Summary of Study ST003500
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002146. The data can be accessed directly via it's Project DOI: 10.21228/M8783Z This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
Study ID | ST003500 |
Study Title | A UHPLC-MS/MS Method for Profiling of Urinary Mercapturic Acids using Positive Ion Mode |
Study Summary | We report the first application of a UHPLC-MS/MS method using positive ion mode detection for the unbiased characterization of mercapturic acids. The proposed method utilizes a neutral loss monitoring paradigm to monitor for two diagnostic fragmentation pathways for this class of compound. Using a cohort of 20 nonsmokers and 20 smokers, we detected 180 putative mercapturic acid signatures that exhibited a high degree of reproducibility from the complex urine metabolome background. Following a combination of multivariate and univariate statistics, we found 33 putative mercapturic acids associated with smoking status. |
Institute | University of Minnesota |
Last Name | Murray |
First Name | Kevin |
Address | 2-210 CCRB, 2231 6th St SE, Minneapolis, MN 55455 |
murra668@umn.edu | |
Phone | 612-626-2182 |
Submit Date | 2024-08-01 |
Num Groups | 2 |
Total Subjects | 20 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | LC-MS |
Release Date | 2025-02-03 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
Analysis ID | AN005745 |
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Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Thermo Dionex Ultimate 3000 RS |
Column | Self-packed C18 column Dr. Maisch GmbH ReproSil-PUR (450 mm x 100 µm, 1.9 µm, 120 Å C18aq) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Orbitrap Fusion Lumos Tribrid |
Ion Mode | POSITIVE |
Units | Peak heights |
MS:
MS ID: | MS005468 |
Analysis ID: | AN005745 |
Instrument Name: | Thermo Orbitrap Fusion Lumos Tribrid |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Discovery DDA-CNL-MS3 analyses of experimental samples were performed using full-scan detection followed by data-dependent MS2 acquisition and a conditional neutral loss-triggered MS3 acquisition. All analyses were performed in positive ion mode. Full-scan detection was performed using Orbitrap detection at a resolution of 120,000, AGC targeted setting of 4 × 105, a maximum ion injection time of 50 ms, and an S-Lens RF setting of 40%. Scan ranges of 170 m/z – 600 m/z were used for full-scan detection. MS2 spectra were collected using a DDA design with a 2 sec cycle time in centroid mode with a 15 sec dynamic exclusion list. Fragment spectra were acquired with quadrupole isolation of 0.8 m/z, Orbitrap detection at a resolution of 30,000, an AGC setting of 1 × 105, and a 100 ms maximum injection time. The analysis utilized HCD fragmentation at a fixed collision energy of 30%. MS3 spectra were collected using a conditional neutral loss design that acquired an additional fragmentation scan on ions exhibiting a neutral loss of 131.0582 Da or 105.0426 Da from the selected precursor. MS3 spectra were acquired with a full-scan MS isolation of 1.5 m/z and MS2 isolation of 2.0 m/z, Orbitrap detection at a resolution of 30,000, AGC setting of 2 × 105, and a 200 ms maximum injection time. The MS3 analysis utilized HCD fragmentation at a fixed collision energy of 50%. Data processing: Fragmentation filtering was performed using the DFBuilder module incorporated in the open-source software MZmine to monitor diagnostic neutral loss and fragment ions characteristic of mercapturic acid conjugates. Putative mercapturic acid detection required the observation of a neutral loss of 131.0582 Da (C5H9NO3) or 105.0426 Da (C3H7NO3) in acquired MS/MS spectrum. A complete list of the processing parameters is summarized in Table S2. Fragmentation filtering using the DFBuilder module was performed for the specified neutral loss using a 5 ppm mass tolerance and minimum fragment ion intensity of 1 x 104 with a 1% base peak threshold. A targeted chromatogram was drawn around detected precursor masses using a 1.0 min retention time window. Masses of interest were detected using the centroid detector and noise threshold of 1 x 105. Chromatogram traces were computed using the ADAP chromatogram builder module with a mass tolerance of 5 ppm. Chromatographic peaks were detected using the Local Minimum search algorithm using a 30% chromatographic threshold, 0.1 min retention time minimum search range, a minimum peak height of 1 x 105, a minimum peak top/edge ratio of 10, and minimum peak width tolerance of 0.1 min. Duplicate peaks were removed using a 0.1 min retention time tolerance. Feature lists were deisotoped using the 13C isotope filter module. All samples and pooled replicate feature lists were aligned using the Join Aligner module with a mass tolerance of 5 ppm and retention time tolerance of 0.4 min. Commonly observed in-source fragments, adducts, and multimer complexes were detected and removed from consideration. Missing peak annotations were replaced using the Gap-Filling algorithm. Acquired MS/MS spectra were matched against the NIST mass spectral library (version 2020) to remove unrelated metabolic signatures. Finally, the remaining features were exported as CSV files for downstream analysis. |
Ion Mode: | POSITIVE |
Collision Energy: | NCE 30% |
Fragmentation Method: | HCD |
Ion Spray Voltage: | 2.1 kV |
Ionization: | ESI |
Mass Accuracy: | 5 ppm |
Precursor Type: | [M+H]+ |