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MB Sample ID: SA175344
Local Sample ID: | 900483-011-112 |
Subject ID: | SU001966 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | C57BL/6NCrl |
Age Or Age Range: | 92 weeks old |
Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Combined analysis:
Analysis ID | AN003057 | AN003058 | AN003059 | AN003060 | AN003061 |
---|---|---|---|---|---|
Analysis type | MS | MS | MS | MS | MS |
Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase | GC |
Chromatography system | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish | Agilent 6890N |
Column | Waters XBridge Amide (100 x 4.6mm,3.5um) | Waters XBridge Amide (100 x 4.6mm,3.5um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
MS Type | ESI | ESI | ESI | ESI | EI |
MS instrument type | Orbitrap | LTQ-FT | Orbitrap | Ion trap | GC-TOF |
MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Leco Pegasus IV TOF |
Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE | POSITIVE |
Units | Peak height | Peak height | Peak height | Peak height | Peak height |
MS:
MS ID: | MS002844 |
Analysis ID: | AN003057 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | The ion source conditions were set as follows: spray voltage, 3.6 kV; sheath gas flow rate, 60 arbitrary units; aux gas flow rate, 25 arbitrary units; sweep gas flow rate, 2 arbitrary units; capillary temp, 300 °C; S-lens RF level, 50; Aux gas heater temp, 370 °C. The following acquisition parameters were used for MS1 analysis: resolution, 60000, AGC target, 1e6; Maximum IT, 100 ms; scan range 60-900 m/z; spectrum data type, centroid. Data dependent MS/MS parameters: resolution, 15000; AGC target, 1e5; maximum IT, 50 ms; loop count, 4; TopN, 4; isolation window, 1.0 m/z; fixed first mass, 70.0 m/z; (N)CE/ stepped nce, 20, 30, 40; spectrum data type, centroid; minimum AGC target, 8e3; intensity threshold, 1.6e5; exclude isotopes, on; dynamic exclusion, 3.0 s. To increase the total number of MS/MS spectra, five runs with iterative MS/MS exclusions were performed using the R package “IE-Omics”18 for both positive and negative electrospray conditions. All the LC-MS raw data files were converted into ABF format using ABF converter (https://www.reifycs.com/AbfConverter/). MS-DIAL ver.4.00 software was used for deconvolution, peak picking, alignment, and compound identification19. The detailed parameter setting was as follows: MS1 tolerance, 0.005 Da; MS2 tolerance, 0.01 Da; minimum peak height, 20000 amplitude; mass slice width, 0.1 Da; smoothing method, linear weighted moving average; smoothing level, 5 scans; minimum peak width, 10 scans. [M+H]+, [M+NH4]+, [M+Na]+, [2M+H]+,[2M+NH4]+, [2M+Na]+ were included in adduct ion setting for positive mode lipidomics and HILIC analysis, [M-H]-, [M+Cl]-, [M+Hac-H]- for negative mode lipidomics, and [M-H]-, [M+Cl]-, [M+FA-H]-, [2M-H]- for negative mode HILIC analysis. Compounds were annotated by matching retention times, accurate precursor masses and MS/MS spectra against libraries in MassBank of North America and NIST17. Retention time libraries were produced from authentic standards and extrapolated for lipids as published before. The primary result data matrix was processed with MS-FLO software to identify ion adducts, duplicate peaks, and isotopic features. Systematic error removal by random forest (SERRF software) was employed to correct for batch effects or instrument signal drifts. Statistical analysis was performed by normalization to the median intensity of all identified compounds, log transformation and Pareto scaling. PCA was used for multivariate statistics and visualization, specifically for outlier detection. Two outliers, including one medulla sample from a female early adult and one basal ganglia sample from a female late adult, were removed. Results from Kruskal-Wallis tests were followed by Dunn’s multiple comparison confinement. Results from Mann–Whitney U tests were corrected by the Benjamini–Hochberg procedure to control the false discovery rate. Spearman rank correlation analyses and fold change calculations were conducted using R. |
Ion Mode: | POSITIVE |
MS ID: | MS002845 |
Analysis ID: | AN003058 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | LTQ-FT |
MS Type: | ESI |
