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rename, add protocol refs

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# ISA Metadata as markdown tables
:warning: This is just for convenience since .xlsx files are not shown in GitLab. Check the original `isa.*.xlsx` for latest metadata.
## Convert xlsx to md
For convenience (i.e. since `.xlsx` are not shown in GitLab), I wrote a [little helper tool](https://github.com/nfdi4plants/xlsx2markdownTable) that converts all xlsx into markdown tables.
```bash
xlsx2md -e "isa" -o _isa-md -d -di
```
:bulb: This collects all "isa" metadata it will find in a separate folder (in root).
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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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| 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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| Source Name | Parameter [scan polarity] | Parameter [scan window lower limit] | Parameter [scan window upper limit] | Parameter [scan rate] | Unit | Parameter [instrument model] | Parameter [ionization type] | Parameter [mass analyzer type] | Parameter [detector type] | Data File Name |
|--------------:|:----------------------------|--------------------------------------:|--------------------------------------:|------------------------:|:-------|:------------------------------------|:------------------------------|:---------------------------------|:----------------------------|:-----------------|
| 150112_03 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_03.D |
| 150112_04 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_04.D |
| 150112_15 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_15.D |
| 150112_16 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_16.D |
| 150112_55 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_55.D |
| 150112_56 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_56.D |
| 150112_61 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_61.D |
| 150112_62 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_62.D |
| 150112_65 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_65.D |
| 150112_66 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_66.D |
| 150115_03 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_03.D |
| 150115_04 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_04.D |
| 150115_11 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_11.D |
| 150115_12 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_12.D |
| 150115_13 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_13.D |
| 150115_14 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_14.D |
| 150115_15 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_15.D |
| 150115_16 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_16.D |
| 150115_25 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_25.D |
| 150115_26 | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_26.D |
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| Source Name | Protocol REF | Protocol Type | 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 | gas_chromatography.md | assay protocol | | 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 | gas_chromatography.md | assay protocol | | 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 | gas_chromatography.md | assay protocol | | 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 | gas_chromatography.md | assay protocol | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-436 | helium(0) | 1 | microliter | split | gradient elution | 150112_16 |
| DB23 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | | 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 | gas_chromatography.md | assay protocol | | Agilent 7890B GC | GERSTEL MultiPurpose Sampler (MPS) Dual Head | low polarity | Agilent 19091S-444 | helium(0) | 1 | microliter | split | gradient elution | 150115_04 |
| DB39 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | 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 | gas_chromatography.md | assay protocol | | 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 | gas_chromatography.md | assay protocol | | 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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| Source Name | Protocol Type | Protocol REF | Parameter [scan polarity] | Parameter [scan window lower limit] | Parameter [scan window upper limit] | Parameter [scan rate] | Unit | Parameter [instrument model] | Parameter [ionization type] | Parameter [mass analyzer type] | Parameter [detector type] | Data File Name |
|--------------:|:----------------|:---------------|:----------------------------|--------------------------------------:|--------------------------------------:|------------------------:|:-------|:------------------------------------|:------------------------------|:---------------------------------|:----------------------------|:-----------------|
| 150112_03 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_03.D |
| 150112_04 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_04.D |
| 150112_15 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_15.D |
| 150112_16 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_16.D |
| 150112_55 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_55.D |
| 150112_56 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_56.D |
| 150112_61 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_61.D |
| 150112_62 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_62.D |
| 150112_65 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_65.D |
| 150112_66 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150112_66.D |
| 150115_03 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_03.D |
| 150115_04 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_04.D |
| 150115_11 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_11.D |
| 150115_12 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_12.D |
| 150115_13 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_13.D |
| 150115_14 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_14.D |
| 150115_15 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_15.D |
| 150115_16 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_16.D |
| 150115_25 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_25.D |
| 150115_26 | assay protocol | mass_spec.md | positive | 60 | 800 | 20 | hertz | 7200 GC-QTOF (Agilent Technologies) | electron ionization | quadrupole | electron multiplier | 150115_26.D |
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| Source Name | Protocol Type | Protocol REF | 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 | extraction protocol | metabolite_extraction.md | 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 | extraction protocol | metabolite_extraction.md | 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 | extraction protocol | metabolite_extraction.md | 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 | extraction protocol | metabolite_extraction.md | 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 | extraction protocol | metabolite_extraction.md | 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 | extraction protocol | metabolite_extraction.md | 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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> ARC Note:
> - This is a somewhat polished protocol as found in a publication's "materials and methods" section.
