#METABOLOMICS WORKBENCH Xinyu_Zhang_20200818_170706 DATATRACK_ID:2129 STUDY_ID:ST001450 ANALYSIS_ID:AN002422 PROJECT_ID:PR000996 VERSION 1 CREATED_ON August 21, 2020, 11:29 am #PROJECT PR:PROJECT_TITLE Five Easy Metrics of Data Quality for LC-MS based Global Metabolomics PR:PROJECT_TYPE MS global profiling PR:PROJECT_SUMMARY Data quality in global metabolomics is of great importance for biomarker PR:PROJECT_SUMMARY discovery and systems biology studies. However, comprehensive metrics and PR:PROJECT_SUMMARY methods to evaluate and compare the data quality of global metabolomics data PR:PROJECT_SUMMARY sets are lacking. In this work, we combine newly developed metrics, along with PR:PROJECT_SUMMARY well-known measures, to comprehensively and quantitatively characterize the data PR:PROJECT_SUMMARY quality across two similar LC-MS platforms, with the goal of providing an PR:PROJECT_SUMMARY efficient and improved ability to evaluate the data quality in global metabolite PR:PROJECT_SUMMARY profiling experiments. A pooled human serum sample was run 50 times on two PR:PROJECT_SUMMARY high-resolution LC-QTOF-MS platforms to provide profile and centroid MS data. PR:PROJECT_SUMMARY These data were processed using Progenesis Qi software and then analyzed using PR:PROJECT_SUMMARY five important data quality measures, including retention time drift, compound PR:PROJECT_SUMMARY coverage, missing values and MS reproducibility (2 measures). The coverage was PR:PROJECT_SUMMARY fit to a Gamma distribution versus compound abundance, which was normalized to PR:PROJECT_SUMMARY allow comparison of different platforms. To evaluate missing values, PR:PROJECT_SUMMARY characteristic curves were obtained by plotting the compound detection PR:PROJECT_SUMMARY percentage versus extraction frequency. To characterize reproducibility, the PR:PROJECT_SUMMARY accumulative coefficient of variation (CV) versus percentage of total compounds PR:PROJECT_SUMMARY detected and CV vs intra-class correlation coefficient (ICC) were investigated. PR:PROJECT_SUMMARY Key findings include significantly better performance using profile mode data PR:PROJECT_SUMMARY compared to centroid mode as well quantitatively better performance from the PR:PROJECT_SUMMARY newer, higher resolution instrument. A summary of the results given in tabulated PR:PROJECT_SUMMARY form gives a snapshot of the experimental results and provides a template to PR:PROJECT_SUMMARY evaluate the global metabolite profiling workflow. In total, these measures give PR:PROJECT_SUMMARY a good overall view of data quality in global profiling and allow comparisons of PR:PROJECT_SUMMARY data acquisition strategies and platforms as well as optimization of parameters. PR:INSTITUTE University of Washington PR:DEPARTMENT Anesthesiology and Pain PR:LABORATORY Daniel Raftery PR:LAST_NAME Zhang PR:FIRST_NAME Xinyu PR:ADDRESS 850 Republican Street, Seattle, WA, 98109, USA PR:EMAIL xinyu.z@live.com PR:PHONE 8505672757 #STUDY ST:STUDY_TITLE Five Easy Metrics of Data Quality for LC-MS based Global Metabolomics ST:STUDY_SUMMARY Data quality in global metabolomics is of great importance for biomarker ST:STUDY_SUMMARY discovery and systems biology studies. However, comprehensive metrics and ST:STUDY_SUMMARY