MS Comments: | The ion source conditions were set as follows: spray voltage, -3.0 kV; sheath gas flow rate, 60 arbitrary units; aux gas flow rate, 25 arbitrary units; sweep gas flow rate, 2 arbitrary units; capillary temp, 300 °C; S-lens RF level, 50; Aux gas heater temp, 370 °C. The following acquisition parameters were used for MS1 analysis: resolution, 60000, AGC target, 1e6; Maximum IT, 100 ms; scan range 60-900 m/z; spectrum data type, centroid. Data dependent MS/MS parameters: resolution, 15000; AGC target, 1e5; maximum IT, 50 ms; loop count, 4; TopN, 4; isolation window, 1.0 m/z; fixed first mass, 70.0 m/z; (N)CE/ stepped nce, 20, 30, 40; spectrum data type, centroid; minimum AGC target, 8e3; intensity threshold, 1.6e5; exclude isotopes, on; dynamic exclusion, 3.0 s. To increase the total number of MS/MS spectra, five runs with iterative MS/MS exclusions were performed using the R package “IE-Omics”18 for both positive and negative electrospray conditions. All the LC-MS raw data files were converted into ABF format using ABF converter (https://www.reifycs.com/AbfConverter/). MS-DIAL ver.4.00 software was used for deconvolution, peak picking, alignment, and compound identification19. The detailed parameter setting was as follows: MS1 tolerance, 0.005 Da; MS2 tolerance, 0.01 Da; minimum peak height, 20000 amplitude; mass slice width, 0.1 Da; smoothing method, linear weighted moving average; smoothing level, 5 scans; minimum peak width, 10 scans. [M+H]+, [M+NH4]+, [M+Na]+, [2M+H]+,[2M+NH4]+, [2M+Na]+ were included in adduct ion setting for positive mode lipidomics and HILIC analysis, [M-H]-, [M+Cl]-, [M+Hac-H]- for negative mode lipidomics, and [M-H]-, [M+Cl]-, [M+FA-H]-, [2M-H]- for negative mode HILIC analysis. Compounds were annotated by matching retention times, accurate precursor masses and MS/MS spectra against libraries in MassBank of North America and NIST17. Retention time libraries were produced from authentic standards and extrapolated for lipids as published before. The primary result data matrix was processed with MS-FLO software to identify ion adducts, duplicate peaks, and isotopic features. Systematic error removal by random forest (SERRF software) was employed to correct for batch effects or instrument signal drifts. Statistical analysis was performed by normalization to the median intensity of all identified compounds, log transformation and Pareto scaling. PCA was used for multivariate statistics and visualization, specifically for outlier detection. Two outliers, including one medulla sample from a female early adult and one basal ganglia sample from a female late adult, were removed. Results from Kruskal-Wallis tests were followed by Dunn’s multiple comparison confinement. Results from Mann–Whitney U tests were corrected by the Benjamini–Hochberg procedure to control the false discovery rate. Spearman rank correlation analyses and fold change calculations were conducted using R. |
Ion Mode: | NEGATIVE |
MS ID: | MS002846 |
Analysis ID: | AN003059 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | The ion source conditions were set as follows: spray voltage, 3.6 kV; sheath gas flow rate, 60 arbitrary units; aux gas flow rate, 25 arbitrary units; sweep gas flow rate, 2 arbitrary units; capillary temp, 300 °C; S-lens RF level, 50; Aux gas heater temp, 370 °C. The following acquisition parameters were used for MS1 analysis: resolution, 60000, AGC target, 1e6; Maximum IT, 100 ms; scan range 150-1700 m/z; spectrum data type, centroid. Data dependent MS/MS parameters: resolution, 15000; AGC target, 1e5; maximum IT, 50 ms; loop count, 4; TopN, 4; isolation window, 1.0 m/z; fixed first mass, 70.0 m/z; (N)CE/ stepped nce, 20, 30, 40; spectrum data type, centroid; minimum AGC target, 8e3; intensity threshold, 1.6e5; exclude isotopes, on; dynamic exclusion, 3.0 s. To increase the total number of MS/MS spectra, five runs with iterative MS/MS exclusions were performed using the R package “IE-Omics”18 for both positive and negative electrospray conditions. All the LC-MS raw data files were converted into ABF format using ABF converter (https://www.reifycs.com/AbfConverter/). MS-DIAL ver.4.00 software was used for deconvolution, peak picking, alignment, and compound identification19. The detailed parameter setting was as follows: MS1 tolerance, 0.005 Da; MS2 tolerance, 0.01 Da; minimum peak height, 20000 amplitude; mass slice width, 0.1 Da; smoothing method, linear weighted moving average; smoothing level, 5 scans; minimum peak width, 10 scans. [M+H]+, [M+NH4]+, [M+Na]+, [2M+H]+,[2M+NH4]+, [2M+Na]+ were included in adduct ion setting for positive mode lipidomics and HILIC analysis, [M-H]-, [M+Cl]-, [M+Hac-H]- for negative mode lipidomics, and [M-H]-, [M+Cl]-, [M+FA-H]-, [2M-H]- for negative mode HILIC analysis. Compounds were annotated by matching retention times, accurate precursor masses and MS/MS spectra against libraries in MassBank of North America and NIST17. Retention time libraries were produced from authentic standards and extrapolated for lipids as published before. The primary result data matrix was processed with MS-FLO software to identify ion adducts, duplicate peaks, and isotopic features. Systematic error removal by random forest (SERRF software) was employed to correct for batch effects or instrument signal drifts. Statistical analysis was performed by normalization to the median intensity of all identified compounds, log transformation and Pareto scaling. PCA was used for multivariate statistics and visualization, specifically for outlier detection. Two outliers, including one medulla sample from a female early adult and one basal ganglia sample from a female late adult, were removed. Results from Kruskal-Wallis tests were followed by Dunn’s multiple comparison confinement. Results from Mann–Whitney U tests were corrected by the Benjamini–Hochberg procedure to control the false discovery rate. Spearman rank correlation analyses and fold change calculations were conducted using R. |
