Summary of Study ST003921

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002454. The data can be accessed directly via it's Project DOI: 10.21228/M8F846 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study ID	ST003921
Study Title	Metabolic fingerprinting enables rapid, label-free histopathology in gastric cancer diagnosis and prognostic prediction
Study Summary	Histopathological evaluation is a cornerstone of cancer identification but often involves time-consuming labeling processes (~days per sample) and experience-dependent interpretation. Herein, we introduce a rapid (~40 minutes per sample) label-free method based on nanoparticle-enhanced LDI metabolic fingerprinting for gastric cancer (GC) assessment. Untargeted metabolomics of 284 paired tissues distinguishes malignant from benign tissues (AUC of 0.979), identifies tumor subtypes (AUC of 0.963), and assesses prognosis (p < 0.05) without specialized pathologists. This approach marks a substantial advancement in histopathological evaluation and shows great potential for large-scale clinical applications.
Institute	Fudan University
Department	Minhang Hospital
Last Name	Teng
First Name	Fei
Address	170 Xinsong Road
Email	prof_tengfei@fudan.edu.cn
Phone	18817618785
Submit Date	2025-05-16
Analysis Type Detail	MS(Dir. Inf.)
Release Date	2025-05-28
Release Version	1

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Project:

Project ID:	PR002454
Project DOI:	doi: 10.21228/M8F846
Project Title:	Metabolic fingerprinting enables rapid, label-free histopathology in gastric cancer diagnosis and prognostic prediction
Project Summary:	Nanoparticle-enhanced-LDI-MS-based metabolic profiling of formalin-fixed-paraffin-embedded tissues identifies diagnostic fingerprints for gastric cancer, correlating with pentose phosphate pathway dysregulation
Institute:	Fudan University
Department:	Minhang Hospital
Last Name:	Teng
First Name:	Fei
Address:	170 Xinsong Road
Email:	prof_tengfei@fudan.edu.cn
Phone:	18817618785

Subject:

