ MZmine version 3.9 mzio https://mzio.io/mzmine-news/ GNPS2 GNPS2 https://gnps2.org/homepage PanReDU El Abiead et al.59 https://redu.gnps2.org/selection/ (Continued on next page) 18 Cell Reports 45, 117499, June 23, 2026 .. As previously described,55 8-weeks-old wild-type C57BL/6J mice (The Jackson Laboratory, Cat#000664), homozygous 3xTg22 [B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax] (The Jackson Laboratory, Cat#004807) and hemizygous 5xFAD23 [B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax] (The Jackson Laboratory, Cat#034848) mice were obtained from the Jackson Laboratory and maintained in the laboratory of S.K.M at the California Institute of Technology (Caltech).
Targeted Proteomics:Article Title: Protocol for high-throughput, automated, solid-phase extraction of sphingolipids from human urine.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Acetonitrile (ACN, LC–MS grade) Fisher Chemical Cat# A955-4 Ammonium formate Sigma-Aldrich Cat# 70221 Formic acid (Optima LC–MS grade) Fisher Chemical Cat# A117-50 Isopropanol (IPA, LC–MS grade) Fisher Chemical Cat# A464-4 Methanol (MeOH, LC–MS grade) Fisher Chemical Cat# A456-4 Methyl tert-butyl ether (MTBE) Sigma-Aldrich Cat# 34875 PBS, pH 7.4 Thermo Fisher Cat# 10010023 1-Propanol (PrOH, LC–MS grade) Fisher Chemical Cat# A399-4 Sphingolipid internal standards Avanti Polar Lipids See recipe Water (H 2 O, LC-MS grade) Fisher Chemical Cat# W6-4 Critical commercial assays/Consumables Agilent Captiva EMR-Lipid 96-well plate Agilent Technologies Cat# 5191-4110 96-well deep-well plates (1 mL) Eppendorf or VWR e.g., VWR Cat# 82054-142 Captiva 96-deep well collection plate (1 mL) Agilent Cat# A696001000 Adhesive sealing foil Thermo Fisher Cat# AB0625 Positive-displacement pipette tips Gilson Depends on model Autosampler vials with inserts or polypropylene 96-well LC plate Agilent Cat# 5182-0554 and 5183-2086 or Cat# 5042-8502 Experimental models: Organisms/strains Human urine samples University of Utah IRB-approved protocol NCT03335865 Software and algorithms Agilent MassHunter Acquisition (for QQQ/QTOF) Agilent Technologies Version 10.1 Agilent MassHunter Quantitative Analysis Agilent Technologies Version B.07.00 Prism 10 Graphpad N/A Excel Microsoft N/A Other Tecan Resolvex A200 positive-pressure manifold Tecan N/A Agilent 6490 Triple Quadrupole LC–MS Agilent Technologies G6490A Agilent 1290 Bin Pump Agilent Technologies G4220A Agilent 1290 Sampler Agilent Technologies G4226A Agilent Column Compartment Agilent Technologies G1316A Waters Acquity UPLC CSH C18 column (2.1 3 100 mm, 1.7 μm) Waters Cat# 186005297 Nitrogen evaporator (e.g., Biotage, Organomation) Various N/A Sonicator VWR or Branson N/A Benchtop centrifuge Eppendorf N/A − 80 ◦ C freezer Thermo Fisher N/A 2 STAR Protocols 7, 104644, September 18, 2026 ..
