#METABOLOMICS WORKBENCH ax1_20251126_051028 DATATRACK_ID:6769 STUDY_ID:ST004479 ANALYSIS_ID:AN007512 PROJECT_ID:PR002826
VERSION             	1
CREATED_ON             	December 18, 2025, 6:36 pm
#PROJECT
PR:PROJECT_TITLE                 	Untargeted metabolomics analysis of fermented milk
PR:PROJECT_SUMMARY               	This project employed untargeted metabolomics to decipher the impact of the
PR:PROJECT_SUMMARY               	adjunct culture Lactiplantibacillus plantarum NDF28B2 on yoghurt quality.
PR:PROJECT_SUMMARY               	Co-fermentation induced a profound metabolic reprogramming of the yoghurt
PR:PROJECT_SUMMARY               	metabolome. This was characterized by a marked enrichment of key flavor
PR:PROJECT_SUMMARY               	compounds, particularly 2,3-butanedione, which imparts desirable buttery and
PR:PROJECT_SUMMARY               	creamy notes. Concurrently, we observed a broad accumulation of amino acids,
PR:PROJECT_SUMMARY               	peptides, and lipids, alongside the selective depletion of specific precursors.
PR:PROJECT_SUMMARY               	These changes are consistent with enhanced proteolytic and lipolytic activities,
PR:PROJECT_SUMMARY               	which contribute to both the development of a superior, complex flavor profile
PR:PROJECT_SUMMARY               	and significant alterations in texture. The findings demonstrate that L.
PR:PROJECT_SUMMARY               	plantarum NDF28B2 acts as a powerful metabolic driver, collectively reshaping
PR:PROJECT_SUMMARY               	the sensory and nutritional landscape of yoghurt through targeted modulation of
PR:PROJECT_SUMMARY               	its biochemical composition.
PR:INSTITUTE                     	Jiangnan University
PR:DEPARTMENT                    	school of food science and technology
PR:LAST_NAME                     	Xiao
PR:FIRST_NAME                    	Nan
PR:ADDRESS                       	Jiangnan University, No.1800 Lihu Avenue, Wuxi City, Jiangsu Province, Wuxi,
PR:ADDRESS                       	Jiangsu, 214000, China
PR:EMAIL                         	6230112091@stu.jiangnan.edu.cn
PR:PHONE                         	19850160696
#STUDY
ST:STUDY_TITLE                   	Metabolomics to decipher the impact of the adjunct culture Lactiplantibacillus
ST:STUDY_TITLE                   	plantarum NDF28B2 on yoghurt quality
ST:STUDY_SUMMARY                 	This project employed untargeted metabolomics to decipher the impact of the
ST:STUDY_SUMMARY                 	adjunct culture Lactiplantibacillus plantarum NDF28B2 on yoghurt quality.
ST:STUDY_SUMMARY                 	Co-fermentation induced a profound metabolic reprogramming of the yoghurt
ST:STUDY_SUMMARY                 	metabolome. This was characterized by a marked enrichment of key flavor
ST:STUDY_SUMMARY                 	compounds, particularly 2,3-butanedione, which imparts desirable buttery and
ST:STUDY_SUMMARY                 	creamy notes. Concurrently, we observed a broad accumulation of amino acids,
ST:STUDY_SUMMARY                 	peptides, and lipids, alongside the selective depletion of specific precursors.
ST:STUDY_SUMMARY                 	These changes are consistent with enhanced proteolytic and lipolytic activities,
ST:STUDY_SUMMARY                 	which contribute to both the development of a superior, complex flavor profile
ST:STUDY_SUMMARY                 	and significant alterations in texture. The findings demonstrate that L.
ST:STUDY_SUMMARY                 	plantarum NDF28B2 acts as a powerful metabolic driver, collectively reshaping
ST:STUDY_SUMMARY                 	the sensory and nutritional landscape of yoghurt through targeted modulation of
ST:STUDY_SUMMARY                 	its biochemical composition.