Subject ID:	SU004056
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Diagnosis	Sample source
SA444017	ANT_100	Benign	FFPE tissue
SA444018	ANT_94	Benign	FFPE tissue
SA444019	ANT_95	Benign	FFPE tissue
SA444020	ANT_96	Benign	FFPE tissue
SA444021	ANT_97	Benign	FFPE tissue
SA444022	ANT_98	Benign	FFPE tissue
SA444023	ANT_99	Benign	FFPE tissue
SA444024	ANT_101	Benign	FFPE tissue
SA444025	ANT_92	Benign	FFPE tissue
SA444026	ANT_102	Benign	FFPE tissue
SA444027	ANT_103	Benign	FFPE tissue
SA444028	ANT_104	Benign	FFPE tissue
SA444029	ANT_105	Benign	FFPE tissue
SA444030	ANT_106	Benign	FFPE tissue
SA444031	ANT_107	Benign	FFPE tissue
SA444032	ANT_93	Benign	FFPE tissue
SA444033	ANT_91	Benign	FFPE tissue
SA444034	ANT_109	Benign	FFPE tissue
SA444035	ANT_82	Benign	FFPE tissue
SA444036	ANT_76	Benign	FFPE tissue
SA444037	ANT_77	Benign	FFPE tissue
SA444038	ANT_78	Benign	FFPE tissue
SA444039	ANT_79	Benign	FFPE tissue
SA444040	ANT_80	Benign	FFPE tissue
SA444041	ANT_81	Benign	FFPE tissue
SA444042	ANT_83	Benign	FFPE tissue
SA444043	ANT_90	Benign	FFPE tissue
SA444044	ANT_84	Benign	FFPE tissue
SA444045	ANT_85	Benign	FFPE tissue
SA444046	ANT_86	Benign	FFPE tissue
SA444047	ANT_87	Benign	FFPE tissue
SA444048	ANT_88	Benign	FFPE tissue
SA444049	ANT_89	Benign	FFPE tissue
SA444050	ANT_108	Benign	FFPE tissue
SA444051	ANT_110	Benign	FFPE tissue
SA444052	ANT_74	Benign	FFPE tissue
SA444053	ANT_136	Benign	FFPE tissue
SA444054	ANT_130	Benign	FFPE tissue
SA444055	ANT_131	Benign	FFPE tissue
SA444056	ANT_132	Benign	FFPE tissue
SA444057	ANT_133	Benign	FFPE tissue
SA444058	ANT_134	Benign	FFPE tissue
SA444059	ANT_135	Benign	FFPE tissue
SA444060	ANT_137	Benign	FFPE tissue
SA444061	ANT_128	Benign	FFPE tissue
SA444062	ANT_138	Benign	FFPE tissue
SA444063	ANT_139	Benign	FFPE tissue
SA444064	ANT_140	Benign	FFPE tissue
SA444065	ANT_141	Benign	FFPE tissue
SA444066	ANT_142	Benign	FFPE tissue
SA444067	ANT_2	Benign	FFPE tissue
SA444068	ANT_129	Benign	FFPE tissue
SA444069	ANT_127	Benign	FFPE tissue
SA444070	ANT_111	Benign	FFPE tissue
SA444071	ANT_118	Benign	FFPE tissue
SA444072	ANT_112	Benign	FFPE tissue
SA444073	ANT_113	Benign	FFPE tissue
SA444074	ANT_114	Benign	FFPE tissue
SA444075	ANT_115	Benign	FFPE tissue
SA444076	ANT_116	Benign	FFPE tissue
SA444077	ANT_117	Benign	FFPE tissue
SA444078	ANT_119	Benign	FFPE tissue
SA444079	ANT_126	Benign	FFPE tissue
SA444080	ANT_120	Benign	FFPE tissue
SA444081	ANT_121	Benign	FFPE tissue
SA444082	ANT_122	Benign	FFPE tissue
SA444083	ANT_123	Benign	FFPE tissue
SA444084	ANT_124	Benign	FFPE tissue
SA444085	ANT_125	Benign	FFPE tissue
SA444086	ANT_75	Benign	FFPE tissue
SA444087	ANT_1	Benign	FFPE tissue
SA444088	ANT_73	Benign	FFPE tissue
SA444089	ANT_27	Benign	FFPE tissue
SA444090	ANT_21	Benign	FFPE tissue
SA444091	ANT_22	Benign	FFPE tissue
SA444092	ANT_23	Benign	FFPE tissue
SA444093	ANT_24	Benign	FFPE tissue
SA444094	ANT_25	Benign	FFPE tissue
SA444095	ANT_26	Benign	FFPE tissue
SA444096	ANT_28	Benign	FFPE tissue
SA444097	ANT_19	Benign	FFPE tissue
SA444098	ANT_29	Benign	FFPE tissue
SA444099	ANT_30	Benign	FFPE tissue
SA444100	ANT_31	Benign	FFPE tissue
SA444101	ANT_32	Benign	FFPE tissue
SA444102	ANT_33	Benign	FFPE tissue
SA444103	ANT_34	Benign	FFPE tissue
SA444104	ANT_20	Benign	FFPE tissue
SA444105	ANT_18	Benign	FFPE tissue
SA444106	ANT_36	Benign	FFPE tissue
SA444107	ANT_9	Benign	FFPE tissue
SA444108	ANT_72	Benign	FFPE tissue
SA444109	ANT_4	Benign	FFPE tissue
SA444110	ANT_5	Benign	FFPE tissue
SA444111	ANT_6	Benign	FFPE tissue
SA444112	ANT_7	Benign	FFPE tissue
SA444113	ANT_8	Benign	FFPE tissue
SA444114	ANT_10	Benign	FFPE tissue
SA444115	ANT_17	Benign	FFPE tissue
SA444116	ANT_11	Benign	FFPE tissue