methods to evaluate and compare the data quality of global metabolomics data ST:STUDY_SUMMARY sets are lacking. In this work, we combine newly developed metrics, along with ST:STUDY_SUMMARY well-known measures, to comprehensively and quantitatively characterize the data ST:STUDY_SUMMARY quality across two similar LC-MS platforms, with the goal of providing an ST:STUDY_SUMMARY efficient and improved ability to evaluate the data quality in global metabolite ST:STUDY_SUMMARY profiling experiments. A pooled human serum sample was run 50 times on two ST:STUDY_SUMMARY high-resolution LC-QTOF-MS platforms to provide profile and centroid MS data. ST:STUDY_SUMMARY These data were processed using Progenesis Qi software and then analyzed using ST:STUDY_SUMMARY five important data quality measures, including retention time drift, compound ST:STUDY_SUMMARY coverage, missing values and MS reproducibility (2 measures). The coverage was ST:STUDY_SUMMARY fit to a Gamma distribution versus compound abundance, which was normalized to ST:STUDY_SUMMARY allow comparison of different platforms. To evaluate missing values, ST:STUDY_SUMMARY characteristic curves were obtained by plotting the compound detection ST:STUDY_SUMMARY percentage versus extraction frequency. To characterize reproducibility, the ST:STUDY_SUMMARY accumulative coefficient of variation (CV) versus percentage of total compounds ST:STUDY_SUMMARY detected and CV vs intra-class correlation coefficient (ICC) were investigated. ST:STUDY_SUMMARY Key findings include significantly better performance using profile mode data ST:STUDY_SUMMARY compared to centroid mode as well quantitatively better performance from the ST:STUDY_SUMMARY newer, higher resolution instrument. A summary of the results given in tabulated ST:STUDY_SUMMARY form gives a snapshot of the experimental results and provides a template to ST:STUDY_SUMMARY evaluate the global metabolite profiling workflow. In total, these measures give ST:STUDY_SUMMARY a good overall view of data quality in global profiling and allow comparisons of ST:STUDY_SUMMARY data acquisition strategies and platforms as well as optimization of parameters. ST:INSTITUTE University of Washington ST:DEPARTMENT Anesthesiology and Pain ST:LABORATORY Daniel Raftery ST:LAST_NAME Zhang ST:FIRST_NAME Xinyu ST:ADDRESS 850 Republican Street, Seattle, Washington 98109, United States ST:EMAIL xinyu.z@live.com ST:PHONE 850-567-2757 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #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 - 1 Data type:Agilent 6520 profile data RAW_FILE_NAME=1 SUBJECT_SAMPLE_FACTORS - 2 Data type:Agilent 6520 profile data RAW_FILE_NAME=2 SUBJECT_SAMPLE_FACTORS - 3 Data type:Agilent 6520 profile data RAW_FILE_NAME=3 SUBJECT_SAMPLE_FACTORS - 4 Data type:Agilent 6520 profile data RAW_FILE_NAME=4 SUBJECT_SAMPLE_FACTORS - 5 Data type:Agilent 6520 profile data RAW_FILE_NAME=5 SUBJECT_SAMPLE_FACTORS - 6 Data type:Agilent 6520 profile data RAW_FILE_NAME=6 SUBJECT_SAMPLE_FACTORS - 7 Data type:Agilent 6520 profile data RAW_FILE_NAME=7 SUBJECT_SAMPLE_FACTORS - 8 Data type:Agilent 6520 profile data RAW_FILE_NAME=8 SUBJECT_SAMPLE_FACTORS - 9 Data type:Agilent 6520 profile data RAW_FILE_NAME=9 SUBJECT_SAMPLE_FACTORS - 10 Data type:Agilent 6520 profile data RAW_FILE_NAME=10 SUBJECT_SAMPLE_FACTORS - 11 Data type:Agilent 6520 profile data RAW_FILE_NAME=11 SUBJECT_SAMPLE_FACTORS - 12 Data type:Agilent 6520 profile data RAW_FILE_NAME=12 SUBJECT_SAMPLE_FACTORS - 13 Data type:Agilent 6520 profile data RAW_FILE_NAME=13 SUBJECT_SAMPLE_FACTORS - 14 Data type:Agilent 6520 profile data RAW_FILE_NAME=14 SUBJECT_SAMPLE_FACTORS - 15 Data type:Agilent 6520 profile data RAW_FILE_NAME=15 SUBJECT_SAMPLE_FACTORS - 16 Data type:Agilent 6520 profile data RAW_FILE_NAME=16 SUBJECT_SAMPLE_FACTORS - 17 Data type:Agilent 6520 profile data RAW_FILE_NAME=17 SUBJECT_SAMPLE_FACTORS - 18 Data type:Agilent 6520 profile data RAW_FILE_NAME=18 SUBJECT_SAMPLE_FACTORS - 19 Data type:Agilent 6520 profile data RAW_FILE_NAME=19 SUBJECT_SAMPLE_FACTORS - 20 Data type:Agilent 6520 profile data RAW_FILE_NAME=20 SUBJECT_SAMPLE_FACTORS - 21 Data type:Agilent 6520 profile data RAW_FILE_NAME=21 SUBJECT_SAMPLE_FACTORS - 22 Data type:Agilent 6520 profile data RAW_FILE_NAME=22 SUBJECT_SAMPLE_FACTORS - 23 Data type:Agilent 6520 profile data RAW_FILE_NAME=23 SUBJECT_SAMPLE_FACTORS - 24 Data type:Agilent 6520 profile data RAW_FILE_NAME=24 SUBJECT_SAMPLE_FACTORS - 25 Data type:Agilent 6520 profile data RAW_FILE_NAME=25 SUBJECT_SAMPLE_FACTORS - 26 Data type:Agilent 6520 profile data RAW_FILE_NAME=26 SUBJECT_SAMPLE_FACTORS - 27 Data type:Agilent 6520 profile data RAW_FILE_NAME=27 SUBJECT_SAMPLE_FACTORS - 28 Data type:Agilent 6520 profile data RAW_FILE_NAME=28 SUBJECT_SAMPLE_FACTORS - 29 Data type:Agilent 6520 profile data RAW_FILE_NAME=29 SUBJECT_SAMPLE_FACTORS - 30 Data type:Agilent 6520 profile data RAW_FILE_NAME=30 SUBJECT_SAMPLE_FACTORS - 31 Data type:Agilent 6520 profile data RAW_FILE_NAME=31 SUBJECT_SAMPLE_FACTORS - 32 Data type:Agilent 6520 profile data RAW_FILE_NAME=32 SUBJECT_SAMPLE_FACTORS - 33 Data type:Agilent 6520 profile data RAW_FILE_NAME=33 SUBJECT_SAMPLE_FACTORS - 34 Data type:Agilent 6520 profile data RAW_FILE_NAME=34 SUBJECT_SAMPLE_FACTORS - 35 Data type:Agilent 6520 profile data RAW_FILE_NAME=35 SUBJECT_SAMPLE_FACTORS - 36 Data type:Agilent 6520 profile data RAW_FILE_NAME=36 SUBJECT_SAMPLE_FACTORS - 37 Data type:Agilent 6520 profile data RAW_FILE_NAME=37 SUBJECT_SAMPLE_FACTORS - 38 Data type:Agilent 6520 profile data RAW_FILE_NAME=38 SUBJECT_SAMPLE_FACTORS - 39 Data type:Agilent 6520 profile data RAW_FILE_NAME=39 SUBJECT_SAMPLE_FACTORS - 40 Data type:Agilent 6520 profile data RAW_FILE_NAME=40 SUBJECT_SAMPLE_FACTORS - 41 Data type:Agilent 6520 profile data RAW_FILE_NAME=41 SUBJECT_SAMPLE_FACTORS - 42 Data type:Agilent 6520 profile data RAW_FILE_NAME=42 SUBJECT_SAMPLE_FACTORS - 43 Data type:Agilent 6520 profile data RAW_FILE_NAME=43 SUBJECT_SAMPLE_FACTORS - 44 Data type:Agilent 6520 profile data RAW_FILE_NAME=44 SUBJECT_SAMPLE_FACTORS - 45 Data type:Agilent 6520 profile data RAW_FILE_NAME=45 SUBJECT_SAMPLE_FACTORS - 46 Data type:Agilent 6520 profile data RAW_FILE_NAME=46 SUBJECT_SAMPLE_FACTORS - 47 Data type:Agilent 6520 profile data RAW_FILE_NAME=47 SUBJECT_SAMPLE_FACTORS - 48 Data type:Agilent 6520 profile data RAW_FILE_NAME=48 SUBJECT_SAMPLE_FACTORS - 49 Data type:Agilent 6520 profile data RAW_FILE_NAME=49 SUBJECT_SAMPLE_FACTORS - 50 Data