REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Surgical tissue samples from 30 CD patients and 5 non-CD controls	Shanghai 10th People’s Hospital	This paper (Table S1)
Serum and fecal samples from 30 active CD patients and 30 healthy donors	Shanghai 10th People’s Hospital	This paper (Table S1)
Chemicals, peptides, and recombinant proteins
Triethylammonium bicarbonate buffer (TEAB)	Sigma-Aldrich	Cat #T7408
Urea	Sigma-Aldrich	Cat #U1250
Thiourea	Sigma-Aldrich	Cat #T8656
Tris (2-carboxyethyl) phosphine (TCEP)	Adamas-beta	Cat # 61820E
Iodoacetamide (IAA)	Sigma-Aldrich	Cat #I6125
Trypsin	Hualishi Tech	Cat # HLS TRY001C
Trifluoroacetic acid (TFA)	Thermo Fisher Scientific	Cat # 85183
Water	Thermo Fisher Scientific	Cat #W6-4
Acetonitrile	Thermo Fisher Scientific	Cat # A955-4
Formic acid (FA)	Thermo Fisher Scientific	Cat # A117-50
Ammonium hydroxide solution	Sigma-Aldrich	Cat # 221228
Methanol	Sigma-Aldrich	Cat # 3486
E.Z.N.A.® stool kit	Omega Bio-tek	Cat #D4015-02
TransStart FastPfu DNA Polymerase	TransGen	Cat # AP221-03
Miseq Reagent Kit V3	Illumina	Cat # MS-102-3003
Critical commercial assays
Ultracel-3 regenerated cellulose membrane	Millipore	Cat # UFC500324
XBridge Peptide BEH C18 column	Waters	Cat # 186003570
High SelectTM Top-14 Abundant Protein Depletion Mini Spin Columns	Thermo Fisher Scientific	Cat # A36370
96-well SOLAμ™ SPE plate	Thermo Fisher Scientific	Cat # 60209-001
μ-Precolumn™ Catridge	Thermo Fisher Scientific	Cat # DX163593
Pierce™ C18 Spin Column	Thermo Fisher Scientific	Cat # 89870
TMTpro 16plex reagents	Thermo Fisher Scientific	Cat # A44520
Emitter column, 15 cm × 75 μm	New Objective	N/A
C18 resin, 1.9 μm	Fresh Biosciences	N/A
Deposited data
Mass spectrometry data	This paper	https://www.iprox.org
16S amplicon sequencing (tissue)	NODE: OEP003464	https://www.biosino.org/node/
16S amplicon sequencing (feces)	NODE: OEP003463	https://www.biosino.org/node/
Software and algorithms
QIIME2 v2019.07	Bolyen et al., 2019a65	https://qiime2.org
PICRUSt v2.0	Douglas et al., 2020b66	https://github.com/picrust/picrust2
Sparcc	Friedman and Alm, 2012a67	https://bitbucket.org/yonatanf/sparcc
FEAST	Shenhav et al., 201968	https://github.com/cozygene/FEAST
R package ClusterProfile v4.0	Wu et al., 2021a69	https://bioconductor.org/packages/clusterProfiler/
R package decontam	Davis et al., 201870	https://github.com/benjjneb/decontam
R package phyloseq v1.22.3	McMurdie and Holmes, 201371	https://github.com/joey711/phyloseq
R package mfuzz v2.50.0	Futschik and Carlisle, 200572	http://mfuzz.sysbiolab.eu
R package vegan v2.5-7	Dixon, 200373	https://github.com/vegandevs/vegan
Proteome Discoverer (Version 2.4.0.305)	Thermo Fisher Scientific	N/A
Spectronaut (Version 14.6.201001.47784)	Biognosys	N/A
R v4.0.2	R project	https://www.r-project.org/
String	Szklarczyk et al., 202174	https://string-db.org/
Cytoscape (version 3.6.1)	Shannon et al., 200375	NA
Ingenuine pathway analysis (version 51963813)	Kramer et al., 201476	https://www.qiagen.com/cn/
R v3.6.3	R project	https://www.r-project.org/
Python package scikit-learn v0.21	Pedregosa et al., 201177	https://scikit-learn.org/0.21/
Other
timsTOF Pro mass spectrometer	Bruker Daltonics	N/A
nanoElute liquid chromatographer	Bruker Daltonics	N/A
DIONEX UltiMate 3000 RSLCnano liquid chromatographer	Thermo Fisher Scientific	N/A
Q Exactive HF-Orbitrap	Thermo Fisher Scientific	N/A
NanoDrop Eight	Thermo Fisher Scientific	N/A
QuantiFluor™-ST	Promega	N/A
MiSeq System	Illumina	N/A