Summary of Study ST001753
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 PR001124. The data can be accessed directly via it's Project DOI: 10.21228/M8DQ30 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 | ST001753 |
| Study Title | Modifying Chromatography Conditions for Improved Unknown Feature Identification in Untargeted Metabolomics |
| Study Summary | Project represents an effort to modify chromatographic conditions for improved compound identification in untargeted metabolomics. Two different modes of chromatograph (HILIC and RPLC) and multiple run conditions (sample loading, gradient duration, iterative acquisition) were evaluated. All relevant data from different conditions are contained within the raw data archive file attached to this submission. Metadata associated with this Metabolomics Workbench submission reflects only the manually reviewed identifications obtained using modified HILIC conditions. See protocol file Mod_vs_Con_Chrom_IDs_Protocol.pdf for details. |
| Institute | University of Michigan |
| Department | Chemistry/Internal Medicine/CCMB/Biomedical Research Core Facilities |
| Laboratory | Michigan Compound Identification Development Core/BRCF Metabolomics Core |
| Last Name | Anderson |
| First Name | Brady |
| Address | 1000 Wall St., Ann Arbor, MI 48105 |
| anderbra@umich.edu | |
| Phone | 734-232-8177 |
| Submit Date | 2021-09-09 |
| Raw Data Available | Yes |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-11-12 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001124 |
| Project DOI: | doi: 10.21228/M8DQ30 |
| Project Title: | Modifying Chromatography Conditions for Improved Unknown Feature Identification in Untargeted Metabolomics |
| Project Summary: | Project represents an effort to modify chromatographic conditions for improved compound identification in untargeted metabolomics. Two different modes of chromatograph (HILIC and RPLC) and multiple run conditions (sample loading, gradient duration, iterative acquisition) were evaluated. All relevant data from different conditions are contained within the raw data archive file attached to this submission. Metadata associated with this Metabolomics Workbench submission reflects only the manually reviewed identifications obtained using modified HILIC conditions. See protocol file Mod_vs_Con_Chrom_IDs_Protocol.pdf for details. |
| Institute: | University of Michigan |
| Department: | Chemistry/Internal Medicine/CCMB/Biomedical Research Core Facilities |
| Laboratory: | Michigan Compound Identification Development Core/BRCF Metabolomics Core |
| Last Name: | Anderson |
| First Name: | Brady |
| Address: | 1000 Wall St. Ann Arbor, MI 48105 |
| Email: | anderbra@umich.edu |
| Phone: | 734-232-8177 |
| Funding Source: | NIH Common Fund Metabolomics program grant U2CES030164/NIH NIDDK grant R01DK101473-01A1 |
| Contributors: | Brady G. Anderson, Alexander Raskind, Hani Habra, Robert T. Kennedy, Charles R. Evans |
Subject:
| Subject ID: | SU002061 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Pooled |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Iteration number |
|---|---|---|
| SA185572 | Pooled Human Plasma 1 | 1 |
| SA185573 | Pooled Human Plasma 2 | 2 |
| SA185574 | Pooled Human Plasma 3 | 3 |
| SA185575 | Pooled Human Plasma 4 | 4 |
| SA185576 | Pooled Human Plasma 5 | 5 |
| SA185577 | Pooled Human Plasma 6 | 6 |
| SA185578 | Pooled Human Plasma 7 | 7 |
| SA185579 | Pooled Human Plasma 8 | 8 |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO002054 |
| Collection Summary: | A pooled sample of human plasma compiled from hundreds of de-identified consented donors was obtained from the Red Cross of Michigan. |
| Sample Type: | Blood (plasma) |
| Storage Conditions: | -80℃ |
| Additives: | EDTA |
Treatment:
| Treatment ID: | TR002073 |
| Treatment Summary: | All studies were performed on a pooled plasma sample as received. |
