#METABOLOMICS WORKBENCH jmmitc06_20240215_092030 DATATRACK_ID:4644 STUDY_ID:ST003075 ANALYSIS_ID:AN005033 VERSION 1 CREATED_ON 03-02-2024 #PROJECT PR:PROJECT_TITLE Evaluation of a python-centric metabolomics data processing pipeline based on PR:PROJECT_TITLE Asari. PR:PROJECT_SUMMARY To standardize metabolomics data analysis and facilitate future computational PR:PROJECT_SUMMARY developments, it is essential is have a set of well-defined templates for common PR:PROJECT_SUMMARY data structures. Here we describe a collection of data structures involved in PR:PROJECT_SUMMARY metabolomics data processing and illustrate how they are utilized in a PR:PROJECT_SUMMARY full-featured Python-centric pipeline. We demonstrate the performance of the PR:PROJECT_SUMMARY pipeline, and the details in annotation and quality control using large-scale PR:PROJECT_SUMMARY LC-MS metabolomics and lipidomics data and LC-MS/MS data. Multiple previously PR:PROJECT_SUMMARY published datasets are also reanalyzed to showcase its utility in biological PR:PROJECT_SUMMARY data analysis. This pipeline allows users to streamline data processing, quality PR:PROJECT_SUMMARY control, annotation, and standardization in an efficient and transparent manner. PR:PROJECT_SUMMARY This work fills a major gap in the Python ecosystem for computational PR:PROJECT_SUMMARY metabolomics. The uploaded datasets include previously unreleased datasets used PR:PROJECT_SUMMARY for the evaluation of this pipeline including two large plasma datasets taken PR:PROJECT_SUMMARY from recipients of one of two herpes zoster vaccines, analyzed as 17 separate PR:PROJECT_SUMMARY batches, and a lipidomics dataset collected on a subset of these patients. PR:INSTITUTE Jackson Laboratory for Genomic Medicine PR:LABORATORY Shuzhao Li Laboratory PR:LAST_NAME Joshua PR:FIRST_NAME Mitchell PR:ADDRESS 10 Discovery Dr, Farmington CT 06032 PR:EMAIL joshua.mitchell@jax.org PR:PHONE 8608372474 PR:FUNDING_SOURCE NIH grants U01 CA235493 (NCI), R01 AI149746 and AI149746 S1 (NIAID), and UM1 PR:FUNDING_SOURCE HG012651 (NHGRI). PR:PUBLICATIONS Common data models to streamline metabolomics processing and annotation, and PR:PUBLICATIONS implementation in a Python pipeline (BioRxiv) Joshua Mitchell, Yuanye Chi, PR:PUBLICATIONS Maheshwor Thapa, Zhiqiang Pang, Jianguo Xia, Shuzhao Li; doi: PR:PUBLICATIONS https://doi.org/10.1101/2024.02.13.580048 PR:DOI http://dx.doi.org/10.21228/M86137 PR:CONTRIBUTORS Joshua Mitchell, Yuanye Chi, Maheshwor Thapa, Shuzhao Li #STUDY ST:STUDY_TITLE HZV029 TwoPhase Metabolomics and Lipidomics ST:STUDY_SUMMARY In this study, a subset of plasma samples were processed using an in-house two ST:STUDY_SUMMARY phase extraction protocol based on the protocol originally proposed by Matayash ST:STUDY_SUMMARY et al. The resulting non-polar layer was then analyzed on a Thermo ScientificTM ST:STUDY_SUMMARY TranscendTM Duo LX-2 UHPLC system interfaced with high resolution Thermo ST:STUDY_SUMMARY ScientificTM Orbitrap ID-XTM TribidTM mass spectrometer with a HESI ionization ST:STUDY_SUMMARY source. This dataset was collected as a single batch and was used for the ST:STUDY_SUMMARY pipeline's ability to detect failed injections, which in this study, was ST:STUDY_SUMMARY simulated through the substitution of an empty vial for a missing study sample. ST:INSTITUTE Jackson Laboratory for Genomic Medicine ST:LABORATORY Shuzhao Li Laboratory ST:LAST_NAME Joshua ST:FIRST_NAME Mitchell ST:ADDRESS 10 Discovery Dr, Farmington CT 06032 ST:EMAIL joshua.mitchell@jax.org ST:PHONE 8608372474 ST:SUBMIT_DATE 2024-02-15 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - pooledsample_DDA_01 Factor:DDA | Sample source:Pooled Study Plasma RAW_FILE_NAME=pooledsample_DDA_01.mzML SUBJECT_SAMPLE_FACTORS - pooledsample_DDA_02 Factor:DDA | Sample source:Pooled Study Plasma RAW_FILE_NAME=pooledsample_DDA_02.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_007 Factor:NIST | Sample source:Pooled NIST Reference Plasma RAW_FILE_NAME=MT_20230807_007.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_008 Factor:NIST | Sample source:Pooled NIST Reference Plasma RAW_FILE_NAME=MT_20230807_008.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_009 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_009.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_010 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_010.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_031 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_031.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_032 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_032.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_053 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_053.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_054 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_054.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_075 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_075.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_076 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_076.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_097 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_097.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_098 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_098.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_123 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_123.