ST:INSTITUTE                     	Jiangnan University
ST:LAST_NAME                     	Xiao
ST:FIRST_NAME                    	Nan
ST:ADDRESS                       	Jiangnan University, No.1800 Lihu Avenue, Wuxi City, Jiangsu Province, Wuxi,
ST:ADDRESS                       	Jiangsu, 214000, China
ST:EMAIL                         	6230112091@stu.jiangnan.edu.cn
ST:PHONE                         	19850160696
#SUBJECT
SU:SUBJECT_TYPE                  	Food item
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	SEF	SEF_1	Sample source:Fermented milk | Treatment:control	RAW_FILE_NAME=SEF_1.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SEF	SEF_2	Sample source:Fermented milk | Treatment:control	RAW_FILE_NAME=SEF_2.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SEF	SEF_3	Sample source:Fermented milk | Treatment:control	RAW_FILE_NAME=SEF_3.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SEF	SEF_4	Sample source:Fermented milk | Treatment:control	RAW_FILE_NAME=SEF_4.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SER	SER_1	Sample source:Fermented milk | Treatment:control	RAW_FILE_NAME=SER_1.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SER	SER_2	Sample source:Fermented milk | Treatment:control	RAW_FILE_NAME=SER_2.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SER	SER_3	Sample source:Fermented milk | Treatment:control	RAW_FILE_NAME=SER_3.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SER	SER_4	Sample source:Fermented milk | Treatment:control	RAW_FILE_NAME=SER_4.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SFEF	SFEF_1	Sample source:Fermented milk | Treatment:co-fermented	RAW_FILE_NAME=SFEF_1.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SFEF	SFEF_2	Sample source:Fermented milk | Treatment:co-fermented	RAW_FILE_NAME=SFEF_2.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SFEF	SFEF_3	Sample source:Fermented milk | Treatment:co-fermented	RAW_FILE_NAME=SFEF_3.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SFEF	SFEF_4	Sample source:Fermented milk | Treatment:co-fermented	RAW_FILE_NAME=SFEF_4.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SFER	SFER_1	Sample source:Fermented milk | Treatment:co-fermented	RAW_FILE_NAME=SFER_1.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SFER	SFER_2	Sample source:Fermented milk | Treatment:co-fermented	RAW_FILE_NAME=SFER_2.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SFER	SFER_3	Sample source:Fermented milk | Treatment:co-fermented	RAW_FILE_NAME=SFER_3.raw; m/z_RT=m/z_RT
SUBJECT_SAMPLE_FACTORS           	SFER	SFER_4	Sample source:Fermented milk | Treatment:co-fermented	RAW_FILE_NAME=SFER_4.raw; m/z_RT=m/z_RT
#COLLECTION
CO:COLLECTION_SUMMARY            	Fermented milk samples collected at fermentation endpoint (EF) and ripening
CO:COLLECTION_SUMMARY            	endpoint (ER). Samples were directly transferred and immediately stored at
CO:COLLECTION_SUMMARY            	-80°C until analysis.
CO:COLLECTION_PROTOCOL_COMMENTS  	Sampling at two time points: EF (end of fermentation) and ER (end of ripening).
CO:COLLECTION_PROTOCOL_COMMENTS  	No subpackaging after fermentation. Immediate freezing at -80°C. Thawed at 4°C
CO:COLLECTION_PROTOCOL_COMMENTS  	prior to analysis.
CO:SAMPLE_TYPE                   	Milk
CO:COLLECTION_LOCATION           	lab
CO:COLLECTION_FREQUENCY          	At two specific endpoints (EF and ER)
CO:COLLECTION_DURATION           	24 hours
CO:VOLUMEORAMOUNT_COLLECTED      	8 mL
CO:STORAGE_CONDITIONS            	-80℃
CO:COLLECTION_TUBE_TEMP          	37℃
CO:ADDITIVES                     	none
#TREATMENT
TR:TREATMENT_SUMMARY             	No experimental treatment applied post-collection. Samples were immediately
TR:TREATMENT_SUMMARY             	frozen and stored at -80°C until analysis.
TR:TREATMENT_PROTOCOL_COMMENTS   	Samples are endpoint products of fermentation/ripening and were not subjected to
TR:TREATMENT_PROTOCOL_COMMENTS   	any further treatment.