Cell Surface Hydrophobicity:Article Title: Protocol for high-throughput, automated, solid-phase extraction of sphingolipids from human urine.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Acetonitrile (ACN, LC–MS grade) Fisher Chemical Cat# A955-4 Ammonium formate Sigma-Aldrich Cat# 70221 Formic acid (Optima LC–MS grade) Fisher Chemical Cat# A117-50 Isopropanol (IPA, LC–MS grade) Fisher Chemical Cat# A464-4 Methanol (MeOH, LC–MS grade) Fisher Chemical Cat# A456-4 Methyl tert-butyl ether (MTBE) Sigma-Aldrich Cat# 34875 PBS, pH 7.4 Thermo Fisher Cat# 10010023 1-Propanol (PrOH, LC–MS grade) Fisher Chemical Cat# A399-4 Sphingolipid internal standards Avanti Polar Lipids See recipe Water (H 2 O, LC-MS grade) Fisher Chemical Cat# W6-4 Critical commercial assays/Consumables Agilent Captiva EMR-Lipid 96-well plate Agilent Technologies Cat# 5191-4110 96-well deep-well plates (1 mL) Eppendorf or VWR e.g., VWR Cat# 82054-142 Captiva 96-deep well collection plate (1 mL) Agilent Cat# A696001000 Adhesive sealing foil Thermo Fisher Cat# AB0625 Positive-displacement pipette tips Gilson Depends on model Autosampler vials with inserts or polypropylene 96-well LC plate Agilent Cat# 5182-0554 and 5183-2086 or Cat# 5042-8502 Experimental models: Organisms/strains Human urine samples University of Utah IRB-approved protocol NCT03335865 Software and algorithms Agilent MassHunter Acquisition (for QQQ/QTOF) Agilent Technologies Version 10.1 Agilent MassHunter Quantitative Analysis Agilent Technologies Version B.07.00 Prism 10 Graphpad N/A Excel Microsoft N/A Other Tecan Resolvex A200 positive-pressure manifold Tecan N/A Agilent 6490 Triple Quadrupole LC–MS Agilent Technologies G6490A Agilent 1290 Bin Pump Agilent Technologies G4220A Agilent 1290 Sampler Agilent Technologies G4226A Agilent Column Compartment Agilent Technologies G1316A Waters Acquity UPLC CSH C18 column (2.1 3 100 mm, 1.7 μm) Waters Cat# 186005297 Nitrogen evaporator (e.g., Biotage, Organomation) Various N/A Sonicator VWR or Branson N/A Benchtop centrifuge Eppendorf N/A − 80 ◦ C freezer Thermo Fisher N/A 2 STAR Protocols 7, 104644, September 18, 2026 ..
Isolation:Article Title: A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Mouse - Brain Caltech, Pasadena N/A Mouse - Liver Caltech, Pasadena N/A Mouse - Serum Caltech, Pasadena N/A Mouse - Cecal content Caltech, Pasadena N/A Mouse - Feces Caltech, Pasadena N/A Human - Serum/Plasma Alzheimer Gut Microbiome Project N/A Chemicals, peptides, and recombinant proteins Water, OptimaTM LC/MS Grade Fisher Chemical W6-4 Methanol, OptimaTM LC/MS Grade Fisher Chemical A456-500 L-Carnitine hydrochloride MilliporeSigma 6645-46-1 Phenylpropionyl chloride MilliporeSigma 645-45-4 Phenylacetyl chloride MilliporeSigma 103-80-0 Benzoyl chloride MilliporeSigma 98-88-4 Pyridine MilliporeSigma 110-86-1 Critical commercial assays Phree Phospholipid Removal Phenomenex 8E-S133-TGB MagMAX Microbiome Ultra Total Nucleic Acid Isolation Kit Thermo Fisher Scientific Cat#A42357 Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Scientific Cat#P11496 KAPA HyperPlus Roche Cat#KK8514 NovaSeq 6000 S4 flowcell v1.5 (300-cycle) Illumina Cat#20028312 Deposited data LC-MS/MS - Mouse Brain This paper MassIVE: MSV000096035 LC-MS/MS - Mouse Liver This paper MassIVE: MSV000096037 LC-MS/MS - Mouse Serum This paper MassIVE: MSV000096036 LC-MS/MS - Mouse Cecal Content This paper MassIVE: MSV000096038 LC-MS/MS - GF Mouse Feces This paper MassIVE: MSV000096039 LC-MS/MS - 3xTg Mouse Feces This paper MassIVE: MSV000093230 LC-MS/MS - 5xFAD Mouse Feces This paper MassIVE: MSV000093168 Metagenomics - 3xTg Mouse Feces This paper ENA: ERP165389 Metagenomics - 5xFAD Mouse Feces This paper ENA; ERP165388 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax The Jackson Laboratory Cat#004807 Mouse: B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax The Jackson Laboratory Cat#034848 Software and algorithms R version 4.5.2 The R Foundation https://www.r-project.org/ MZmine version 3.9 mzio https://mzio.io/mzmine-news/ GNPS2 GNPS2 https://gnps2.org/homepage PanReDU El Abiead et al.59 https://redu.gnps2.org/selection/ (Continued on next page) 18 Cell Reports 45, 117499, June 23, 2026 .. As previously described,55 8-weeks-old wild-type C57BL/6J mice (The Jackson Laboratory, Cat#000664), homozygous 3xTg22 [B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax] (The Jackson Laboratory, Cat#004807) and hemizygous 5xFAD23 [B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax] (The Jackson Laboratory, Cat#034848) mice were obtained from the Jackson Laboratory and maintained in the laboratory of S.K.M at the California Institute of Technology (Caltech).