type:Agilent 6520 profile data RAW_FILE_NAME=50 SUBJECT_SAMPLE_FACTORS - 51 Data type:Agilent 6520 centroid data RAW_FILE_NAME=51 SUBJECT_SAMPLE_FACTORS - 52 Data type:Agilent 6520 centroid data RAW_FILE_NAME=52 SUBJECT_SAMPLE_FACTORS - 53 Data type:Agilent 6520 centroid data RAW_FILE_NAME=53 SUBJECT_SAMPLE_FACTORS - 54 Data type:Agilent 6520 centroid data RAW_FILE_NAME=54 SUBJECT_SAMPLE_FACTORS - 55 Data type:Agilent 6520 centroid data RAW_FILE_NAME=55 SUBJECT_SAMPLE_FACTORS - 56 Data type:Agilent 6520 centroid data RAW_FILE_NAME=56 SUBJECT_SAMPLE_FACTORS - 57 Data type:Agilent 6520 centroid data RAW_FILE_NAME=57 SUBJECT_SAMPLE_FACTORS - 58 Data type:Agilent 6520 centroid data RAW_FILE_NAME=58 SUBJECT_SAMPLE_FACTORS - 59 Data type:Agilent 6520 centroid data RAW_FILE_NAME=59 SUBJECT_SAMPLE_FACTORS - 60 Data type:Agilent 6520 centroid data RAW_FILE_NAME=60 SUBJECT_SAMPLE_FACTORS - 61 Data type:Agilent 6520 centroid data RAW_FILE_NAME=61 SUBJECT_SAMPLE_FACTORS - 62 Data type:Agilent 6520 centroid data RAW_FILE_NAME=62 SUBJECT_SAMPLE_FACTORS - 63 Data type:Agilent 6520 centroid data RAW_FILE_NAME=63 SUBJECT_SAMPLE_FACTORS - 64 Data type:Agilent 6520 centroid data RAW_FILE_NAME=64 SUBJECT_SAMPLE_FACTORS - 65 Data type:Agilent 6520 centroid data RAW_FILE_NAME=65 SUBJECT_SAMPLE_FACTORS - 66 Data type:Agilent 6520 centroid data RAW_FILE_NAME=66 SUBJECT_SAMPLE_FACTORS - 67 Data type:Agilent 6520 centroid data RAW_FILE_NAME=67 SUBJECT_SAMPLE_FACTORS - 68 Data type:Agilent 6520 centroid data RAW_FILE_NAME=68 SUBJECT_SAMPLE_FACTORS - 69 Data type:Agilent 6520 centroid data RAW_FILE_NAME=69 SUBJECT_SAMPLE_FACTORS - 70 Data type:Agilent 6520 centroid data RAW_FILE_NAME=70 SUBJECT_SAMPLE_FACTORS - 71 Data type:Agilent 6520 centroid data RAW_FILE_NAME=71 SUBJECT_SAMPLE_FACTORS - 72 Data type:Agilent 6520 centroid data RAW_FILE_NAME=72 SUBJECT_SAMPLE_FACTORS - 73 Data type:Agilent 6520 centroid data RAW_FILE_NAME=73 SUBJECT_SAMPLE_FACTORS - 74 Data type:Agilent 6520 centroid data RAW_FILE_NAME=74 SUBJECT_SAMPLE_FACTORS - 75 Data type:Agilent 6520 centroid data RAW_FILE_NAME=75 SUBJECT_SAMPLE_FACTORS - 76 Data type:Agilent 6520 centroid data RAW_FILE_NAME=76 SUBJECT_SAMPLE_FACTORS - 77 Data type:Agilent 6520 centroid data RAW_FILE_NAME=77 SUBJECT_SAMPLE_FACTORS - 78 Data type:Agilent 6520 centroid data RAW_FILE_NAME=78 SUBJECT_SAMPLE_FACTORS - 79 Data type:Agilent 6520 centroid data RAW_FILE_NAME=79 SUBJECT_SAMPLE_FACTORS - 80 Data type:Agilent 6520 centroid data RAW_FILE_NAME=80 SUBJECT_SAMPLE_FACTORS - 81 Data type:Agilent 6520 centroid data RAW_FILE_NAME=81 SUBJECT_SAMPLE_FACTORS - 82 Data type:Agilent 6520 centroid data RAW_FILE_NAME=82 SUBJECT_SAMPLE_FACTORS - 83 Data type:Agilent 6520 centroid data RAW_FILE_NAME=83 SUBJECT_SAMPLE_FACTORS - 84 Data type:Agilent 6520 centroid data RAW_FILE_NAME=84 SUBJECT_SAMPLE_FACTORS - 85 Data type:Agilent 6520 centroid data RAW_FILE_NAME=85 SUBJECT_SAMPLE_FACTORS - 86 Data type:Agilent 6520 centroid data RAW_FILE_NAME=86 SUBJECT_SAMPLE_FACTORS - 87 Data type:Agilent 6520 centroid data RAW_FILE_NAME=87 SUBJECT_SAMPLE_FACTORS - 88 Data type:Agilent 6520 centroid data RAW_FILE_NAME=88 SUBJECT_SAMPLE_FACTORS - 89 Data type:Agilent 6520 centroid data RAW_FILE_NAME=89 