#METABOLOMICS WORKBENCH FernandezGarcia_M_20230625_114427 DATATRACK_ID:4111 STUDY_ID:ST002763 ANALYSIS_ID:AN004496 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 Chromatography was performed according to DOI: 10.1128/msphere.00184-22 CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1290 Infinity CH:COLUMN_NAME Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) CH:SOLVENT_A 10 mM Ammonium acetate and 0.2 mM ammonium fluoride in 9:1 H2O:MeOH (v/v) CH:SOLVENT_B 10 mM Ammonium acetate and 0.2 mM ammonium fluoride in 2:3:5 ACN:MeOH:IPA (v/v) CH:SOLVENT_C N/A CH:FLOW_GRADIENT 70%B held 1 min; then increase up to 86 %B at 3.5 min; then hold 10 min; Next, CH:FLOW_GRADIENT incerase in %B up to 100 %B at 11 min; then, held for 6 min. Then, switched to CH:FLOW_GRADIENT initial conditions (1.84 min of re-equilibration time) CH:FLOW_RATE 0.6 mL/min CH:COLUMN_TEMPERATURE 50 ºC CH:SAMPLE_INJECTION 2 uL (ESI+, MS1, ITMS with default inj. volume) and 5 uL (ESI-, MS1, ITMS with CH:SAMPLE_INJECTION default inj. volume), 7 uL (ESI+ ITMS with increased inj. volume), 10 uL (ESI- CH:SAMPLE_INJECTION ITMS with increased inj. volume) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6545 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Drying gas T = 300 ºC; drying gas flow rate = 12 L/min; Capillary V = 3500 V; MS:MS_COMMENTS fragmentor V = 150 V; skimmer V = 65 V; octopole RFV = 750 V. MS acquisition MS:MS_COMMENTS mode = Auto MS/MS, isolation width = narrow (1.3 Da); collision energy (ramp) = MS:MS_COMMENTS 3.8; offset (ramp) = 4 6. Data processed with Agilent MassHunter Profinder MS:MS_COMMENTS B.10.00 and Agilent MassHunter Qualitative Analysis (B.08.00). Feature MS:MS_COMMENTS annotation performed with Agilent MassHunter Lipid Annotator (v.1.0) MS:MS_RESULTS_FILE ST002763_AN004496_Results.txt UNITS:raw abundance Has m/z:Neutral masses Has RT:Yes RT units:Minutes #END