#METABOLOMICS WORKBENCH eamonnk_20190419_170344 DATATRACK_ID:1707 STUDY_ID:ST001173 ANALYSIS_ID:AN001948 PROJECT_ID:PR000785 VERSION 1 CREATED_ON April 25, 2019, 2:23 pm #PROJECT PR:PROJECT_TITLE Combinatorial metabolic mixtures for encoding abstract digital data PR:PROJECT_TYPE FTICR-MS acquisition of 1536-spot MALDI plates, comprising thousands of mixtures PR:PROJECT_TYPE of common metabolites PR:PROJECT_SUMMARY This data comprises FT-ICR MS readouts of 1536-spot MALDI plates. Each spectra PR:PROJECT_SUMMARY is a measure of a specific metabolic mixture from a library of 36 common PR:PROJECT_SUMMARY metabolites. The combinatorial mixtures of metabolites are used to encode PR:PROJECT_SUMMARY abstract digital data (images). A comprehensive list of the metabolites and PR:PROJECT_SUMMARY specific mixture present in each spot on each plate are provided in metadata PR:PROJECT_SUMMARY files. Data is provided in open-source .hdf5 files. PR:INSTITUTE Brown University PR:DEPARTMENT Engineering PR:LABORATORY Rosenstein Lab PR:LAST_NAME Kennedy PR:FIRST_NAME Eamonn PR:ADDRESS Barus & Holley room 446, 184 Hope St PR:EMAIL eamonn_kennedy@brown.edu PR:PHONE 7737507192 PR:FUNDING_SOURCE DARPA PR:PUBLICATIONS E. Kennedy et al. “Encoding information in synthetic metabolomes” Plos One, PR:PUBLICATIONS accepted, 2019 PR:CONTRIBUTORS Eamonn Kennedy, Christopher E. Arcadia, Joseph Geiser Peter M. Weber, PR:CONTRIBUTORS Christopher Rose, Brenda M. Rubenstein and Jacob K. Rosenstein #STUDY ST:STUDY_TITLE Combinatorial metabolic mixtures for encoding abstract digital data ST:STUDY_TYPE MALDI MS ST:STUDY_SUMMARY We present several kilobyte-scale image datasets stored in synthetic ST:STUDY_SUMMARY metabolomes, which are decoded with accuracy exceeding 98-99% using multi-mass ST:STUDY_SUMMARY logistic regression. ST:INSTITUTE Brown University ST:DEPARTMENT Engineering ST:LABORATORY Rosenstein Lab ST:LAST_NAME Kennedy ST:FIRST_NAME Eamonn ST:ADDRESS Barus & Holley room 353, 184 Hope St ST:EMAIL eamonn_kennedy@brown.edu ST:PHONE 7737507192 ST:PUBLICATIONS E. Kennedy et al. “Encoding information in synthetic metabolomes” Plos One, ST:PUBLICATIONS accepted, 2019 #SUBJECT SU:SUBJECT_TYPE Synthetic SU:SUBJECT_SPECIES Escherichia coli SU:TAXONOMY_ID 562 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - e0117p01t01 Sample Type:standard # of metabolites=36; Max metabolites in 1 spot=3; # spots/spectra=1400; concs (mM)=25 SUBJECT_SAMPLE_FACTORS - e0112p01t01 Sample Type:standard # of metabolites=6; Max metabolites in 1 spot=6; # spots/spectra=1024; concs (mM)=25 SUBJECT_SAMPLE_FACTORS - e0114p03t02 Sample Type:standard # of metabolites=12; Max metabolites in 1 spot=12; # spots/spectra=1452; concs (mM)=25 #COLLECTION CO:COLLECTION_SUMMARY Extensive details of the collection parameters are provided in metadata .mat CO:COLLECTION_SUMMARY files (see in raw data zip file : README.pdf). Briefly, a Solarix 7T was used to CO:COLLECTION_SUMMARY collect FTICR MS data of thousands of MALDI spots comprised of synthetic CO:COLLECTION_SUMMARY metabolite mixtures. CO:COLLECTION_PROTOCOL_ID NA CO:COLLECTION_PROTOCOL_FILENAME There are multiple provided, e.g. please see : raw data zip file, CO:COLLECTION_PROTOCOL_FILENAME e0114p03t02_instrument_settings.mat CO:SAMPLE_TYPE Synthetic Mixture CO:COLLECTION_METHOD FTICR MS CO:COLLECTION_LOCATION Brown University CO:COLLECTION_FREQUENCY 2000 CO:COLLECTION_DURATION shot_count: 500, 4x averaging, 1 second duration CO:VOLUMEORAMOUNT_COLLECTED 0.1 nL CO:STORAGE_CONDITIONS Room temperature CO:COLLECTION_VIALS 1 CO:STORAGE_VIALS 36 CO:COLLECTION_TUBE_TEMP RT CO:ADDITIVES Aminoacridine matrix #TREATMENT TR:TREATMENT_SUMMARY Combinatorial mixtures of metabolites were deposited using a Labcyte Echo 550 on TR:TREATMENT_SUMMARY to a MALDI steel plate at 30-60 nL volumes. Aminoacridine matrix was added in TR:TREATMENT_SUMMARY the ratio 0.7:1 to 1:.7 to metabolite concentrations. The spot droplets were air TR:TREATMENT_SUMMARY dried. No further treatments were performed prior to data acquisition. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Combinatorial mixtures of metabolites were deposited using a Labcyte Echo 550 on SP:SAMPLEPREP_SUMMARY to a MALDI steel plate at 30-60 nL volumes. Aminoacridine matrix was added in SP:SAMPLEPREP_SUMMARY the ratio 0.7:1 to 1:.7 to metabolite concentrations. The spot droplets were air SP:SAMPLEPREP_SUMMARY dried. No further preparations were performed prior to data acquisition. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE None (Direct infusion) CH:INSTRUMENT_NAME none CH:COLUMN_NAME none #ANALYSIS AN:ANALYSIS_TYPE MS AN:LABORATORY_NAME BH Solarix laboratory AN:OPERATOR_NAME Joseph Geiser #MS MS:INSTRUMENT_NAME Bruker Solarix FT-ICR-MS MS:INSTRUMENT_TYPE FT-ICR MS:MS_TYPE MALDI MS:ION_MODE POSITIVE MS:MS_COMMENTS Extensive details of the data processing are provided in the readme.pdf file, MS:MS_COMMENTS and scripts for directly reading the data in Python are also provided. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS mM MS_METABOLITE_DATA_START Samples e0117p01t01 e0112p01t01 e0114p03t02 Factors Sample Type:standard Sample Type:standard Sample Type:standard Imidazolepropionic acid 25 0 25 Glutamine 25 0 0 Sodium ethyl sulfate 25 0 0 Methionine 25 0 0 D-(-)-Ribose 25 0 0 Histidine 25 0 0 Disodium succinate 25 0 25 Phenylalanine 25 0 0 cis-Aconitic acid 25 0 25 L-(+)-Arginine 25 0 0 4-Hydroxyphenylpyruvic acid 25 0 0 D-(+)-Galactose 25 0 25 Tyrosine 25 0 0 Sorbitol 25 25 25 N-Acetyl-L-glutamic acid 25 25 25 Tryptophan 25 25 25 2'-Deoxycytidine 25 0 0 2'-Deoxyuridine 25 0 0 Thymidine 25 0 0 Cytidine 25 25 25 Uridine 25 0 25 2'-Deoxyadenosine 25 0 0 5-Methyluridine 25 0 25 Adenosine 25 0 0 2'-Deoxyadenosine monohydrate 25 0 0 D-Glucose 6-phosphate (Na) 25 0 0 Guanosine 25 25 25 2'-Deoxyguanosine hydrate 25 25 25 Sodium Citrate 25 0 0 Thiamine hydrochloride 25 0 0 Roboflavin 25 0 0 Adenosine 5_-diphosphate sodium 25 0 0 Phylloquinone (Vitamin K1) 25 0 0 Cytidine 5'-triphosphate disodium salt 25 0 0 NADP (2x Na) 25 0 0 Creatine monohydrate 25 0 0 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name CID Monoisotopic mass Imidazolepropionic acid 70630 140.059 Glutamine 738 146.069 Sodium ethyl sulfate 23680278 147.981 Methionine 6137 149.051 D-(-)-Ribose 5311110 150.053 Histidine 6274 155.0695 Disodium succinate 9020 161.99 Phenylalanine 6140 165.079 cis-Aconitic acid 643757 174.016 L-(+)-Arginine 6322 174.1117 4-Hydroxyphenylpyruvic acid 979 180.042 D-(+)-Galactose 6036 180.063 Tyrosine 6057 181.0739 Sorbitol 5780 182.079 N-Acetyl-L-glutamic acid 70914 189.064 Tryptophan 6305 204.0899 2'-Deoxycytidine 13711 227.091 2'-Deoxyuridine 13712 228.075 Thymidine 5789 242.09 Cytidine 6175 243.086 Uridine 6029 244.07 2'-Deoxyadenosine 13730 251.102 5-Methyluridine 445408 258.085 Adenosine 60961 267.097 2'-Deoxyadenosine monohydrate 9549172 269.112 D-Glucose 6-phosphate (Na) 439958 282.0198 Guanosine 6802 283.092 2'-Deoxyguanosine hydrate 16218597 267.24 Sodium Citrate 6224 293.994 Thiamine hydrochloride 6202 336.058 Roboflavin 493570 376.138 Adenosine 5_-diphosphate sodium 6022 427.029 Phylloquinone (Vitamin K1) 5284607 450.35 Cytidine 5'-triphosphate disodium salt 16219171 526.948 NADP (2x Na) 5885 787.039 Creatine monohydrate 80116 149.08 METABOLITES_END #END