Picogreen Assay:Article Title: A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Mouse - Brain Caltech, Pasadena N/A Mouse - Liver Caltech, Pasadena N/A Mouse - Serum Caltech, Pasadena N/A Mouse - Cecal content Caltech, Pasadena N/A Mouse - Feces Caltech, Pasadena N/A Human - Serum/Plasma Alzheimer Gut Microbiome Project N/A Chemicals, peptides, and recombinant proteins Water, OptimaTM LC/MS Grade Fisher Chemical W6-4 Methanol, OptimaTM LC/MS Grade Fisher Chemical A456-500 L-Carnitine hydrochloride MilliporeSigma 6645-46-1 Phenylpropionyl chloride MilliporeSigma 645-45-4 Phenylacetyl chloride MilliporeSigma 103-80-0 Benzoyl chloride MilliporeSigma 98-88-4 Pyridine MilliporeSigma 110-86-1 Critical commercial assays Phree Phospholipid Removal Phenomenex 8E-S133-TGB MagMAX Microbiome Ultra Total Nucleic Acid Isolation Kit Thermo Fisher Scientific Cat#A42357 Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Scientific Cat#P11496 KAPA HyperPlus Roche Cat#KK8514 NovaSeq 6000 S4 flowcell v1.5 (300-cycle) Illumina Cat#20028312 Deposited data LC-MS/MS - Mouse Brain This paper MassIVE: MSV000096035 LC-MS/MS - Mouse Liver This paper MassIVE: MSV000096037 LC-MS/MS - Mouse Serum This paper MassIVE: MSV000096036 LC-MS/MS - Mouse Cecal Content This paper MassIVE: MSV000096038 LC-MS/MS - GF Mouse Feces This paper MassIVE: MSV000096039 LC-MS/MS - 3xTg Mouse Feces This paper MassIVE: MSV000093230 LC-MS/MS - 5xFAD Mouse Feces This paper MassIVE: MSV000093168 Metagenomics - 3xTg Mouse Feces This paper ENA: ERP165389 Metagenomics - 5xFAD Mouse Feces This paper ENA; ERP165388 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax The Jackson Laboratory Cat#004807 Mouse: B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax The Jackson Laboratory Cat#034848 Software and algorithms R version 4.5.2 The R Foundation https://www.r-project.org/ MZmine version 3.9 mzio https://mzio.io/mzmine-news/ GNPS2 GNPS2 https://gnps2.org/homepage PanReDU El Abiead et al.59 https://redu.gnps2.org/selection/ (Continued on next page) 18 Cell Reports 45, 117499, June 23, 2026 .. As previously described,55 8-weeks-old wild-type C57BL/6J mice (The Jackson Laboratory, Cat#000664), homozygous 3xTg22 [B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax] (The Jackson Laboratory, Cat#004807) and hemizygous 5xFAD23 [B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax] (The Jackson Laboratory, Cat#034848) mice were obtained from the Jackson Laboratory and maintained in the laboratory of S.K.M at the California Institute of Technology (Caltech).