SUBJECT_SAMPLE_FACTORS - 90 Data type:Agilent 6520 centroid data RAW_FILE_NAME=90 SUBJECT_SAMPLE_FACTORS - 91 Data type:Agilent 6520 centroid data RAW_FILE_NAME=91 SUBJECT_SAMPLE_FACTORS - 92 Data type:Agilent 6520 centroid data RAW_FILE_NAME=92 SUBJECT_SAMPLE_FACTORS - 93 Data type:Agilent 6520 centroid data RAW_FILE_NAME=93 SUBJECT_SAMPLE_FACTORS - 94 Data type:Agilent 6520 centroid data RAW_FILE_NAME=94 SUBJECT_SAMPLE_FACTORS - 95 Data type:Agilent 6520 centroid data RAW_FILE_NAME=95 SUBJECT_SAMPLE_FACTORS - 96 Data type:Agilent 6520 centroid data RAW_FILE_NAME=96 SUBJECT_SAMPLE_FACTORS - 97 Data type:Agilent 6520 centroid data RAW_FILE_NAME=97 SUBJECT_SAMPLE_FACTORS - 98 Data type:Agilent 6520 centroid data RAW_FILE_NAME=98 SUBJECT_SAMPLE_FACTORS - 99 Data type:Agilent 6520 centroid data RAW_FILE_NAME=99 SUBJECT_SAMPLE_FACTORS - 100 Data type:Agilent 6520 centroid data RAW_FILE_NAME=100 SUBJECT_SAMPLE_FACTORS - 101 Data type:Agilent 6545 profile data RAW_FILE_NAME=101 SUBJECT_SAMPLE_FACTORS - 102 Data type:Agilent 6545 profile data RAW_FILE_NAME=102 SUBJECT_SAMPLE_FACTORS - 103 Data type:Agilent 6545 profile data RAW_FILE_NAME=103 SUBJECT_SAMPLE_FACTORS - 104 Data type:Agilent 6545 profile data RAW_FILE_NAME=104 SUBJECT_SAMPLE_FACTORS - 105 Data type:Agilent 6545 profile data RAW_FILE_NAME=105 SUBJECT_SAMPLE_FACTORS - 106 Data type:Agilent 6545 profile data RAW_FILE_NAME=106 SUBJECT_SAMPLE_FACTORS - 107 Data type:Agilent 6545 profile data RAW_FILE_NAME=107 SUBJECT_SAMPLE_FACTORS - 108 Data type:Agilent 6545 profile data RAW_FILE_NAME=108 SUBJECT_SAMPLE_FACTORS - 109 Data type:Agilent 6545 profile data RAW_FILE_NAME=109 SUBJECT_SAMPLE_FACTORS - 110 Data type:Agilent 6545 profile data RAW_FILE_NAME=110 SUBJECT_SAMPLE_FACTORS - 111 Data type:Agilent 6545 profile data RAW_FILE_NAME=111 SUBJECT_SAMPLE_FACTORS - 112 Data type:Agilent 6545 profile data RAW_FILE_NAME=112 SUBJECT_SAMPLE_FACTORS - 113 Data type:Agilent 6545 profile data RAW_FILE_NAME=113 SUBJECT_SAMPLE_FACTORS - 114 Data type:Agilent 6545 profile data RAW_FILE_NAME=114 SUBJECT_SAMPLE_FACTORS - 115 Data type:Agilent 6545 profile data RAW_FILE_NAME=115 SUBJECT_SAMPLE_FACTORS - 116 Data type:Agilent 6545 profile data RAW_FILE_NAME=116 SUBJECT_SAMPLE_FACTORS - 117 Data type:Agilent 6545 profile data RAW_FILE_NAME=117 SUBJECT_SAMPLE_FACTORS - 118 Data type:Agilent 6545 profile data RAW_FILE_NAME=118 SUBJECT_SAMPLE_FACTORS - 119 Data type:Agilent 6545 profile data RAW_FILE_NAME=119 SUBJECT_SAMPLE_FACTORS - 120 Data type:Agilent 6545 profile data RAW_FILE_NAME=120 SUBJECT_SAMPLE_FACTORS - 121 Data type:Agilent 6545 profile data RAW_FILE_NAME=121 SUBJECT_SAMPLE_FACTORS - 122 Data type:Agilent 6545 profile data RAW_FILE_NAME=122 SUBJECT_SAMPLE_FACTORS - 123 Data type:Agilent 6545 profile data RAW_FILE_NAME=123 SUBJECT_SAMPLE_FACTORS - 124 Data type:Agilent 6545 profile data RAW_FILE_NAME=124 SUBJECT_SAMPLE_FACTORS - 125 Data type:Agilent 6545 profile data RAW_FILE_NAME=125 SUBJECT_SAMPLE_FACTORS - 126 Data type:Agilent 6545 profile data RAW_FILE_NAME=126 SUBJECT_SAMPLE_FACTORS - 127 Data type:Agilent 6545 profile data RAW_FILE_NAME=127 SUBJECT_SAMPLE_FACTORS - 128 Data type:Agilent 6545 profile data RAW_FILE_NAME=128 SUBJECT_SAMPLE_FACTORS - 129 Data