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_124 Factor:Pooled | Sample source:Pooled Study Plasma RAW_FILE_NAME=MT_20230807_124.mzML SUBJECT_SAMPLE_FACTORS - Blank_20230807_001 Factor:Process_Blank | Sample source:Process Blank RAW_FILE_NAME=Blank_20230807_001.mzML SUBJECT_SAMPLE_FACTORS - Blank_20230807_002 Factor:Process_Blank | Sample source:Process Blank RAW_FILE_NAME=Blank_20230807_002.mzML SUBJECT_SAMPLE_FACTORS - Blank_20230807_003 Factor:Process_Blank | Sample source:Process Blank RAW_FILE_NAME=Blank_20230807_003.mzML SUBJECT_SAMPLE_FACTORS - Blank_20230807_004 Factor:Process_Blank | Sample source:Process Blank RAW_FILE_NAME=Blank_20230807_004.mzML SUBJECT_SAMPLE_FACTORS - Blank_20230807_005 Factor:Process_Blank | Sample source:Process Blank RAW_FILE_NAME=Blank_20230807_005.mzML SUBJECT_SAMPLE_FACTORS - Blank_20230807_006 Factor:Process_Blank | Sample source:Process Blank RAW_FILE_NAME=Blank_20230807_006.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_001 Factor:QC | Sample source:Pooled Commercial Plasma Sample RAW_FILE_NAME=MT_20230807_001.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_002 Factor:QC | Sample source:Pooled Commercial Plasma Sample RAW_FILE_NAME=MT_20230807_002.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_003 Factor:QC | Sample source:Pooled Commercial Plasma Sample RAW_FILE_NAME=MT_20230807_003.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_004 Factor:QC | Sample source:Pooled Commercial Plasma Sample RAW_FILE_NAME=MT_20230807_004.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_005 Factor:QC | Sample source:Pooled Commercial Plasma Sample RAW_FILE_NAME=MT_20230807_005.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_006 Factor:QC | Sample source:Pooled Commercial Plasma Sample RAW_FILE_NAME=MT_20230807_006.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_125 Factor:QC | Sample source:Pooled Commercial Plasma Sample RAW_FILE_NAME=MT_20230807_125.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_126 Factor:QC | Sample source:Pooled Commercial Plasma Sample RAW_FILE_NAME=MT_20230807_126.mzML SUBJECT_SAMPLE_FACTORS - Sol_blank_20230807_001 Factor:Solvent_Blank | Sample source:Solvent Blank RAW_FILE_NAME=Sol_blank_20230807_001.mzML SUBJECT_SAMPLE_FACTORS - Sol_blank_20230807_002 Factor:Solvent_Blank | Sample source:Solvent Blank RAW_FILE_NAME=Sol_blank_20230807_002.mzML SUBJECT_SAMPLE_FACTORS - Sol_blank_20230807_003 Factor:Solvent_Blank | Sample source:Solvent Blank RAW_FILE_NAME=Sol_blank_20230807_003.mzML SUBJECT_SAMPLE_FACTORS - Sol_blank_20230807_004 Factor:Solvent_Blank | Sample source:Solvent Blank RAW_FILE_NAME=Sol_blank_20230807_004.mzML SUBJECT_SAMPLE_FACTORS - Blank_std_20230807_1_001 Factor:Standards_Blank | Sample source:Blank w/ Stds RAW_FILE_NAME=Blank_std_20230807_1_001.mzML SUBJECT_SAMPLE_FACTORS - Blank_std_20230807_1_002 Factor:Standards_Blank | Sample source:Blank w/ Stds RAW_FILE_NAME=Blank_std_20230807_1_002.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_011 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_011.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_012 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_012.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_013 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_013.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_014 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_014.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_015 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_015.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_016 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_016.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_017 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_017.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_018 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_018.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_019 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_019.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_020 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_020.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_021 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_021.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_022 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_022.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_023 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_023.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_024 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_024.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_025 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_025.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_026 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_026.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_027 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_027.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_028 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_028.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_029 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_029.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_030 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_030.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_033 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_033.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_034 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_034.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_035 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_035.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_036 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_036.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_037 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_037.