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tandem mass tag (tmt) 16plex isobaric label reagents  (Thermo Fisher)


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    Thermo Fisher tandem mass tag (tmt) 16plex isobaric label reagents
    Tandem Mass Tag (Tmt) 16plex Isobaric Label Reagents, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/tandem+mass+tag+(tmt)+16plex+reagents/bio_rxiv__2024__11__20__624444-226-7-15
    Average 90 stars, based on 1 article reviews
    tandem mass tag (tmt) 16plex isobaric label reagents - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Polymerase Chain Reaction:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    SYBR Green Assay:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Thin Layer Chromatography:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Saline:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Purification:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Gel Extraction:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Plasmid Preparation:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Multiplex sample analysis:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Concentration Assay:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Recombinant:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Staining:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Lysis:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Flow Cytometry:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Imaging:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Fractionation:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Cell Culture:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Extraction:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Electrophoresis:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Software:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Labeling:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.

    Multiplex Assay:

    Article Title: Genome homeostasis defects drive enlarged cells into senescence
    Article Snippet: Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Cell Cycle Progression Defects and Impaired DNA Damage Signaling Drive Enlarged Cells into Senescence
    Article Snippet: 607 Tandem mass tag (TMT) isobaric reagents (TMTpro 16plex Thermo Fisher Scientific 44522) 608 were dissolved in anhydrous ACN to a final concentration of 20 mg/mL, of which a unique 609 TMT label was added at a 2:1 label:peptide ratio.

    Article Title: Optimizing PSC culture for generating neural organoids
    Article Snippet: Thereafter the peptide samples were labeled with Tandem Mass Tag (TMT) 16plex Isobaric label Reagents (Thermo Scientific) according to the manufacturer’s instructions.

    Article Title: A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER EDTA Sigma Aldrich Cat# E6758 Nitrilotriacetic acid Thermo Scientific Cat# AAA1193622 L-Glutathione Sigma Aldrich Cat# G4251 (NH4)2SO4 Thermo Scientific Cat# BP212R NaCl Thermo Scientific Cat# S271-1 Tyrosine Thermo Scientific Cat# AAA1114118 Biotin Thermo Scientific Cat# AC230090010 Thiamine Sigma Aldrich Cat# T4625 Riboflavin Sigma Aldrich Cat# R7649 NEBNext High-fidelity 2X PCR Master Mix New England Biolabs Cat# M0541 NEBuilder HiFiDNA assembly Master mix New England Biolabs Cat# E2621 BamHI New England Biolabs Cat# R3136 SalI New England Biolabs Cat# R0138 SacI New England Biolabs Cat# R3156 SYBR Green Master Mix Life Technologies Cat# A25778 SuperScript IV VILO Master Mix Life Technologies Cat# 11756500 TLC Silica gel 60 F254 Sigma Aldrich Cat# 1055540001 Butanol Sigma Aldrich Cat# 537993 Acetic acid Sigma Aldrich Cat# 695092 Diphenylamine Sigma Aldrich Cat# 112763 Aniline Sigma Aldrich Cat# 242284 Phosphoric acid VWR Cat# 2796 Hydrochloric acid Sigma Aldrich Cat# 258148 Deoxy-D-Glucose Sigma Aldrich Cat# D8375 D-Galactose Sigma Aldrich Cat# G0625 L-Fucose Sigma Aldrich Cat# F2252 D-lactose Sigma Aldrich Cat# L254 Sialic acid (Neu5AC) Biosynth Cat# MA00746 Dulbecco’s Phosphate Buffered Saline with calcium and magnesium (1X) Thermo Scientific Cat# MT21030CV BugBuster Millipore Cat# 705843 RNAlater stabilization solution Thermo Scientific Cat# am7021 Anthranilamide Thermo Scientific Cat# 104905000 Sodium cyanoborohydride Sigma Aldrich Cat# 156159 Acetic acid Sigma Aldrich Cat# A6283 Tandem Mass Tag (TMT) 10plex reagents Thermo Scientific Cat# 90110; lot# WH329135 Tandem Mass Tag (TMT) 16plex reagents Thermo Scientific Cat# A44520; lot# XA341491 C4 5 mm Stationary phase Sepax Cat# 109045-0000 C18 3 mm Stationary phase Sepax Cat# 101183-0000 C18 1.8 mm Stationary phase Sepax Cat# 101181-0000 Critical commercial assays QIAquick PCR purification kit Qiagen Cat# 28106 QIAquick Gel extraction kit Qiagen Cat# 28706 Nucleospin Plasmid kit Macherey Nagel Cat# 740588 Quick-DNA Fecal/Soil Microbe Miniprep kit Genesee Scientific Cat# 11-322 NucleoSpin Microbial DNA kit Macherey Nagel Cat# 740235 Nucleospin RNA kit Macherey Nagel Cat# 740955 ProtiFi S-Trap columns ProtiFi Cat# C02-mini SepPak C18 columns Waters Cat# WAT054960 Pierce Quantitative Colorimetric Peptide Assay Thermo Scientific Cat# 23275 (Continued on next page) Cell Host & Microbe 32, 181–190.e1–e9, February 14, 2024 e3

    Article Title: A bacterial sialidase mediates early life colonization by a pioneering gut commensal
    Article Snippet: Samples were labeled using Tandem Mass Tag (TMT) 16plex reagents (Thermo Scientific, A44520; lot number XA341491) following manufacturer protocol, then combined into a single multiplex.



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    Tandem Mass Tags (Tmt) 16plex Reagent, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    tandem mass tag (tmt) 16plex label reagent set  (Thermo Fisher)
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    Thermo Fisher tandem mass tag (tmt) 16plex label reagent set
    Tandem Mass Tag (Tmt) 16plex Label Reagent Set, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/tandem+mass+tag+(tmt)+16plex+reagents/tmt+reagent/pm37670295-95-0-24
    Average 90 stars, based on 1 article reviews
    tandem mass tag (tmt) 16plex label reagent set - by Bioz Stars, 2026-10
    90/100 stars
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    tandem mass tag (tmt) 16plex reagents  (Thermo Fisher)
    90
    Thermo Fisher tandem mass tag (tmt) 16plex reagents
    Tandem Mass Tag (Tmt) 16plex Reagents, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/tandem+mass+tag+(tmt)+16plex+reagents/bio_rxiv__2023__08__08__552477-203-4-10
    Average 90 stars, based on 1 article reviews
    tandem mass tag (tmt) 16plex reagents - by Bioz Stars, 2026-10
    90/100 stars
    		  Buy from Supplier
    tandem mass tag (tmt) pro 16plex reagent set  (Thermo Fisher)
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    Thermo Fisher tandem mass tag (tmt) pro 16plex reagent set
    Tandem Mass Tag (Tmt) Pro 16plex Reagent Set, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/tandem+mass+tag+(tmt)+16plex+reagents/tmt+reagent/pmc08321680-208-7-15
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    tandem mass tag (tmt) pro 16plex reagent set - by Bioz Stars, 2026-10
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