Metagenomics:Article Title: A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Mouse - Brain Caltech, Pasadena N/A Mouse - Liver Caltech, Pasadena N/A Mouse - Serum Caltech, Pasadena N/A Mouse - Cecal content Caltech, Pasadena N/A Mouse - Feces Caltech, Pasadena N/A Human - Serum/Plasma Alzheimer Gut Microbiome Project N/A Chemicals, peptides, and recombinant proteins Water, OptimaTM LC/MS Grade Fisher Chemical W6-4 Methanol, OptimaTM LC/MS Grade Fisher Chemical A456-500 L-Carnitine hydrochloride MilliporeSigma 6645-46-1 Phenylpropionyl chloride MilliporeSigma 645-45-4 Phenylacetyl chloride MilliporeSigma 103-80-0 Benzoyl chloride MilliporeSigma 98-88-4 Pyridine MilliporeSigma 110-86-1 Critical commercial assays Phree Phospholipid Removal Phenomenex 8E-S133-TGB MagMAX Microbiome Ultra Total Nucleic Acid Isolation Kit Thermo Fisher Scientific Cat#A42357 Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Scientific Cat#P11496 KAPA HyperPlus Roche Cat#KK8514 NovaSeq 6000 S4 flowcell v1.5 (300-cycle) Illumina Cat#20028312 Deposited data LC-MS/MS - Mouse Brain This paper MassIVE: MSV000096035 LC-MS/MS - Mouse Liver This paper MassIVE: MSV000096037 LC-MS/MS - Mouse Serum This paper MassIVE: MSV000096036 LC-MS/MS - Mouse Cecal Content This paper MassIVE: MSV000096038 LC-MS/MS - GF Mouse Feces This paper MassIVE: MSV000096039 LC-MS/MS - 3xTg Mouse Feces This paper MassIVE: MSV000093230 LC-MS/MS - 5xFAD Mouse Feces This paper MassIVE: MSV000093168 Metagenomics - 3xTg Mouse Feces This paper ENA: ERP165389 Metagenomics - 5xFAD Mouse Feces This paper ENA; ERP165388 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax The Jackson Laboratory Cat#004807 Mouse: B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax The Jackson Laboratory Cat#034848 Software and algorithms R version 4.5.2 The R Foundation https://www.r-project.org/ MZmine version 3.9 mzio https://mzio.io/mzmine-news/ GNPS2 GNPS2 https://gnps2.org/homepage PanReDU El Abiead et al.59 https://redu.gnps2.org/selection/ (Continued on next page) 18 Cell Reports 45, 117499, June 23, 2026 .. As previously described,55 8-weeks-old wild-type C57BL/6J mice (The Jackson Laboratory, Cat#000664), homozygous 3xTg22 [B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax] (The Jackson Laboratory, Cat#004807) and hemizygous 5xFAD23 [B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax] (The Jackson Laboratory, Cat#034848) mice were obtained from the Jackson Laboratory and maintained in the laboratory of S.K.M at the California Institute of Technology (Caltech).
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![Reaction schemes <t>and</t> <t>LC-MS</t> analysis of Pp UGTs reactions with diosgenin and pennogenin . ( a ) Biosynthesis of trillin mediated by UGT91BP2 and UGT703R1–3 through transferring glucose from UDP-glucose to the C-3 OH position of diosgenin. ( b ) Extracted ion chromatograms (EICs) of the in vitro enzyme activity assays of recombinant UGT91BP2 and UGT703R1–3 with UDP-glucose and diosgenin showing the formation of trillin, as compared to the authentic trillin standard. Control is the empty expression vector. ( c ) MS spectra of the enzymatic reaction products in hydrogen and sodium ion adducts compared to the fragmentation pattern of the trillin standard. The product molecular ions [M + H] + and [M +Na] + and the feature fragment ion [M + H − Glc] + with m / z 415.32 are marked. Of note, additional peaks observed in the diosgenin EIC ( m / z 415.32) for UGT703R1–3 might correspond to substrate isomeric impurities, in-source adducts, or minor non-enzymatic by-products; these peaks, which arose from the extracted ion flow of the substrate m / z , did not co-elute with the product, trillin , and therefore did not affect the interpretation of the product formation. ( d ) Biosynthesis of pennogenin 3- O -glucoside mediated by the UGT703R1–3 through transferring glucose from UDP-glucose to the C-3 OH position of pennogenin. ( e ) EICs of the in vitro enzyme activity assays of recombinant UGT91BP2 and UGT703R1–3 with UDP-glucose and pennogenin showing the formation of pennogenin 3- O -glucoside, compared to the control empty expression vector. ( f ) MS/MS spectra ([M + H – Glc] + and [M + H – Glc − H 2 O] + ) of the enzymatic reaction products.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_3502/pmc13123502/pmc13123502__gr2.jpg)