type:Agilent 6545 profile data RAW_FILE_NAME=129 SUBJECT_SAMPLE_FACTORS - 130 Data type:Agilent 6545 profile data RAW_FILE_NAME=130 SUBJECT_SAMPLE_FACTORS - 131 Data type:Agilent 6545 profile data RAW_FILE_NAME=131 SUBJECT_SAMPLE_FACTORS - 132 Data type:Agilent 6545 profile data RAW_FILE_NAME=132 SUBJECT_SAMPLE_FACTORS - 133 Data type:Agilent 6545 profile data RAW_FILE_NAME=133 SUBJECT_SAMPLE_FACTORS - 134 Data type:Agilent 6545 profile data RAW_FILE_NAME=134 SUBJECT_SAMPLE_FACTORS - 135 Data type:Agilent 6545 profile data RAW_FILE_NAME=135 SUBJECT_SAMPLE_FACTORS - 136 Data type:Agilent 6545 profile data RAW_FILE_NAME=136 SUBJECT_SAMPLE_FACTORS - 137 Data type:Agilent 6545 profile data RAW_FILE_NAME=137 SUBJECT_SAMPLE_FACTORS - 138 Data type:Agilent 6545 profile data RAW_FILE_NAME=138 SUBJECT_SAMPLE_FACTORS - 139 Data type:Agilent 6545 profile data RAW_FILE_NAME=139 SUBJECT_SAMPLE_FACTORS - 140 Data type:Agilent 6545 profile data RAW_FILE_NAME=140 SUBJECT_SAMPLE_FACTORS - 141 Data type:Agilent 6545 profile data RAW_FILE_NAME=141 SUBJECT_SAMPLE_FACTORS - 142 Data type:Agilent 6545 profile data RAW_FILE_NAME=142 SUBJECT_SAMPLE_FACTORS - 143 Data type:Agilent 6545 profile data RAW_FILE_NAME=143 SUBJECT_SAMPLE_FACTORS - 144 Data type:Agilent 6545 profile data RAW_FILE_NAME=144 SUBJECT_SAMPLE_FACTORS - 145 Data type:Agilent 6545 profile data RAW_FILE_NAME=145 SUBJECT_SAMPLE_FACTORS - 146 Data type:Agilent 6545 profile data RAW_FILE_NAME=146 SUBJECT_SAMPLE_FACTORS - 147 Data type:Agilent 6545 profile data RAW_FILE_NAME=147 SUBJECT_SAMPLE_FACTORS - 148 Data type:Agilent 6545 profile data RAW_FILE_NAME=148 SUBJECT_SAMPLE_FACTORS - 149 Data type:Agilent 6545 profile data RAW_FILE_NAME=149 SUBJECT_SAMPLE_FACTORS - 150 Data type:Agilent 6545 profile data RAW_FILE_NAME=150 SUBJECT_SAMPLE_FACTORS - 151 Data type:Agilent 6545 centroid data RAW_FILE_NAME=151 SUBJECT_SAMPLE_FACTORS - 152 Data type:Agilent 6545 centroid data RAW_FILE_NAME=152 SUBJECT_SAMPLE_FACTORS - 153 Data type:Agilent 6545 centroid data RAW_FILE_NAME=153 SUBJECT_SAMPLE_FACTORS - 154 Data type:Agilent 6545 centroid data RAW_FILE_NAME=154 SUBJECT_SAMPLE_FACTORS - 155 Data type:Agilent 6545 centroid data RAW_FILE_NAME=155 SUBJECT_SAMPLE_FACTORS - 156 Data type:Agilent 6545 centroid data RAW_FILE_NAME=156 SUBJECT_SAMPLE_FACTORS - 157 Data type:Agilent 6545 centroid data RAW_FILE_NAME=157 SUBJECT_SAMPLE_FACTORS - 158 Data type:Agilent 6545 centroid data RAW_FILE_NAME=158 SUBJECT_SAMPLE_FACTORS - 159 Data type:Agilent 6545 centroid data RAW_FILE_NAME=159 SUBJECT_SAMPLE_FACTORS - 160 Data type:Agilent 6545 centroid data RAW_FILE_NAME=160 SUBJECT_SAMPLE_FACTORS - 161 Data type:Agilent 6545 centroid data RAW_FILE_NAME=161 SUBJECT_SAMPLE_FACTORS - 162 Data type:Agilent 6545 centroid data RAW_FILE_NAME=162 SUBJECT_SAMPLE_FACTORS - 163 Data type:Agilent 6545 centroid data RAW_FILE_NAME=163 SUBJECT_SAMPLE_FACTORS - 164 Data type:Agilent 6545 centroid data RAW_FILE_NAME=164 SUBJECT_SAMPLE_FACTORS - 165 Data type:Agilent 6545 centroid data RAW_FILE_NAME=165 SUBJECT_SAMPLE_FACTORS - 166 Data type:Agilent 6545 centroid data RAW_FILE_NAME=166 SUBJECT_SAMPLE_FACTORS - 167 Data type:Agilent 6545 centroid data RAW_FILE_NAME=167 SUBJECT_SAMPLE_FACTORS - 168 Data