#METABOLOMICS WORKBENCH FernandezGarcia_M_20230625_114427 DATATRACK_ID:4111 STUDY_ID:ST002763 ANALYSIS_ID:AN004493 PROJECT_ID:PR001721 VERSION 1 CREATED_ON June 29, 2023, 12:50 pm #PROJECT PR:PROJECT_TITLE Multi-omics of Haemophilus influenzae Rd KW20 PR:PROJECT_SUMMARY This project aims to characterize at different levels the modifications ocurring PR:PROJECT_SUMMARY during compensatory evolution of bacteria upon plasmid transformation and to PR:PROJECT_SUMMARY characterize the metabolome of H. influenzae at a global level. PR:INSTITUTE CEU San Pablo University PR:LAST_NAME García PR:FIRST_NAME Antonia PR:ADDRESS Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, PR:ADDRESS Universidad San Pablo-CEU, Urbanización Montepríncipe, 28660, Boadilla del PR:ADDRESS Monte, España PR:EMAIL miguel.fernandezgarcia@ceu.es PR:PHONE 913724711 #STUDY ST:STUDY_TITLE Metabolomic and lipidomic characterization of Haemophilus influenzae Rd KW20 ST:STUDY_SUMMARY This study aims to comprehensively characterize the polar metabolome and the ST:STUDY_SUMMARY phosphlipidome of Haemophilus influenzae Rd Kw20, to provide an improved ST:STUDY_SUMMARY understanding of this bacterial metabolome by comparison with data inferred from ST:STUDY_SUMMARY genome annotation data. ST:INSTITUTE Universidad CEU San Pablo ST:LAST_NAME García ST:FIRST_NAME Antonia ST:ADDRESS Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, ST:ADDRESS Universidad San Pablo-CEU, Urbanización Montepríncipe, 28660, Boadilla del ST:ADDRESS Monte, España ST:EMAIL miguel.fernandezgarcia@ceu.es ST:PHONE 913724711 #SUBJECT SU:SUBJECT_TYPE Bacteria SU:SUBJECT_SPECIES Haemophilus influenzae SU:GENOTYPE_STRAIN Rd KW20 #FACTORS #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 A1 A1_GC-MS Population:A Analytical platform=GC-MS; RAW_FILE_NAME=A1_GC-MS.mzML SUBJECT_SAMPLE_FACTORS A2 A2_GC-MS Population:A Analytical platform=GC-MS; RAW_FILE_NAME=A2_GC-MS.mzML SUBJECT_SAMPLE_FACTORS A3 A3_GC-MS Population:A Analytical platform=GC-MS; RAW_FILE_NAME=A3_GC-MS.mzML SUBJECT_SAMPLE_FACTORS A4 A4_GC-MS Population:A Analytical platform=GC-MS; RAW_FILE_NAME=A4_GC-MS.mzML SUBJECT_SAMPLE_FACTORS A5 A5_GC-MS Population:A Analytical platform=GC-MS; 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RAW_FILE_NAME=QC_vol_ITMS_neg_8.mzML #COLLECTION CO:COLLECTION_SUMMARY H. influenzae Rd KW20 (NC_000907.1) was cultured in HTM broth and bacterial CO:COLLECTION_SUMMARY pellets were obtained by centrifugation. CO:SAMPLE_TYPE Bacterial cells #TREATMENT TR:TREATMENT_SUMMARY In this case, samples were not treated as the study is a characterization. We TR:TREATMENT_SUMMARY performed independent evolution of five biological replicate populations. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Sample preparation was performed following Ares-Arroyo, M. et al. SP:SAMPLEPREP_SUMMARY (https://doi.org/10.1128/msphere.00184-22) #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Separation was performed according to DOI: 10.1128/msphere.00184-22 CH:CHROMATOGRAPHY_TYPE CE CH:INSTRUMENT_NAME Agilent 7100 CE CH:COLUMN_NAME fused silica capillary (70 cm; 50 um i.d.), Agilent Technologies CH:SOLVENT_A N/A for CE-MS CH:SOLVENT_B N/A for CE-MS CH:SOLVENT_C N/A for CE-MS CH:FLOW_GRADIENT N/A for CE-MS CH:FLOW_RATE N/A for CE-MS CH:COLUMN_TEMPERATURE RT CH:INTERNAL_STANDARD Methionine sulfone CH:SAMPLE_INJECTION hydrodynamic injection: 50 mbar for 100 s CH:CAPILLARY_VOLTAGE 30 kV CH:RUNNING_BUFFER 1M HCOOH in MeOH:H2O 1:9 (v/v) (BGE) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6224 TOF MS:INSTRUMENT_TYPE TOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS drying gas T = 200 ºC; drying gas flow rate = 10 L/min; nebulizer pressure = 10 MS:MS_COMMENTS psi; capillary V = 5500 V; fragmentor V = 125 V; skimmer V = 65 V; octopole RFV MS:MS_COMMENTS = 650 V; Acquisition mode: Full-MS scan, m/z range from 70 to 1000; acquisition MS:MS_COMMENTS rate = 1.36 spectra/s. Data processed with Agilent MassHunter Profinder B.10.00, MS:MS_COMMENTS feature assignment performed with CEU Mass Mediator Exp RMT Search and CEU Mass MS:MS_COMMENTS Mediator Batch Search. MS:MS_RESULTS_FILE ST002763_AN004493_Results.txt UNITS:raw abundance Has m/z:Neutral masses Has RT:Yes RT units:Minutes #END