> - This is not an example for a typical lab protocol or method.
# Metabolite Profiling - Chromatography # Metabolite Profiling - Chromatography
After incubation for 2 hours at room temperature, 1 μl of derivatized compounds were injected at a flow of 1 ml/min with an automatic liner exchange system in conjunction with a cold injection system (Gerstel) in splitless mode (ramping from 50 ◦C to 250 ◦C at 12 ◦C/s) into the GC. Chromatography was performed using a 7890B GC system (Agilent Technologies) with a 30 m long, 0.25 mm internal diameter, HP-5MS column with 5% phenyl methyl siloxane film (Agilent 19091S-433). The oven temperature was held constant at 70◦C for 2 min and then ramped at 12.5◦C/min to 320◦C at which it was held constant for 5 min; resulting in a total run time of 27 minutes. After incubation for 2 hours at room temperature, 1 μl of derivatized compounds were injected at a flow of 1 ml/min with an automatic liner exchange system in conjunction with a cold injection system (Gerstel) in splitless mode (ramping from 50 ◦C to 250 ◦C at 12 ◦C/s) into the GC. Chromatography was performed using a 7890B GC system (Agilent Technologies) with a 30 m long, 0.25 mm internal diameter, HP-5MS column with 5% phenyl methyl siloxane film (Agilent 19091S-433). The oven temperature was held constant at 70◦C for 2 min and then ramped at 12.5◦C/min to 320◦C at which it was held constant for 5 min; resulting in a total run time of 27 minutes.
assays/GCqTOF_targets/protocols/ProtRef04_MassSpec.md → assays/GCqTOF_targets/protocols/mass_spec.md
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> ARC Note:
> - This is a somewhat polished protocol as found in a publication's "materials and methods" section.
> - This is not an example for a typical lab protocol or method.
# Metabolite Profiling - Mass Spectrometry # Metabolite Profiling - Mass Spectrometry
Metabolites were ionized with an electron impact source at 70V and 200 ◦C source temperature and recorded in a mass range of m/z 60 to m/z 800 at 20 scans per second with a 7200 GC-QTOF (Agilent Technologies). Metabolites were ionized with an electron impact source at 70V and 200 ◦C source temperature and recorded in a mass range of m/z 60 to m/z 800 at 20 scans per second with a 7200 GC-QTOF (Agilent Technologies).
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assays/GCqTOF_targets/protocols/ProtRef02_extraction.md → assays/GCqTOF_targets/protocols/metabolite_extraction.md
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> ARC Note:
> - This is a somewhat polished protocol as found in a publication's "materials and methods" section.
> - This is not an example for a typical lab protocol or method.
# Metabolite Profiling - Extraction # Metabolite Profiling - Extraction
Each of the samples was analyzed one time via gas chromatography-mass spectrometry (GC-MS) using an adapted protocol from Lisec et al. (2006). Metabolites were extracted from Each of the samples was analyzed one time via gas chromatography-mass spectrometry (GC-MS) using an adapted protocol from Lisec et al. (2006). Metabolites were extracted from
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assays/MassHunter_targets/protocols/ProtRef05_DataTransformation.md → assays/MassHunter_targets/protocols/DataTransformation.md
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> ARC Note:
> - This is a somewhat polished protocol as found in a publication's "materials and methods" section.
> - This is not an example for a typical lab protocol or method.
# Metabolite Profiling - Data transformation # Metabolite Profiling - Data transformation
Raw data files exported from MassHunter Qualitative (v b07, Agilent Technologies) in the Agilent data file format (*.D/) Raw data files exported from MassHunter Qualitative (v b07, Agilent Technologies) in the Agilent data file format (*.D/)
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assays/MassHunter_targets/protocols/MetaboliteIdentification.md 0 → 100644
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# Metabolite Profiling - Identification
assays/MassHunter_targets/protocols/ProtRef06_MetaboliteIdentification.md deleted 100644 → 0
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> ARC Note:
> - This is a somewhat polished protocol as found in a publication's "materials and methods" section.
> - This is not an example for a typical lab protocol or method.
# Metabolite Profiling - Identification
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