type:Agilent 6545 centroid data RAW_FILE_NAME=168 SUBJECT_SAMPLE_FACTORS - 169 Data type:Agilent 6545 centroid data RAW_FILE_NAME=169 SUBJECT_SAMPLE_FACTORS - 170 Data type:Agilent 6545 centroid data RAW_FILE_NAME=170 SUBJECT_SAMPLE_FACTORS - 171 Data type:Agilent 6545 centroid data RAW_FILE_NAME=171 SUBJECT_SAMPLE_FACTORS - 172 Data type:Agilent 6545 centroid data RAW_FILE_NAME=172 SUBJECT_SAMPLE_FACTORS - 173 Data type:Agilent 6545 centroid data RAW_FILE_NAME=173 SUBJECT_SAMPLE_FACTORS - 174 Data type:Agilent 6545 centroid data RAW_FILE_NAME=174 SUBJECT_SAMPLE_FACTORS - 175 Data type:Agilent 6545 centroid data RAW_FILE_NAME=175 SUBJECT_SAMPLE_FACTORS - 176 Data type:Agilent 6545 centroid data RAW_FILE_NAME=176 SUBJECT_SAMPLE_FACTORS - 177 Data type:Agilent 6545 centroid data RAW_FILE_NAME=177 SUBJECT_SAMPLE_FACTORS - 178 Data type:Agilent 6545 centroid data RAW_FILE_NAME=178 SUBJECT_SAMPLE_FACTORS - 179 Data type:Agilent 6545 centroid data RAW_FILE_NAME=179 SUBJECT_SAMPLE_FACTORS - 180 Data type:Agilent 6545 centroid data RAW_FILE_NAME=180 SUBJECT_SAMPLE_FACTORS - 181 Data type:Agilent 6545 centroid data RAW_FILE_NAME=181 SUBJECT_SAMPLE_FACTORS - 182 Data type:Agilent 6545 centroid data RAW_FILE_NAME=182 SUBJECT_SAMPLE_FACTORS - 183 Data type:Agilent 6545 centroid data RAW_FILE_NAME=183 SUBJECT_SAMPLE_FACTORS - 184 Data type:Agilent 6545 centroid data RAW_FILE_NAME=184 SUBJECT_SAMPLE_FACTORS - 185 Data type:Agilent 6545 centroid data RAW_FILE_NAME=185 SUBJECT_SAMPLE_FACTORS - 186 Data type:Agilent 6545 centroid data RAW_FILE_NAME=186 SUBJECT_SAMPLE_FACTORS - 187 Data type:Agilent 6545 centroid data RAW_FILE_NAME=187 SUBJECT_SAMPLE_FACTORS - 188 Data type:Agilent 6545 centroid data RAW_FILE_NAME=188 SUBJECT_SAMPLE_FACTORS - 189 Data type:Agilent 6545 centroid data RAW_FILE_NAME=189 SUBJECT_SAMPLE_FACTORS - 190 Data type:Agilent 6545 centroid data RAW_FILE_NAME=190 SUBJECT_SAMPLE_FACTORS - 191 Data type:Agilent 6545 centroid data RAW_FILE_NAME=191 SUBJECT_SAMPLE_FACTORS - 192 Data type:Agilent 6545 centroid data RAW_FILE_NAME=192 SUBJECT_SAMPLE_FACTORS - 193 Data type:Agilent 6545 centroid data RAW_FILE_NAME=193 SUBJECT_SAMPLE_FACTORS - 194 Data type:Agilent 6545 centroid data RAW_FILE_NAME=194 SUBJECT_SAMPLE_FACTORS - 195 Data type:Agilent 6545 centroid data RAW_FILE_NAME=195 SUBJECT_SAMPLE_FACTORS - 196 Data type:Agilent 6545 centroid data RAW_FILE_NAME=196 SUBJECT_SAMPLE_FACTORS - 197 Data type:Agilent 6545 centroid data RAW_FILE_NAME=197 SUBJECT_SAMPLE_FACTORS - 198 Data type:Agilent 6545 centroid data RAW_FILE_NAME=198 SUBJECT_SAMPLE_FACTORS - 199 Data type:Agilent 6545 centroid data RAW_FILE_NAME=199 SUBJECT_SAMPLE_FACTORS - 200 Data type:Agilent 6545 centroid data RAW_FILE_NAME=200 #COLLECTION CO:COLLECTION_SUMMARY Human serum was frozen at -80 C. CO:SAMPLE_TYPE Blood (serum) #TREATMENT TR:TREATMENT_SUMMARY See sampleprep #SAMPLEPREP SP:SAMPLEPREP_SUMMARY 4 mL frozen commercial pooled human serum (Innovative Research, Novi, MI, USA) SP:SAMPLEPREP_SUMMARY was thawed at 4 °C, vortexed and aliquoted into 50 µL portions in 2 mL SP:SAMPLEPREP_SUMMARY Eppendorf vials. Every 50 µL portion was mixed with 250 µL cold methanol and SP:SAMPLEPREP_SUMMARY vortexed to precipitate proteins.38 After 20 min