Showing page 1 of 3 Results: 1 2 3 Next Showing results 1 to 100 of 284

Collection:

Collection ID:	CO004049
Collection Summary:	Formalin-fixed paraffin-embedded (FFPE) gastric cancer tissues and paired adjacent normal (benign) tissues (>2 cm from tumor margins) were collected under standardized surgical protocols. Tissue cores (1 mm diameter, 20 μm thickness) were microdissected using a tissue microarray platform, validated by histopathological review to ensure purity.
Sample Type:	gastric cancer tissue

Treatment:

Treatment ID:	TR004065
Treatment Summary:	None

Sample Preparation:

Sampleprep ID:	SP004062
Sampleprep Summary:	（1）Tissue samples were dissolved in 80% methanol to release metabolites. (2) Samples were heated at 70°C for 20 minutes to remove paraffin wax, a step that can be performed in batches to enhance throughput. (3) Samples were placed in an ice bath for 10 minutes to solidify the wax. (4) Centrifugation was performed at 10,000 rpm for 10 minutes at 4°C to separate the wax. (5) The supernatant containing the extracted metabolites was carefully collected. (6) The supernatant was mixed with a matrix and spotted onto an LDI plate. (7) The plate was inserted into the mass spectrometer for metabolic fingerprint acquisition.

Sampleprep ID:

SP004062

Sampleprep Summary:

（1）Tissue samples were dissolved in 80% methanol to release metabolites. (2) Samples were heated at 70°C for 20 minutes to remove paraffin wax, a step that can be performed in batches to enhance throughput. (3) Samples were placed in an ice bath for 10 minutes to solidify the wax. (4) Centrifugation was performed at 10,000 rpm for 10 minutes at 4°C to separate the wax. (5) The supernatant containing the extracted metabolites was carefully collected. (6) The supernatant was mixed with a matrix and spotted onto an LDI plate. (7) The plate was inserted into the mass spectrometer for metabolic fingerprint acquisition.

Combined analysis:

Analysis ID	AN006438
Chromatography ID	CH004886
MS ID	MS006139
Analysis type	MS
Chromatography type	None (Direct infusion)
Chromatography system	none
Column	none
MS Type	MALDI
MS instrument type	TOF
MS instrument name	Bruker Autoflex speed TOF/TOF
Ion Mode	POSITIVE
Units	Peak intensity

Chromatography:

Chromatography ID:	CH004886
Instrument Name:	none
Column Name:	none
Column Temperature:	none
Flow Gradient:	none
Flow Rate:	none
Solvent A:	none
Solvent B:	none
Chromatography Type:	None (Direct infusion)

MS:

MS ID:	MS006139
Analysis ID:	AN006438
Instrument Name:	Bruker Autoflex speed TOF/TOF
Instrument Type:	TOF
MS Type:	MALDI
MS Comments:	Metabolites extracted from FFPE tissue samples were directly detected without the need for further sample pretreatment, following a standardized profiling workflow. In a typical metabolic analysis process based on NPELDI MS, 1 µL of the FFPE tissue metabolite solution was deposited onto the microarray chip. Subsequently, ferric nanoparticle solution (1 µL) with a concentration of 1 mg mL-1 was distributed onto the dried FFPE tissue metabolites. Mass spectra of metabolites were recorded using a Bruker Autoflex MALDI TOF/TOF mass spectrometer (Bruker Daltonics, Bremen, Germany), with Nd:YAG lasers of 355 nm. During detection, the pulse laser was optimized at a frequency of 1000 Hz (2000 shots), a delay time of 200 ns, and an acceleration voltage of 20 kV. Biomarker identification was performed on Solarix 7.0T (Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, FT-ICR-MS). The related molecular formulas were confirmed in the Bruker Compass Data Analysis software (version 5.0) based on accurate mass (< 10 ppm). The Human Metabolome Database (HMDB) was utilized for searching candidate metabolites. All MALDI-MS data were acquired using the reflectron mode.
Ion Mode:	POSITIVE