Sample Preparation:
| Sampleprep ID: | SP002067 |
| Sampleprep Summary: | Four parts of 1:1:1 methanol:acetonitrile:acetone were added to one part human plasma in 15 mL polypropylene centrifuge tubes and the suspension was vortexed for 20 seconds and allowed to rest on ice for an additional 10 minutes. The extract was centrifuged at 5000 x g for 10 minutes, and the supernatant was divided into 1.5 mL aliquots which were completely dried under a gentle stream of nitrogen gas. Dried samples were reconstituted in varied volumes of 90:10 water:methanol (for RPLC analyses) and 85:15 methanol:water (for HILIC). |
| Sampleprep Protocol Filename: | Mod_vs_Con_Chrom_IDs_Protocol.pdf |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Solvent precipitation with 4 parts 1:1:1 methanol:acetonitrile:acetone to 1 part human plasma |
| Extract Cleanup: | Centrifugation 5000 g for 10 min |
| Extract Storage: | 4℃ |
| Sample Resuspension: | 90:10 water:methanol (RPLC)/85:15 methanol:water (HILIC) volume varied |
Combined analysis:
| Analysis ID | AN002856 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Agilent 1290 Infinity II |
| Column | Waters Acquity BEH Amide (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6545 QTOF |
| Ion Mode | POSITIVE |
| Units | Total Intensity Units |
Chromatography:
| Chromatography ID: | CH002383 |
| Chromatography Summary: | HILIC separations were performed on a Waters Acquity UPLC BEH amide column (2.1 x 100 mm 1.7 m) with a matching Vanguard precolumn. The flow rate was set to 0.3 mL/min and mobile phases consisted of (A) 95:5 acetonitrile/water with 0.125% v/v formic acid and 10 mM ammonium formate and (B) 95:5 water/acetonitrile with 0.125% v/v formic acid and 10 mM ammonium formate. Gradient specified in protocol file. |
| Methods Filename: | 2 mm amide pos MS2 70%H2O 120min_PC6.m |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Waters Acquity BEH Amide (100 x 2.1mm,1.7um) |
| Column Pressure: | 300 bar |
| Column Temperature: | 55 |
| Flow Rate: | 0.3 mL/min |
| Sampling Cone: | 175 V |
| Solvent A: | 95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate |
| Solvent B: | 5% acetonitrile/95% water; 0.125% formic acid; 10 mM ammonium formate |
| Analytical Time: | 120 min |
| Capillary Voltage: | 3500 V |
| Weak Wash Solvent Name: | 85:15 acetonitrile:water |
| Target Sample Temperature: | 4 |
| Sample Loop Size: | 20 uL |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003005 |
| Analysis ID: | AN002856 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Instrument settings for positive ionization mode following electrospray ionization were as follows: Sheath gas flow rate, 11 L/min; Drying gas, 8 L/min; Drying gas temperature, 320 ºC; Nebulizer, 35 psi; Capillary voltage, 3500 V; Nozzle voltage, 1000 V; Fragmentor, 175 V; Skimmer, 65 V; Octupole 1 RF Vpp, 750 V; Collision energy, 20; Iterative MS/MS mass error tolerance, ± 20 ppm; Iterative MS/MS retention time exclusion tolerance, ± 0.5 min; Spectrum data type, centroid. Data de-pendent MS/MS parameters: Mass range, 25-1200 m/z; Rate, 2 spectra/s; Max precursor ions per cycle, 3; Absolute precursor threshold, 5000 counts; Relative precursor threshold, 0.001%; Active exclusion enabled after 2 spectra and released after 0.5 min; Isolation width, narrow (~1.3 m/z). Iterative LC-MS/MS data acquired from the modified HILIC separation conditions was loaded into a pre-release version of an in-house software tool, MetIDTracker for feature detection. This software uses MSPepSearch (NIST) for database searching and score assignment. |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3500 V |
| Collision Energy: | 20 |
| Collision Gas: | N2 |
| Dry Gas Flow: | 8L/min |
| Dry Gas Temp: | 320 C |
| Fragment Voltage: | 175 V |
| Fragmentation Method: | CID |
| Ionization: | ESI |
| Mass Accuracy: | <20 ppm |