incubation at −20 °C, these SP:SAMPLEPREP_SUMMARY mixtures were centrifuged at 20,800 x g for 10 min at 4 °C. The supernatants SP:SAMPLEPREP_SUMMARY were transferred into clean 2.0 mL Eppendorf vials and then dried in an SP:SAMPLEPREP_SUMMARY Eppendorf Vacufuge (Brinkmann Instruments, Westbury, NY, USA). The residue in SP:SAMPLEPREP_SUMMARY each Eppendorf vial was reconstituted in 50 µL H2O:ACN (2:3 v/v), vortexed and SP:SAMPLEPREP_SUMMARY centrifuged at 20,800 x g for 10 min at 4 °C. The supernatant in all Eppendorf SP:SAMPLEPREP_SUMMARY vials was pooled into a 5 mL Eppendorf vial, vortexed and centrifuged at xx,xxx SP:SAMPLEPREP_SUMMARY x g (To Dan: I should have used 5000 rpm or a typical rpm in the big centrifuge SP:SAMPLEPREP_SUMMARY in the biosample prep lab) for 10 min at 4 °C to further remove any solid SP:SAMPLEPREP_SUMMARY residue. The resultant supernatant was aliquoted into 50 µL portions in 1.5 mL SP:SAMPLEPREP_SUMMARY Eppendorf vials and stored at −80 °C. Prior to repeated injections to LC-MS SP:SAMPLEPREP_SUMMARY in this work, 8 portions were diluted to 200 µL each with H2O:ACN (2:3 v/v), SP:SAMPLEPREP_SUMMARY pooled into a 2 mL LC vial and vortexed. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY The mobile phase consisted of (A) H2O:ACN (95:5, v/v) with 5 mM ammonium acetate CH:CHROMATOGRAPHY_SUMMARY and 0.1% acetic acid, and (B) H2O:ACN (5:95, v/v), 5 mM ammonium acetate and CH:CHROMATOGRAPHY_SUMMARY 0.1% acetic acid. Gradient elution was performed as follows: 100% mobile phase B CH:CHROMATOGRAPHY_SUMMARY for 1.5 min, 100 to 78% B from 1.5-6.0 min, 78 to 50% B from 6.0-9.0 min, 50% B CH:CHROMATOGRAPHY_SUMMARY from 9.0-15.0 min, restoration to 100% B from 15.0-17.0 min, and continued 100% CH:CHROMATOGRAPHY_SUMMARY B from 17.0-30.0 to equilibrate the LC column. The flow rate was 0.3 mL/min, the CH:CHROMATOGRAPHY_SUMMARY injection volume was 5 µL, followed by an H2O:ACN (5:95, v/v) needle wash for CH:CHROMATOGRAPHY_SUMMARY 10 s, and the column temperature was 35 oC. CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 1260 Infinity CH:COLUMN_NAME Waters XBridge BEH Amide column (15 cm x 2.1 mm, 2.5 µm) #ANALYSIS AN:ANALYSIS_TYPE MS AN:DATA_FORMAT .mzxml (centroid) #MS MS:INSTRUMENT_NAME Agilent 6520 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS The ESI conditions were as follows: Electrospray ion source ESI Agilent Jet MS:MS_COMMENTS Stream Technology in positive ionization mode; voltage 3.8 kV; desolvation MS:MS_COMMENTS temperature 325 °C; cone flow 20 L/h; desolvation gas flow 600 L/h; nebulizer MS:MS_COMMENTS pressure 45 psi, N2 drying gas; MS scan rate of 1.03 spectra/s across the range MS:MS_COMMENTS m/z 60-1000. The software, Progenesis Qi, was used to process raw data. In the MS:MS_COMMENTS results, every compound (feature) had at least two ions, like an ion and its MS:MS_COMMENTS isotope ion or adduct ion. Compounds with single ions were filtered out. If a MS:MS_COMMENTS compound had m/z information only, the m/z was directly used in the compound MS:MS_COMMENTS name. If a compound had neutral mass information, the neutral mass was converted MS:MS_COMMENTS to m/z. MS:MS_RESULTS_FILE ST001450_AN002422_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes #END