#METABOLOMICS WORKBENCH cascam07_20170403_081650 DATATRACK_ID:873 STUDY_ID:ST000602 ANALYSIS_ID:AN001824 PROJECT_ID:PR000439 VERSION 1 CREATED_ON January 10, 2019, 10:42 am #PROJECT PR:PROJECT_TITLE PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and PR:PROJECT_TITLE Collision Cross Section Calculation using Global Data Association PR:PROJECT_SUMMARY Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry PR:PROJECT_SUMMARY (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and PR:PROJECT_SUMMARY new informatics approaches are necessary for processing the associated data. To PR:PROJECT_SUMMARY automatically extract arrival times for molecules measured by DTIMS at multiple PR:PROJECT_SUMMARY electric fields and compute their associated collisional cross sections (CCS), PR:PROJECT_SUMMARY we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary PR:PROJECT_SUMMARY application presented for this algorithm is the extraction of that can then be PR:PROJECT_SUMMARY used to create a reference library of CCS values for use in high throughput PR:PROJECT_SUMMARY omics analyses. Results: We demonstrate the utility of this approach by PR:PROJECT_SUMMARY automatically extracting arrival times and calculating the associated CCSs for a PR:PROJECT_SUMMARY set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values PR:PROJECT_SUMMARY were within error of those calculated using commercially available instrument PR:PROJECT_SUMMARY vendor software. PR:INSTITUTE Pacific Northwest National Laboratory PR:LAST_NAME Casey PR:FIRST_NAME Cameron PR:ADDRESS 902 Battelle Blvd, Richland, WA 99354 PR:EMAIL cameron.casey@pnnl.gov PR:PHONE 5093716612 #STUDY ST:STUDY_TITLE PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and ST:STUDY_TITLE Collision Cross Section Calculation using Global Data Association ST:STUDY_SUMMARY Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry ST:STUDY_SUMMARY (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and ST:STUDY_SUMMARY new informatics approaches are necessary for processing the associated data. To ST:STUDY_SUMMARY automatically extract arrival times for molecules measured by DTIMS at multiple ST:STUDY_SUMMARY electric fields and compute their associated collisional cross sections (CCS), ST:STUDY_SUMMARY we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary ST:STUDY_SUMMARY application presented for this algorithm is the extraction of that can then be ST:STUDY_SUMMARY used to create a reference library of CCS valuesinformation necessary to create ST:STUDY_SUMMARY a reference library containing accurate masses, DTIMS arrival times and CCSs for ST:STUDY_SUMMARY use in high throughput omics analyses. Results: We demonstrate the utility of ST:STUDY_SUMMARY this approach by automatically extracting arrival times and calculating the ST:STUDY_SUMMARY associated CCSs for a set of endogenous metabolites and xenobiotics. The ST:STUDY_SUMMARY PIXiE-generated CCS values were within error of those calculated using ST:STUDY_SUMMARY commercially available instrument vendor software. ST:INSTITUTE Pacific Northwest National Laboratory ST:LAST_NAME Casey ST:FIRST_NAME Cameron ST:ADDRESS 902 Battelle Blvd, Richland, WA 99354 ST:EMAIL cameron.casey@pnnl.gov