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MB Sample ID: SA099252
| Local Sample ID: | Sample_15137 |
| Subject ID: | SU001439 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 21-56 |
| Gender: | Male and female |
| Human Inclusion Criteria: | Cystic Fibrosis, adults |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001439 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 21-56 |
| Gender: | Male and female |
| Human Inclusion Criteria: | Cystic Fibrosis, adults |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Sample_15137 | SA099252 | FL014053 | CF_sample | Factor |
Collection:
| Collection ID: | CO001434 |
| Collection Summary: | Sputum samples from 11 subjects with cystic fibrosis were selected from a larger airway microbiome study that was approved by the University of Michigan Medical School Institutional Review Board. Subjects were 6 males and 5 females, age 21 to 56 years (median 37). Sputum samples were collected by subjects at home and stored at 4˚C for up to 23 days and then transferred to -80˚C. |
| Sample Type: | Sputum |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR001454 |
| Treatment Summary: | The goal of this study was to determine which antibiotics are present in cystic fibrosis sputum using a LC-MS method. There were no experimental conditions. The types of samples included in the LC-MS run were: cystic fibrosis sputum, external standard curve, quality control pools of external standards run every ~50 samples, and washes (blanks). |
Sample Preparation:
| Sampleprep ID: | SP001447 |
| Sampleprep Summary: | The extraction solvent was chilled 1% DTT and spiked with 1.33 µM of both internal standards, linezolid-d3 and levofloxacin-d8. Solvent (150 µL) was added to 50 µL of sputum. The samples were vortexed for 30 seconds, shaken at 4˚C on a shaking platform with moderate agitation for 15 minutes, and centrifuged at 13,200 RCF for 10 minutes at 4˚C. The supernatant was pipetted into amber glass vials and injected directly into the LC-MS. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | On ice |
Combined analysis:
| Analysis ID | AN002272 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity I-Class |
| Column | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Waters Quattro Premier XE |
| Ion Mode | POSITIVE |
| Units | micromolar |
Chromatography:
| Chromatography ID: | CH001671 |
| Methods Filename: | qopt_A2B2_3g_c9_5min.wvhp |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
| Column Temperature: | 50 |
| Flow Rate: | 0.3 ml/min |
| Injection Temperature: | 10 |
| Solvent A: | 100% water; 0.1% acetic acid; 10 mM ammonium acetate |
| Solvent B: | 100% methanol; 0.1% formic acid; 2 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002116 |
| Analysis ID: | AN002272 |
| Instrument Name: | Waters Quattro Premier XE |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | The retention times (RT) and MS/MS parameters for reach antibiotic were determined using the QuanOpt function in the Waters Masslynx software. Peaks were automatically picked and filtered in QuanLynx. Downstream filtering was conducted in R. Data were imported into R and the following criteria for filtering were applied: minimum peak area under the curve of 20 and signal to noise ratio of 10. Because several of the antibiotics had high carry-over rates (including ciprofloxacin, levofloxacin, and trimethoprim), sample peaks were also filtered out when the AUC was lower than the wash ran directly before the sample. Scripts can be found at the following github link: https://github.com/tgallagh/LCMS_Antibiotics. |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3.3 kV |
| Collision Gas: | Nitrogen |
| Source Temperature: | 125 |
| Desolvation Gas Flow: | 800 L/h |
| Desolvation Temperature: | 400 |
| Acquisition Parameters File: | CF_antibiotics.exp |
| Analysis Protocol File: | CF_antibiotics_quant.mdb |
