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Commit 4689716e authored by Dominik Brilhaus's avatar Dominik Brilhaus
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replace deprecated ontology terms

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_isa-md/assays/GCqTOF_targets/isa.assay/02_metabolites_extr.md
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| Source Name | Parameter [Bio entity] | Parameter [Biosource amount] | Unit (#2) | Parameter [Biosource material state] | Parameter [Extraction buffer] | Parameter [Extraction buffer volume] | Parameter [Internal standard] | Parameter [Sample volume] | Unit | Parameter [MS sample post-extraction] | Parameter [MS sample resuspension] | Parameter [MS derivatization] | Parameter [label] | Sample Name |
|:--------------|:-------------------------|-------------------------------:|:------------|:---------------------------------------|:------------------------------------------|---------------------------------------:|:--------------------------------|----------------------------:|:-----------|:----------------------------------------|:-------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------|:--------------------|:--------------|
| CAM_01 | metabolites | 6.1 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | (1) with 10 μl methoxyamine hydrochloride (Acros organics; freshly prepared at 20 mg/ml in pure pyridine (Sigma-Aldrich)) and shaking at 37 ◦C | - | DB23 |
| | | | | | | | | | | | | for 90 min, (2) adding 90 μl N-Methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA; Macherey-Nagel) and shaking at 37 ◦C for 30 min. | | |
| CAM_02 | metabolites | 5.2 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | 10 μl methoxyamine hydrochloride and 90 μl N-Methyl-N-(trimethylsilyl)trifluoroacetamide MSTFA | - | DB24 |
| CAM_03 | metabolites | 8.2 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | MaHCl and MSTFA | - | DB26 |
| reC3_01 | metabolites | 4.9 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | methoxyamination + trimethylsylilation (TMS) | - | DB39 |
| reC3_02 | metabolites | 6 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | methoxyamination + trimethylsylilation (TMS) | - | DB40 |
| reC3_03 | metabolites | 6.2 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | methoxyamination + trimethylsylilation (TMS) | - | DB41 |
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| Source Name | Parameter [Bio entity] | Parameter [Biosource amount] | Unit (#2) | Parameter [Biosource material state] | Parameter [Extraction buffer] | Parameter [Extraction buffer volume] | Parameter [Internal standard] | Parameter [Sample volume] | Unit | Parameter [MS sample post-extraction] | Parameter [MS sample resuspension] | Parameter [MS derivatization] | Sample Name |
|:--------------|:-------------------------|-------------------------------:|:------------|:---------------------------------------|:------------------------------------------|---------------------------------------:|:--------------------------------|----------------------------:|:-----------|:----------------------------------------|:-------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------|:--------------|
| CAM_01 | metabolites | 6.1 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | (1) with 10 μl methoxyamine hydrochloride (Acros organics; freshly prepared at 20 mg/ml in pure pyridine (Sigma-Aldrich)) and shaking at 37 ◦C | DB23 |
| | | | | | | | | | | | | for 90 min, (2) adding 90 μl N-Methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA; Macherey-Nagel) and shaking at 37 ◦C for 30 min. | |
| CAM_02 | metabolites | 5.2 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | 10 μl methoxyamine hydrochloride and 90 μl N-Methyl-N-(trimethylsilyl)trifluoroacetamide MSTFA | DB24 |
| CAM_03 | metabolites | 8.2 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | MaHCl and MSTFA | DB26 |
| reC3_01 | metabolites | 4.9 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | methoxyamination + trimethylsylilation (TMS) | DB39 |
| reC3_02 | metabolites | 6 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | methoxyamination + trimethylsylilation (TMS) | DB40 |
| reC3_03 | metabolites | 6.2 | milligram | Dry material | water:methanol:chloroform 1:2.5:1 (v:v:v) | 1500 | ribitol | 50 | microliter | dried in vacuum concentrator | - | methoxyamination + trimethylsylilation (TMS) | DB41 |
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_isa-md/assays/GCqTOF_targets/isa.assay/03_metabolites_chromatography.md
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| Source Name | Parameter [MS sample type] | Parameter [Chromatography instrument model] | Parameter [Chromatography autosampler model] | Parameter [Chromatography column type] | Parameter [Chromatography column model] | Parameter [Chromatography guard column model] | Parameter [mobile phase] | Parameter [Chromatography injection volume] | Unit | Parameter [Chromatography injection mode] | Parameter [Chromatography gradient] | Sample Name |
|:--------------|:-----------------------------|:----------------------------------------------|:-----------------------------------------------|:-----------------------------------------|:------------------------------------------|:------------------------------------------------|:---------------------------|----------------------------------------------:|:-----------|:--------------------------------------------|:--------------------------------------|--------------:|
| Std. Mix 5µM | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-433 | - | helium(0) | 1 | microliter | splitless | gradient elution | 150112_03 |
| Std. Mix 5µM | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-434 | - | helium(0) | 1 | microliter | split | gradient elution | 150112_04 |
| blank 1 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-435 | - | helium(0) | 1 | microliter | splitless | gradient elution | 150112_15 |
| blank 1 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-436 | - | helium(0) | 1 | microliter | split | gradient elution | 150112_16 |
