diff --git a/_isa-md/README.md b/_isa-md/README.md deleted file mode 100644 index 5b042ab2590eb927eb07a2de284e30489e1ea5fa..0000000000000000000000000000000000000000 --- a/_isa-md/README.md +++ /dev/null @@ -1,14 +0,0 @@ -# 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). \ No newline at end of file diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/02_metabolites_extr.md b/_isa-md/assays/GCqTOF_targets/isa.assay/02_metabolites_extr.md deleted file mode 100644 index 8ab7dca78dcbbb5529d1d13bd01db4decdb1de22..0000000000000000000000000000000000000000 --- a/_isa-md/assays/GCqTOF_targets/isa.assay/02_metabolites_extr.md +++ /dev/null @@ -1,9 +0,0 @@ -| 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 | \ No newline at end of file diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/03_metabolites_chromatography.md b/_isa-md/assays/GCqTOF_targets/isa.assay/03_metabolites_chromatography.md deleted file mode 100644 index 76ee838bd465c67b472ba1d7475ff7de745af2b8..0000000000000000000000000000000000000000 --- a/_isa-md/assays/GCqTOF_targets/isa.assay/03_metabolites_chromatography.md +++ /dev/null @@ -1,22 +0,0 @@ -| 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 | \ No newline at end of file diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/04_metabolites_massspec.md b/_isa-md/assays/GCqTOF_targets/isa.assay/04_metabolites_massspec.md deleted file mode 100644 index b8fbf5b50434a294cb6887f0bb564c7900d877ce..0000000000000000000000000000000000000000 --- a/_isa-md/assays/GCqTOF_targets/isa.assay/04_metabolites_massspec.md +++ /dev/null @@ -1,22 +0,0 @@ -| 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 | \ No newline at end of file diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/gas_chromatography.md b/_isa-md/assays/GCqTOF_targets/isa.assay/gas_chromatography.md new file mode 100644 index 0000000000000000000000000000000000000000..5e7bcfc8e62eac80d11771b1ad315e0c7510b5ef --- /dev/null +++ b/_isa-md/assays/GCqTOF_targets/isa.assay/gas_chromatography.md @@ -0,0 +1,22 @@ +| 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 | \ No newline at end of file diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/mass_spec.md b/_isa-md/assays/GCqTOF_targets/isa.assay/mass_spec.md new file mode 100644 index 0000000000000000000000000000000000000000..9ec4346a00050d18196888294bc8650805cd4298 --- /dev/null +++ b/_isa-md/assays/GCqTOF_targets/isa.assay/mass_spec.md @@ -0,0 +1,22 @@ +| 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 | \ No newline at end of file diff --git a/_isa-md/assays/GCqTOF_targets/isa.assay/metabolite_extraction.md b/_isa-md/assays/GCqTOF_targets/isa.assay/metabolite_extraction.md new file mode 100644 index 0000000000000000000000000000000000000000..2f8c22da2b5aa5207a1c31eefe3423c7e9faf899 --- /dev/null +++ b/_isa-md/assays/GCqTOF_targets/isa.assay/metabolite_extraction.md @@ -0,0 +1,9 @@ +| 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 | \ No newline at end of file diff --git a/assays/GCqTOF_targets/isa.assay.xlsx b/assays/GCqTOF_targets/isa.assay.xlsx index b96d001c466170d5d527a042fb4b22a398a4bea0..9a899eecad80a561b3e5a8c2497dea8ea2317895 100644 Binary files a/assays/GCqTOF_targets/isa.assay.xlsx and b/assays/GCqTOF_targets/isa.assay.xlsx differ diff --git a/assays/GCqTOF_targets/protocols/ProtRef03_chromatography.md b/assays/GCqTOF_targets/protocols/gas_chromatography.md similarity index 79% rename from assays/GCqTOF_targets/protocols/ProtRef03_chromatography.md rename to assays/GCqTOF_targets/protocols/gas_chromatography.md