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_038 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_038.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_039 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_039.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_040 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_040.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_041 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_041.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_042 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_042.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_043 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_043.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_044 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_044.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_045 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_045.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_046 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_046.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_047 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_047.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_048 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_048.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_049 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_049.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_050 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_050.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_051 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_051.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_052 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_052.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_055 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_055.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_056 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_056.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_057 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_057.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_058 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_058.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_059 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_059.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_060 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_060.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_061 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_061.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_062 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_062.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_063 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_063.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_064 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_064.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_065 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_065.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_066 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_066.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_067 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_067.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_068 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_068.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_069 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_069.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_070 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_070.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_071 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_071.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_072 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_072.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_073 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_073.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_074 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_074.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_077 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_077.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_078 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_078.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_079 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_079.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_080 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_080.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_081 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_081.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_082 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_082.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_083 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_083.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_084 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_084.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_085 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_085.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_086 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_086.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_087 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_087.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_088 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_088.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_089 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_089.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_090 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_090.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_091 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_091.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_092 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_092.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_093 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_093.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_094 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_094.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_095 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_095.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_096 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_096.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_099 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_099.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_100 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_100.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_101 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_101.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_102 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_102.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_103 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_103.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_104 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_104.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_105 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_105.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_106 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_106.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_107 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_107.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_108 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_108.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_109 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_109.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_110 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_110.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_111 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_111.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_112 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_112.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_113 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_113.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_114 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_114.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_115 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_115.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_116 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_116.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_117 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_117.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_118 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_118.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_119 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_119.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_120 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_120.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_121 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_121.mzML SUBJECT_SAMPLE_FACTORS - MT_20230807_122 Factor:Unknown | Sample source:Plasma RAW_FILE_NAME=MT_20230807_122.mzML #COLLECTION CO:COLLECTION_SUMMARY Deidentified human plasma samples were used for this study: a) commercial Qstd CO:COLLECTION_SUMMARY and NIST plasma pool ; b) biosamples (from 1R01AI149746 (NIH-NIAID) samples) CO:COLLECTION_SUMMARY plasma, collected through venipuncture. CO:SAMPLE_TYPE Blood (plasma) CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY Not applicable. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Plasma samples were extracted following an in-house two-phase extraction SP:SAMPLEPREP_SUMMARY protocol using methyl tert-butyl ether (MTBE) and methanol as a non-polar and SP:SAMPLEPREP_SUMMARY polar extraction solvent and water as a phase separation solvent. The polar SP:SAMPLEPREP_SUMMARY phase was used for metabolomics and non-polar phase for lipidomics studies. The SP:SAMPLEPREP_SUMMARY MTBE method was introduced by Matayash 2008 which is modified and optimized. SP:SAMPLEPREP_SUMMARY Briefly, 100 ml of ice-cold methanol and 300 ml of ice-cold MTBE was added each SP:SAMPLEPREP_SUMMARY PBMC pellet to extract polar and non-polar lipid molecules, respectively. For a SP:SAMPLEPREP_SUMMARY phase separation, 100 ml of ice-cold water was used. 4 μl of IS solution SP:SAMPLEPREP_SUMMARY prepared by mixing 0.12 mL of 1 M D-Glucose-13C6, 0.2 mL of 5 mM SP:SAMPLEPREP_SUMMARY Caffeine-3-methyl-13C, 0.6 mL of 10 mM L-Methionine-13C5, 0.6 mL of 20 mM SP:SAMPLEPREP_SUMMARY L-Glutamic acid-13C5, 0.8 mL of 10 mM Uracil-15N2, 4 mL of 2 mM L-Tyrosine-15N SP:SAMPLEPREP_SUMMARY and 3.68 mL water in 15-mL tube was added in each sample as spike-in controls SP:SAMPLEPREP_SUMMARY for polar phase extraction. 10 ml of stable isotope labeled standards (Avanti SP:SAMPLEPREP_SUMMARY SPLASH Lipidomix), representing differing lipid classes, were added to each SP:SAMPLEPREP_SUMMARY sample to use as a spike ins quality control for non-polar phase extraction. All SP:SAMPLEPREP_SUMMARY samples were vortexed (Vortex-Genie 2, Scientific Industries, cat. no. SI-0236) SP:SAMPLEPREP_SUMMARY and incubated with shaking ((Eppendorf Thermo Mixer C) at 1000 rpm for SP:SAMPLEPREP_SUMMARY 20 min at 4 °C followed by centrifugation at 4 °C for 15 min at SP:SAMPLEPREP_SUMMARY 20,817 × g (Centrifuge 5430 R, Eppendorf). 