| DB23 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-437 | - | helium(0) | 1 | microliter | splitless | gradient elution | 150112_55 |
| DB23 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-438 | - | helium(0) | 1 | microliter | split | gradient elution | 150112_56 |
| DB24 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-439 | - | helium(0) | 1 | microliter | splitless | gradient elution | 150112_61 |
| DB24 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-440 | - | helium(0) | 1 | microliter | split | gradient elution | 150112_62 |
| DB26 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-441 | - | helium(0) | 1 | microliter | splitless | gradient elution | 150112_65 |
| DB26 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-442 | - | helium(0) | 1 | microliter | split | gradient elution | 150112_66 |
| Std. Mix 5µM | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-443 | - | helium(0) | 1 | microliter | splitless | gradient elution | 150115_03 |
| Std. Mix 5µM | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-444 | - | helium(0) | 1 | microliter | split | gradient elution | 150115_04 |
| DB39 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-445 | - | helium(0) | 1 | microliter | splitless | gradient elution | 150115_11 |
| DB39 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-446 | - | helium(0) | 1 | microliter | split | gradient elution | 150115_12 |
| DB40 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-447 | - | helium(0) | 1 | microliter | splitless | gradient elution | 150115_13 |
| DB40 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-448 | - | helium(0) | 1 | microliter | split | gradient elution | 150115_14 |
| DB41 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-449 | - | helium(0) | 1 | microliter | splitless | gradient elution | 150115_15 |
| DB41 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-450 | - | helium(0) | 1 | microliter | split | gradient elution | 150115_16 |
| blank 2 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-451 | - | helium(0) | 1 | microliter | splitless | gradient elution | 150115_25 |
| blank 2 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-452 | - | helium(0) | 1 | microliter | split | gradient elution | 150115_26 |
\ No newline at end of file
| Source Name | Parameter [MS sample type] | Parameter [Chromatography instrument model] | Parameter [Chromatography autosampler model] | Parameter [Chromatography column type] | Parameter [Chromatography column model] | Parameter [mobile phase] | Parameter [Chromatography injection volume] | Unit | Parameter [Chromatography injection mode] | Parameter [Chromatography gradient] | Sample Name |
|:--------------|:-----------------------------|:----------------------------------------------|:-----------------------------------------------|:-----------------------------------------|:------------------------------------------|:---------------------------|----------------------------------------------:|:-----------|:--------------------------------------------|:--------------------------------------|--------------:|
| Std. Mix 5µM | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-433 | helium(0) | 1 | microliter | splitless | gradient elution | 150112_03 |
| Std. Mix 5µM | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-434 | helium(0) | 1 | microliter | split | gradient elution | 150112_04 |
| blank 1 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-435 | helium(0) | 1 | microliter | splitless | gradient elution | 150112_15 |
| blank 1 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-436 | helium(0) | 1 | microliter | split | gradient elution | 150112_16 |
| DB23 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-437 | helium(0) | 1 | microliter | splitless | gradient elution | 150112_55 |
| DB23 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-438 | helium(0) | 1 | microliter | split | gradient elution | 150112_56 |
| DB24 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-439 | helium(0) | 1 | microliter | splitless | gradient elution | 150112_61 |
| DB24 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-440 | helium(0) | 1 | microliter | split | gradient elution | 150112_62 |
| DB26 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-441 | helium(0) | 1 | microliter | splitless | gradient elution | 150112_65 |
| DB26 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-442 | helium(0) | 1 | microliter | split | gradient elution | 150112_66 |
| Std. Mix 5µM | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-443 | helium(0) | 1 | microliter | splitless | gradient elution | 150115_03 |
| Std. Mix 5µM | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-444 | helium(0) | 1 | microliter | split | gradient elution | 150115_04 |
| DB39 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-445 | helium(0) | 1 | microliter | splitless | gradient elution | 150115_11 |
| DB39 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-446 | helium(0) | 1 | microliter | split | gradient elution | 150115_12 |
| DB40 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-447 | helium(0) | 1 | microliter | splitless | gradient elution | 150115_13 |
| DB40 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-448 | helium(0) | 1 | microliter | split | gradient elution | 150115_14 |
| DB41 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-449 | helium(0) | 1 | microliter | splitless | gradient elution | 150115_15 |
| DB41 | material sample | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-450 | helium(0) | 1 | microliter | split | gradient elution | 150115_16 |
| blank 2 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-451 | helium(0) | 1 | microliter | splitless | gradient elution | 150115_25 |
| blank 2 | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-452 | helium(0) | 1 | microliter | split | gradient elution | 150115_26 |
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assays/GCqTOF_targets/isa.assay.xlsx
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