From 5680b04dddfba0f7e22bcd11762306e8e2b744dc Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Thu, 3 Aug 2023 14:13:33 +0200
Subject: [PATCH] add metabolomics dataset
---
.gitattributes | 21 ++++++++++++
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.../ProtRef06_MetaboliteIdentification.md | 5 +++
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diff --git a/assays/GCqTOF_targets/protocols/ProtRef02_extraction.md b/assays/GCqTOF_targets/protocols/ProtRef02_extraction.md
new file mode 100644
index 0000000..6874abf
--- /dev/null
+++ b/assays/GCqTOF_targets/protocols/ProtRef02_extraction.md
@@ -0,0 +1,14 @@
+> 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
+4.9 - 8.2 mg dry samples with 1.5 ml of a 1:2.5:1 H2O:methanol:chloroform (v:v:v) mixture pre-cooled to -20 â—¦C, then mixed on a rotator for 10 min and centrifuged at
+20,000 g for 2 min (both at 4 ◦C). A total of 50 μl of the supernatant were dried completely in a vacuum concentrator and derivatized in two steps via an MPS-Dual-head
+autosampler (Gerstel): (1) with 10 μl methoxyamine hydrochloride (Acros organics; freshly prepared at 20 mg/ml in pure pyridine (Sigma-Aldrich)) and shaking at 37 ◦C
+for 90 min, (2) adding 90 μl N-Methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA; Macherey-Nagel) and shaking at 37 ◦C for 30 min.
+
+Lisec, J., Schauer, N., Kopka, J., Willmitzer, L., and Fernie, A. R. (2006). Gas chromatography mass spectrometry-based metabolite profiling in plants. Nature Protocols, 1(1):387–396.
\ No newline at end of file
diff --git a/assays/GCqTOF_targets/protocols/ProtRef03_chromatography.md b/assays/GCqTOF_targets/protocols/ProtRef03_chromatography.md
new file mode 100644
index 0000000..fb4c79d
--- /dev/null
+++ b/assays/GCqTOF_targets/protocols/ProtRef03_chromatography.md
@@ -0,0 +1,7 @@
+> 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/ProtRef04_MassSpec.md
new file mode 100644
index 0000000..5c99228
--- /dev/null
+++ b/assays/GCqTOF_targets/protocols/ProtRef04_MassSpec.md
@@ -0,0 +1,7 @@
+> 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 â—¦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/MassHunter_targets/protocols/.gitkeep b/assays/GCqTOF_targets/protocols/README.md
similarity index 100%
rename from assays/MassHunter_targets/protocols/.gitkeep
rename to assays/GCqTOF_targets/protocols/README.md
diff --git a/assays/MassHunter_targets/README.md b/assays/MassHunter_targets/README.md
index e69de29..92b1cbf 100644
--- a/assays/MassHunter_targets/README.md
+++ b/assays/MassHunter_targets/README.md
@@ -0,0 +1,30 @@
+# run1_MassHunter_targets
+
+> This is a placeholder until we have a proper routine to describing `runs` (computations) done with (proprietary or otherwise non-scripted) software.
+
+## File overview
+
+ ```bash
+ tree runs/run1_MassHunter_targets/
+
+ runs/run1_MassHunter_targets/
+ ├── QuantReports
+ │ └── 22-0005_exp001.batch_a.bin
+ │ ├── 190614_QuantReport_ISTD_DB.ReportStatus.xml
+ │ ├── 190614_QuantReport_ISTD_DB.xlsx
+ │ ├── Options.xml
+ │ ├── batch.results.xsd
+ │ └── report.results.xml
+ ├── QuantResults
+ │ └── 22-0005_exp001.batch_a.bin.batch.bin
+ └── README.md
+ ```
+
+## File description
+
+- Directories "QuantReports" and "QuantResults" are automatically created by MassHunter Quant
+- [./QuantReports](./QuantReports)
+- [./QuantResults](./QuantResults)
+ - stores only the "batch" binary
+ -
+
\ No newline at end of file
diff --git a/assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.ReportStatus.xml b/assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.ReportStatus.xml
new file mode 100644
index 0000000..dc29627
--- /dev/null
+++ b/assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.ReportStatus.xml
@@ -0,0 +1,3 @@
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+size 115
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new file mode 100644
index 0000000..c49b138
--- /dev/null
+++ b/assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/190614_QuantReport_ISTD_DB.xlsx
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new file mode 100644
index 0000000..ef8ec7d
--- /dev/null
+++ b/assays/MassHunter_targets/dataset/QuantReports/22-0005_exp001.batch_a.bin/Options.xml
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diff --git a/assays/MassHunter_targets/protocols/ProtRef05_DataTransformation.md b/assays/MassHunter_targets/protocols/ProtRef05_DataTransformation.md
new file mode 100644
index 0000000..eb22b35
--- /dev/null
+++ b/assays/MassHunter_targets/protocols/ProtRef05_DataTransformation.md
@@ -0,0 +1,7 @@
+> 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
new file mode 100644
index 0000000..e9dcfed
--- /dev/null
+++ b/assays/MassHunter_targets/protocols/ProtRef06_MetaboliteIdentification.md
@@ -0,0 +1,5 @@
+> 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
--
GitLab