Return to study ST002297 main page
MB Sample ID: SA220695
| Local Sample ID: | L22_V6 |
| Subject ID: | SU002383 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003752 | AN003753 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
| Column | Waters Atlantis dC18 (100 x 3mm,3um) | Waters Atlantis dC18 (100 x 3mm,3um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6550 QTOF | Agilent 6550 QTOF |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | peak area (pareto-scaled, log2-transformed, 24h creatinine normalised) | peak area (pareto-scaled, log2-transformed, 24h creatinine normalised) |
MS:
| MS ID: | MS003496 |
| Analysis ID: | AN003752 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | MS acquisition conditions detailed in attached Supplementary Materials. Raw data were mined using the targeted feature extraction function in Masshunter Profinder (build 10.00, Agilent) with mass targets based on chemical formulae of known/predicted phe-tyr pathway metabolites from the customised compound databases described below. A combined compound database was compiled using PCDL Manager (Agilent, build 08.00). Accurate mass retention time (AMRT) matched metabolites were present in our published AMRT database, which was generated from chemical standards using the same LC-QTOF-MS methodology employed here: phenylalanine, phenylethylamine, tyrosine, N-acetyl-tyrosine, tyramine, HPPA, HPLA and HGA. Other established phenylalanine metabolites added to the database for mining by accurate mass alone were hydroxyphenylacetic acid, phenylacetaldehyde, phenylacetamide, phenylacetic acid, phenylacetylglutamine, phenylethylamine, phenyllactic acid and phenylpyruvic acid. The remaining formulae were from non-established but theoretically possible phase 1 and 2 biotransformation products derived from phenylalanine (n=74), tyrosine (n=74), HPPA (n=67) and HPLA (n=67) predicted using the Biotransformation Mass Defects tool (Agilent), in addition to the HGA biotransformation products (n=7) previously established by our group. Feature extraction parameters were accurate mass match window ±5 ppm with addition of matched retention time (RT; window ±0.3 min) for AMRT database metabolites. Allowed ion species were: H+, Na+, and NH4+ in positive polarity, and H− and CHO2- in negative polarity. Charge state range was 1–2, and dimers were allowed. ‘Find by formula’ filters were: score >60 in at least 60 % of samples in at least one sample group. Where compounds were detected in both positive and negative ionisation, the polarity with the clearest signal was selected for further analysis. Extracted peak area intensity data were exported in .csv file format and imported into Mass Profiler Professional (MPP; build 15.1, Agilent), in which all statistical analyses were performed unless stated otherwise. In MPP, all data were log2 transformed and pareto scaled. Urine data were normalised to 24-h creatinine values. QC was performed based on compound signal intensity data from the pooled samples interspersed throughout each analytical sequence. Compounds were retained for subsequent statistical analyses if a) observed in 100 % of replicate injections for at least one sample group pool, and b) peak area coefficient of variation (CV) remained <30% across replicate injections for each sample group pool across batches 1 and 2 combined. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003497 |
| Analysis ID: | AN003753 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | MS acquisition conditions detailed in attached Supplementary Materials. Raw data were mined using the targeted feature extraction function in Masshunter Profinder (build 10.00, Agilent) with mass targets based on chemical formulae of known/predicted phe-tyr pathway metabolites from the customised compound databases described below. A combined compound database was compiled using PCDL Manager (Agilent, build 08.00). Accurate mass retention time (AMRT) matched metabolites were present in our published AMRT database, which was generated from chemical standards using the same LC-QTOF-MS methodology employed here: phenylalanine, phenylethylamine, tyrosine, N-acetyl-tyrosine, tyramine, HPPA, HPLA and HGA. Other established phenylalanine metabolites added to the database for mining by accurate mass alone were hydroxyphenylacetic acid, phenylacetaldehyde, phenylacetamide, phenylacetic acid, phenylacetylglutamine, phenylethylamine, phenyllactic acid and phenylpyruvic acid. The remaining formulae were from non-established but theoretically possible phase 1 and 2 biotransformation products derived from phenylalanine (n=74), tyrosine (n=74), HPPA (n=67) and HPLA (n=67) predicted using the Biotransformation Mass Defects tool (Agilent), in addition to the HGA biotransformation products (n=7) previously established by our group. Feature extraction parameters were accurate mass match window ±5 ppm with addition of matched retention time (RT; window ±0.3 min) for AMRT database metabolites. Allowed ion species were: H+, Na+, and NH4+ in positive polarity, and H− and CHO2- in negative polarity. Charge state range was 1–2, and dimers were allowed. ‘Find by formula’ filters were: score >60 in at least 60 % of samples in at least one sample group. Where compounds were detected in both positive and negative ionisation, the polarity with the clearest signal was selected for further analysis. Extracted peak area intensity data were exported in .csv file format and imported into Mass Profiler Professional (MPP; build 15.1, Agilent), in which all statistical analyses were performed unless stated otherwise. In MPP, all data were log2 transformed and pareto scaled. Urine data were normalised to 24-h creatinine values. QC was performed based on compound signal intensity data from the pooled samples interspersed throughout each analytical sequence. Compounds were retained for subsequent statistical analyses if a) observed in 100 % of replicate injections for at least one sample group pool, and b) peak area coefficient of variation (CV) remained <30% across replicate injections for each sample group pool across batches 1 and 2 combined. |
| Ion Mode: | POSITIVE |