ST:PHONE 5093716612 #SUBJECT SU:SUBJECT_TYPE Standards SU:SUBJECT_SPECIES Standard #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - CCS_Neg-1_153-94-6_7Jul16_Beech_Infuse Sample Type:Standard CAS=153-94-6; Compound=D-Tryptophan SUBJECT_SAMPLE_FACTORS - CCS_Neg-1_59-30-3_7Jul16_Beech_Infuse Sample Type:Standard CAS=59-30-3; Compound=Folic acid SUBJECT_SAMPLE_FACTORS - CCS_Neg-2_53-84-9_7Jul16_Beech_Infuse Sample Type:Standard CAS=53-84-9; Compound=NAD SUBJECT_SAMPLE_FACTORS - CCS_Neg-2_57-50-1_7Jul16_Beech_Infuse Sample Type:Standard CAS=57-50-1; Compound=Sucrose SUBJECT_SAMPLE_FACTORS - CCS_Neg-3_137868-52-1_7Jul16_Beech_Infuse Sample Type:Standard CAS=137868-52-1; Compound=UDP-Galactose SUBJECT_SAMPLE_FACTORS - CCS_Neg-3_3616-42-0_7Jul16_Beech_Infuse Sample Type:Standard CAS=3616-42-0; Compound=D-Glucosamine 6-phosphate SUBJECT_SAMPLE_FACTORS - CCS_Neg-3_38099-82-0_7Jul16_Beech_Infuse Sample Type:Standard CAS=38099-82-0; Compound=D-Fructose-1-6-diphosphate SUBJECT_SAMPLE_FACTORS - CCS_Neg-3_51-43-4_7Jul16_Beech_Infuse Sample Type:Standard CAS=51-43-4; Compound=(-)-Epinephrine SUBJECT_SAMPLE_FACTORS - CCS_Neg-3_58-61-7_7Jul16_Beech_Infuse Sample Type:Standard CAS=58-61-7; Compound=Adenosine SUBJECT_SAMPLE_FACTORS - CCS_Pos-1_107-35-7_30Jun16_Beech_Infuse Sample Type:Standard CAS=107-35-7; Compound=Taurine SUBJECT_SAMPLE_FACTORS - CCS_Pos-1_153-94-6_30Jun16_Beech_Infuse Sample Type:Standard CAS=153-94-6; Compound=D-Tryptophan SUBJECT_SAMPLE_FACTORS - CCS_Pos-1_53-84-9_30Jun16_Beech_Infuse Sample Type:Standard CAS=53-84-9; Compound=NAD SUBJECT_SAMPLE_FACTORS - CCS_Pos-1_57-50-1_30Jun16_Beech_Infuse Sample Type:Standard CAS=57-50-1; Compound=Sucrose SUBJECT_SAMPLE_FACTORS - CCS_Pos-1_65-46-3_30Jun16_Beech_Infuse Sample Type:Standard CAS=65-46-3; Compound=Cytidine SUBJECT_SAMPLE_FACTORS - CCS_Pos-2_59-30-3_30Jun16_Beech_Infuse Sample Type:Standard CAS=59-30-3; Compound=Folic acid SUBJECT_SAMPLE_FACTORS - CCS_Pos-3_3616-42-0_7Jul16_Beech_Infuse Sample Type:Standard CAS=3616-42-0; Compound=D-Glucosamine 6-phosphate SUBJECT_SAMPLE_FACTORS - CCS_Pos-3_58-61-7_7Jul16_Beech_Infuse Sample Type:Standard CAS=58-61-7; Compound=Adenosine SUBJECT_SAMPLE_FACTORS - CCS_Pos-3_62-49-7_7Jul16_Beech_Infuse Sample Type:Standard CAS=62-49-7; Compound=Choline SUBJECT_SAMPLE_FACTORS - EXP-PMR_pos2_9Oct14_Columbia_DI Sample Type:Standard CAS=52645-53-1; Compound=Permethrin SUBJECT_SAMPLE_FACTORS - CCS-Neg-1-70-18-8_23Jul16_Beech_Infuse Sample Type:Standard CAS=1-70-18-8; Compound=Glutathione SUBJECT_SAMPLE_FACTORS - CCS-Pos-1-70-18-8_20Jul16_Beech_Infuse Sample Type:Standard CAS=1-70-18-8; Compound=Glutathione #COLLECTION CO:COLLECTION_SUMMARY Authentic standards were purchased from Sigma Aldrich (St. Louis, MO). CO:SAMPLE_TYPE Synthetic Mixture #TREATMENT TR:TREATMENT_SUMMARY Standards were not treated. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Standards were prepared in 100% methanol to a concentration of 1 µM. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Ion Mobility CH:INSTRUMENT_NAME Agilent 6560 CH:COLUMN_NAME N/A #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6560 Ion Mobility MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE UNSPECIFIED MS:MS_COMMENTS None #END