TR:TREATMENT                     	none
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Frozen aliquots were thawed and centrifuged to get 100 μL supernatant, then
SP:SAMPLEPREP_SUMMARY            	mixed with 400 μL of ice-cold methanol/acetonitrile (1:1, v/v). The mixture was
SP:SAMPLEPREP_SUMMARY            	vortexed, kept in an ice bath (10 min), and then stored at -20°C (1 h). After
SP:SAMPLEPREP_SUMMARY            	centrifugation, the supernatant was dried via rotary evaporation. The
SP:SAMPLEPREP_SUMMARY            	precipitate was resoluted with 200 μL of acetonitrile/water (1:1, v/v),
SP:SAMPLEPREP_SUMMARY            	vortexed, centrifuged, and the supernatant was injected.
SP:PROCESSING_METHOD             	Protein precipitation
SP:PROCESSING_STORAGE_CONDITIONS 	-20℃
SP:EXTRACTION_METHOD             	Single-phase liquid extraction with methanol/acetonitrile (1:1, v/v)
SP:EXTRACT_CONCENTRATION_DILUTION	Concentrated by rotary evaporation; Reconstituted in 200 µL (final volume is 2x
SP:EXTRACT_CONCENTRATION_DILUTION	concentrated relative to initial 100 µL sample volume)
SP:EXTRACT_ENRICHMENT            	none
SP:EXTRACT_CLEANUP               	Protein precipitation and centrifugation
SP:EXTRACT_STORAGE               	-80℃
SP:SAMPLE_RESUSPENSION           	200 µL of acetonitrile/water (1:1, v/v)
SP:SAMPLE_DERIVATIZATION         	none
SP:SAMPLE_SPIKING                	none
SP:SUBCELLULAR_LOCATION          	Not applicable
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Waters Acquity
CH:COLUMN_NAME                   	Waters ACQUITY UPLC BEH C18 (100 x 2.1 mm, 1.7 μm)
CH:SOLVENT_A                     	100% Water;0.1% formic acid
CH:SOLVENT_B                     	100% Acetonitrile
CH:FLOW_GRADIENT                 	5% B (0-1 min), 5-60% B (1-5), 60-100% B (5-8), 100% B (8-11), 100-60% B
CH:FLOW_GRADIENT                 	(11-14), 60-5% B (14-15), and 5% B (15-18 min)
CH:FLOW_RATE                     	0.3 mL/min
CH:COLUMN_TEMPERATURE            	40°C
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
AN:DETECTOR_TYPE                 	Orbitrap
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	Use an aqueous solution of formic acid at a concentration of 0.1% (flow phase A)
MS:MS_COMMENTS                   	and acetonitrile (flow phase B) at a flow rate of 0.3 mL/min. The gradient
MS:MS_COMMENTS                   	elution conditions are as follows: 3 minutes, 90% A and 10% B; 6 minutes, 70% A
MS:MS_COMMENTS                   	and 30% B; 8 minutes, 50% A and 50% B; 12 minutes, 40% A and 60% B; 14 minutes,
MS:MS_COMMENTS                   	10% A and 90% B; 15 minutes, 10% A and 90% B; 16 minutes, 90% A and 10% B. Peak
MS:MS_COMMENTS                   	picking, alignment, and feature detection were performed using Compound
MS:MS_COMMENTS                   	Discoverer. Full MS scans (m/z 70-1050) were acquired at 70,000 resolution;
MS:MS_COMMENTS                   	data-dependent MS² scans were performed at 17,500 resolution (AGC target 1e5).
MS:CAPILLARY_TEMPERATURE         	350℃
MS:COLLISION_ENERGY              	30 eV
MS:FRAGMENTATION_METHOD          	HCD
MS:ION_SOURCE_TEMPERATURE        	300°C
MS:ION_SPRAY_VOLTAGE             	3500 V
MS:SPRAY_VOLTAGE                 	3.5 kV
MS:RESOLUTION_SETTING            	70000
MS:SCAN_RANGE_MOVERZ             	70-1050 m/z
MS:MS_RESULTS_FILE               	ST004479_AN007512_Results.txt	UNITS:peak area	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END