100 ml of lower polar phase for SP:SAMPLEPREP_SUMMARY metabolomics were transferred to 1.5 mL autosampler vial and 3 ml injected SP:SAMPLEPREP_SUMMARY directly into UHPLC-MS. 250 ml of upper non-polar MTBE phase was transferred to SP:SAMPLEPREP_SUMMARY new tube and dried for 2 hrs at Labconco CentriVap Centrifugal Vacuum SP:SAMPLEPREP_SUMMARY Concentrator (CentriVap Benchtop Centrifugal Vacuum Concentrator with acrylic SP:SAMPLEPREP_SUMMARY lid, Labconco Corporation, cat. no. 7810010), followed by resuspending in 70 ml SP:SAMPLEPREP_SUMMARY of methanol:toulene (8:1, v/v) solution. 3 ml of reconstituted solution was SP:SAMPLEPREP_SUMMARY injected into UHPLC-MS. For quality control (QC) and assurance (QA), 10 ml of SP:SAMPLEPREP_SUMMARY methanol extract from each sample of batch 1 was collected and pooled together SP:SAMPLEPREP_SUMMARY to prepare QC sample for polar phase metabolomics. Similarly, 10 ml of SP:SAMPLEPREP_SUMMARY reconstituted methanol:toluene (8:1, v/v) solution from each sample of batch 1 SP:SAMPLEPREP_SUMMARY was collected and pooled together to prepare QC sample to be used for non-polar SP:SAMPLEPREP_SUMMARY phase lipidomics. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY The chromatographic separations were performed using Thermo ScientificTM CH:CHROMATOGRAPHY_SUMMARY TranscendTM Duo LX-2 UHPLC system interfaced with high resolution Thermo CH:CHROMATOGRAPHY_SUMMARY ScientificTM Orbitrap ID-XTM TribidTM mass spectrometer with a HESI ionization CH:CHROMATOGRAPHY_SUMMARY source, using both positive and negative ionization mode with a run time of 8.5 CH:CHROMATOGRAPHY_SUMMARY min for polar and 12 min for non-polar extract. All samples were maintained at 4 CH:CHROMATOGRAPHY_SUMMARY °C in the autosampler. Data were acquired for polar and non-polar extract using CH:CHROMATOGRAPHY_SUMMARY HILIC, respectively in full scan mode with mass resolution of 60,000. An CH:CHROMATOGRAPHY_SUMMARY AccucoreTM-150-Amide HILIC column (2.6 mm, 2.1 mm x 100 mm) embedded with CH:CHROMATOGRAPHY_SUMMARY Accucore-150-Amide-HILIC guard column (10 × 2.1 mm, 2.6 μm) (Thermo Fisher CH:CHROMATOGRAPHY_SUMMARY Scientific, MA, USA. Cat. 16726-012105) was used for polar extract. 10 mM CH:CHROMATOGRAPHY_SUMMARY ammonium acetate in acetonitrile:water (95:5, v/v) with 0.1% acetic acid as CH:CHROMATOGRAPHY_SUMMARY mobile phase A and 10 mM ammonium acetate in acetonitrile:water (50:50, v/v) CH:CHROMATOGRAPHY_SUMMARY with 0.1% acetic acid as mobile phase B were used for HILIC method. For HILIC CH:CHROMATOGRAPHY_SUMMARY acquisition, following gradient was applied at a flow rate of 0.55 ml/min: 0-0.2 CH:CHROMATOGRAPHY_SUMMARY min: 0% B, 0.20-8.75 min: 98% B, and 11.25 min for cleaning and equilibration of CH:CHROMATOGRAPHY_SUMMARY column. Mass spectrometry data were collected with the following MS settings: CH:CHROMATOGRAPHY_SUMMARY mass range, 100-1700 m/z for lipidomics and 60-1000 for metabolomics; spray CH:CHROMATOGRAPHY_SUMMARY voltage, 3200 V (ESI+), 2800 V (ESI-); sheath gas, 45 Arb; auxiliary gas, 20 CH:CHROMATOGRAPHY_SUMMARY Arb; sweep gas, 1 Arb; ion transfer tube temperature, 325 °C; vaporizer CH:CHROMATOGRAPHY_SUMMARY temperature, 325 °C; full scan mass resolution, 60,000 (MS1); normalized AGC CH:CHROMATOGRAPHY_SUMMARY target (%), 25; maximum injection time, 100 ms. Data dependent fragmentation CH:CHROMATOGRAPHY_SUMMARY (dd-MS/MS) parameters for each polarity as follows: isolation window (m/z), 1.2; CH:CHROMATOGRAPHY_SUMMARY stepped HCD collision energy (%), 20,40,80; dd-MS/MS resolution, 30,000; CH:CHROMATOGRAPHY_SUMMARY normalized AGC target (%), 20; maximum injection time (ms), 54; micro scan, 1; CH:CHROMATOGRAPHY_SUMMARY cycle time (sec), 1.2. A full scan data-dependent MS2 (ddMS2) method was CH:CHROMATOGRAPHY_SUMMARY utilized to collect MS2 spectra for identification of compounds. CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Thermo Accucore HILIC (100 x 2.1mm,2.6um) CH:COLUMN_TEMPERATURE 45 CH:FLOW_GRADIENT 0-0.2 min: 0% B, 0.20-8.75 min: 98% B, and 11.25 min for cleaning and CH:FLOW_GRADIENT equilibration of column CH:FLOW_RATE 0.55 ml/min CH:SOLVENT_A 95% acetonitrile/5% water; 0.1% acetic acid; 10 mM ammonium acetate CH:SOLVENT_B 50% acetonitrile/50% water; 0.1% acetic acid; 10 mM ammonium acetate CH:CHROMATOGRAPHY_TYPE HILIC #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Orbitrap ID-X tribrid MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:MS_COMMENTS Mass spectrometry data were collected with the following MS settings: mass MS:MS_COMMENTS range, 100-1700 m/z for lipidomics and 60-1000 for metabolomics; spray voltage, MS:MS_COMMENTS 3200 V (ESI+), 2800 V (ESI-); sheath gas, 45 Arb; auxiliary gas, 20 Arb; sweep MS:MS_COMMENTS gas, 1 Arb; ion transfer tube temperature, 325 °C; vaporizer temperature, 325 MS:MS_COMMENTS °C; full scan mass resolution, 60,000 (MS1); normalized AGC target (%), 25; MS:MS_COMMENTS maximum injection time, 100 ms. Data dependent fragmentation (dd-MS/MS) MS:MS_COMMENTS parameters for each polarity as follows: isolation window (m/z), 1.2; stepped MS:MS_COMMENTS HCD collision energy (%), 20,40,80; dd-MS/MS resolution, 30,000; normalized AGC MS:MS_COMMENTS target (%), 20; maximum injection time (ms), 54; micro scan, 1; cycle time MS:MS_COMMENTS (sec), 1.2. A full scan data-dependent MS2 (ddMS2) method was utilized to MS:MS_COMMENTS collect MS2 spectra. MS:ION_MODE NEGATIVE MS:MS_RESULTS_FILE ST003075_AN005033_Results.txt UNITS:peak intensity Has m/z:Yes Has RT:Yes RT units:Seconds #END