index fb4c79d5f7238e04eefe3221cae0e0220e9c067b..9682e590b13ae94c4e6268dcc25631bfa8fc178c 100644 --- a/assays/GCqTOF_targets/protocols/ProtRef03_chromatography.md +++ b/assays/GCqTOF_targets/protocols/gas_chromatography.md @@ -1,7 +1,3 @@ -> 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 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. diff --git a/assays/GCqTOF_targets/protocols/ProtRef04_MassSpec.md b/assays/GCqTOF_targets/protocols/mass_spec.md similarity index 58% rename from assays/GCqTOF_targets/protocols/ProtRef04_MassSpec.md rename to assays/GCqTOF_targets/protocols/mass_spec.md index 5c9922882c6ecf642e615a3e842ae4b6af3ef2ee..26364270bd076a836b78d4d5f52688dfa7ab81e9 100644 --- a/assays/GCqTOF_targets/protocols/ProtRef04_MassSpec.md +++ b/assays/GCqTOF_targets/protocols/mass_spec.md @@ -1,7 +1,3 @@ -> 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 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). \ No newline at end of file diff --git a/assays/GCqTOF_targets/protocols/ProtRef02_extraction.md b/assays/GCqTOF_targets/protocols/metabolite_extraction.md similarity index 85% rename from assays/GCqTOF_targets/protocols/ProtRef02_extraction.md rename to assays/GCqTOF_targets/protocols/metabolite_extraction.md index 6874abf8813b451185def032b1cc2ed935af0ff5..dbe7005e0ed856eb50b48e89a53cc46152ab0028 100644 --- a/assays/GCqTOF_targets/protocols/ProtRef02_extraction.md +++ b/assays/GCqTOF_targets/protocols/metabolite_extraction.md @@ -1,8 +1,3 @@ -> 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 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 diff --git a/assays/MassHunter_targets/protocols/DataTransformation.md b/assays/MassHunter_targets/protocols/DataTransformation.md new file mode 100644 index 0000000000000000000000000000000000000000..b3032d443eb0210d451cf0a89b26d30d48f8afc8 --- /dev/null +++ b/assays/MassHunter_targets/protocols/DataTransformation.md @@ -0,0 +1,3 @@ +# Metabolite Profiling - Data transformation + +Raw data files exported from MassHunter Qualitative (v b07, Agilent Technologies) in the Agilent data file format (*.D/) \ No newline at end of file diff --git a/assays/MassHunter_targets/protocols/MetaboliteIdentification.md b/assays/MassHunter_targets/protocols/MetaboliteIdentification.md new file mode 100644 index 0000000000000000000000000000000000000000..2844e93978f26def42afafaf27dea9a9f91421cd --- /dev/null +++ b/assays/MassHunter_targets/protocols/MetaboliteIdentification.md @@ -0,0 +1 @@ +# Metabolite Profiling - Identification diff --git a/assays/MassHunter_targets/protocols/ProtRef05_DataTransformation.md b/assays/MassHunter_targets/protocols/ProtRef05_DataTransformation.md deleted file mode 100644 index eb22b35fc69bedbcaa7fb19a77ed2bfe48648f3e..0000000000000000000000000000000000000000 --- a/assays/MassHunter_targets/protocols/ProtRef05_DataTransformation.md +++ /dev/null @@ -1,7 +0,0 @@ -> 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 - -Raw data files exported from MassHunter Qualitative (v b07, Agilent Technologies) in the Agilent data file format (*.D/) \ No newline at end of file diff --git a/assays/MassHunter_targets/protocols/ProtRef06_MetaboliteIdentification.md b/assays/MassHunter_targets/protocols/ProtRef06_MetaboliteIdentification.md deleted file mode 100644 index e9dcfed0e36a7e0d04cff92d4d3b7aa3fcb49ce7..0000000000000000000000000000000000000000 --- a/assays/MassHunter_targets/protocols/ProtRef06_MetaboliteIdentification.md +++ /dev/null @@ -1,5 +0,0 @@ -> 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