Ion Mode: | POSITIVE |
MS ID: | MS002847 |
Analysis ID: | AN003060 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Ion trap |
MS Type: | ESI |
MS Comments: | The ion source conditions were set as follows: spray voltage, -3.0 kV; sheath gas flow rate, 60 arbitrary units; aux gas flow rate, 25 arbitrary units; sweep gas flow rate, 2 arbitrary units; capillary temp, 300 °C; S-lens RF level, 50; Aux gas heater temp, 370 °C. The following acquisition parameters were used for MS1 analysis: resolution, 60000, AGC target, 1e6; Maximum IT, 100 ms; scan range 150-1700 m/z; spectrum data type, centroid. Data dependent MS/MS parameters: resolution, 15000; AGC target, 1e5; maximum IT, 50 ms; loop count, 4; TopN, 4; isolation window, 1.0 m/z; fixed first mass, 70.0 m/z; (N)CE/ stepped nce, 20, 30, 40; spectrum data type, centroid; minimum AGC target, 8e3; intensity threshold, 1.6e5; exclude isotopes, on; dynamic exclusion, 3.0 s. To increase the total number of MS/MS spectra, five runs with iterative MS/MS exclusions were performed using the R package “IE-Omics”18 for both positive and negative electrospray conditions. All the LC-MS raw data files were converted into ABF format using ABF converter (https://www.reifycs.com/AbfConverter/). MS-DIAL ver.4.00 software was used for deconvolution, peak picking, alignment, and compound identification19. The detailed parameter setting was as follows: MS1 tolerance, 0.005 Da; MS2 tolerance, 0.01 Da; minimum peak height, 20000 amplitude; mass slice width, 0.1 Da; smoothing method, linear weighted moving average; smoothing level, 5 scans; minimum peak width, 10 scans. [M+H]+, [M+NH4]+, [M+Na]+, [2M+H]+,[2M+NH4]+, [2M+Na]+ were included in adduct ion setting for positive mode lipidomics and HILIC analysis, [M-H]-, [M+Cl]-, [M+Hac-H]- for negative mode lipidomics, and [M-H]-, [M+Cl]-, [M+FA-H]-, [2M-H]- for negative mode HILIC analysis. Compounds were annotated by matching retention times, accurate precursor masses and MS/MS spectra against libraries in MassBank of North America and NIST17. Retention time libraries were produced from authentic standards and extrapolated for lipids as published before. The primary result data matrix was processed with MS-FLO software to identify ion adducts, duplicate peaks, and isotopic features. Systematic error removal by random forest (SERRF software) was employed to correct for batch effects or instrument signal drifts. Statistical analysis was performed by normalization to the median intensity of all identified compounds, log transformation and Pareto scaling. PCA was used for multivariate statistics and visualization, specifically for outlier detection. Two outliers, including one medulla sample from a female early adult and one basal ganglia sample from a female late adult, were removed. Results from Kruskal-Wallis tests were followed by Dunn’s multiple comparison confinement. Results from Mann–Whitney U tests were corrected by the Benjamini–Hochberg procedure to control the false discovery rate. Spearman rank correlation analyses and fold change calculations were conducted using R. |
Ion Mode: | NEGATIVE |
MS ID: | MS002848 |
Analysis ID: | AN003061 |
Instrument Name: | Leco Pegasus IV TOF |
Instrument Type: | GC-TOF |
MS Type: | EI |
MS Comments: | 0.5 μL sample was injected with 25 s splitless time on an Agilent 6890 GC (Agilent Technologies, Santa Clara, CA) using a Restek Rtx-5Sil MS column (30 m x 0.25 mm, 0.25 μm) with 10 m Guard column (10 m x 0.25 mm, 0.25 μm) and 1 mL/min Helium gas flow. Oven temperature was held 50°C for 1 min, ramped up to 330 °C at 20 °C/min and held for 5 min. Data was acquired at 70 eV electron ionization at 17 spectra/s from 85 to 500 Da at 1850 V detector voltage on a Leco Pegasus IV time-of-flight mass spectrometer (Leco Corporation, St. Joseph, MI). The transfer line temperature was held at 280 °C with an ion source temperature set at 250 °C. Standard metabolites mixtures and blank samples were injected at the beginning of the run and every ten samples throughout the run for quality control. Raw data was preprocessed by ChromaTOF version 4.50 for baseline subtraction, deconvolution and peak detection. Binbase was used for metabolite annotation and reporting. |
Ion Mode: | POSITIVE |