Merge pull request #710 from bigbio/dev

Changes in the Enzyme definition PSI accession added. [NOT MERGE YET]

.github/workflows/validate-all.yml

@@ -4,16 +4,13 @@ name: Validate annotations
 
 on:
   push:
+    branches: [ master, dev ]
     paths:
       - 'annotated-projects/**'
-      - 'validate.py'
   pull_request:
-    branches: [ master ]
+    branches: [ master, dev ]
     paths:
       - 'annotated-projects/**'
-      - 'validate.py'
-  schedule:
-      - cron: '0 0 * * *'
 
 jobs:
   sdrf_proteomics_validations:
@@ -55,53 +52,6 @@ jobs:
             python validate.py -v
           else
             export FILELIST=$HOME/filelist.txt
-            cat "$FILELIST"
-            if grep -q '^validate.py' "$FILELIST"; then
-              echo "Validating all projects (script changed)"
-              python validate.py -v
-            else
-              projects=$(cat "$FILELIST" | grep '^annotated-projects' | cut -d/ -f 2)
-              echo "Validating projects:" $projects
-              python validate.py -v $projects
-            fi
+            cat "$FILELIST" | while read line; do echo "Changed file: $line"; parse_sdrf validate-sdrf --sdrf_file $line --skip_factor_validation --skip_experimental_design_validation --use_ols_cache_only; done
           fi
-#  mage_tab_validation:
-#    runs-on: ubuntu-latest
-#    steps:
-#      - uses: actions/checkout@v2
-#      - name: Setup conda
-#        uses: s-weigand/setup-conda@v1
-#        with:
-#          update-conda: true
-#          conda-channels: anaconda, bioconda, conda-forge
-#      - name: Install perl-atlas-modules
-#        run: conda create -n perl-atlas -c ebi-gene-expression-group -c bioconda perl-atlas-modules perl-graphviz
-#      - name: Validate General MAGE-TAB
-#        run: |
-#          . /usr/share/miniconda/bin/activate /usr/share/miniconda/envs/perl-atlas
-#          perl simple_validate_magetab.pl
-#      - name: Archive production artifacts
-#        uses: actions/upload-artifact@v2
-#        with:
-#          name: sdrf-picture
-#          path: graph_file_sdrf.png
-#          retention-days: 5
-#  mage_tab_expression_atlas_validations:
-#    runs-on: ubuntu-latest
-#    steps:
-#      - uses: actions/checkout@v2
-#      - name: Setup conda
-#        uses: s-weigand/setup-conda@v1
-#        with:
-#          update-conda: true
-#          conda-channels: anaconda, bioconda, conda-forge
-#      - name: Install perl-atlas-modules
-#        run: conda create -n perl-atlas -c ebi-gene-expression-group perl-atlas-modules
-#      - name: Validate Expression Atlas MAGE-TAB
-#        id: atlas
-#        run: |
-#          . /usr/share/miniconda/bin/activate /usr/share/miniconda/envs/perl-atlas
-#          perl validate_magetab.pl -i annotated-projects/PXD000288/PXD000288.idf.tsv -x -c -v
-#          RSPEC_RESULT=$?
-#          exit 0
 

README.md

@@ -58,7 +58,7 @@ pip install sdrf-pipelines
 validate the SDRF file
 
 ```bash
-parse_sdrf validate-sdrf --sdrf_file sdrf.tsv
+parse_sdrf validate-sdrf --sdrf_file PXD020294.sdrf.tsv
 ```
 
 You can read more about the validator [here](https://github.com/bigbio/sdrf-pipelines).

annotated-projects/PMID31975593/PMID31975593.sdrf.tsv

@@ -1,11 +1,11 @@
 source name	characteristics[organism]	characteristics[organism part]	characteristics[cell type]	characteristics[disease]	characteristics[pool]	characteristics[enrichment process]	characteristics[ancestry category]	characteristics[age]	characteristics[developmental stage]	characteristics[biological replicate]	characteristics[sex]	assay name	technology type	comment[technical replicate]	comment[fraction identifier]	comment[label]	comment[data file]	comment[file uri]	comment[instrument]	comment[cleavage agent details]	comment[modification parameters]	comment[modification parameters]	comment[modification parameters]	comment[modification parameters]	comment[modification parameters]	comment[modification parameters]	comment[fragment mass tolerance]	comment[precursor mass tolerance]	factor value[pool]
-Sample 1	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	1	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 1	proteomic profiling by mass spectrometry	1	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool1_HCDOT_rep1.raw	https://ftp.ebi.ac.uk/pride-archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool1_HCDOT_rep1.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	1
-Sample 1	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	1	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 2	proteomic profiling by mass spectrometry	2	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool1_HCDOT_rep2.raw	https://ftp.ebi.ac.uk/pride-archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool1_HCDOT_rep2.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	1
-Sample 2	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	2	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 3	proteomic profiling by mass spectrometry	1	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool2_HCDOT_rep1.raw	https://ftp.ebi.ac.uk/pride-archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool2_HCDOT_rep1.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	2
-Sample 2	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	2	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 4	proteomic profiling by mass spectrometry	2	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool2_HCDOT_rep2.raw	https://ftp.ebi.ac.uk/pride-archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool2_HCDOT_rep2.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	2
-Sample 3	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	3	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 5	proteomic profiling by mass spectrometry	1	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool3_HCDOT_rep1.raw	https://ftp.ebi.ac.uk/pride-archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool3_HCDOT_rep1.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	3
-Sample 3	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	3	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 6	proteomic profiling by mass spectrometry	2	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool3_HCDOT_rep2.raw	https://ftp.ebi.ac.uk/pride-archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool3_HCDOT_rep2.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	3
-Sample 4	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	4	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 7	proteomic profiling by mass spectrometry	1	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool4_HCDOT_rep1.raw	https://ftp.ebi.ac.uk/pride-archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool4_HCDOT_rep1.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	4
-Sample 4	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	4	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 8	proteomic profiling by mass spectrometry	2	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool4_HCDOT_rep2.raw	https://ftp.ebi.ac.uk/pride-archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool4_HCDOT_rep2.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	4
-Sample 5	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	5	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 9	proteomic profiling by mass spectrometry	1	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool5_HCDOT_rep1.raw	https://ftp.ebi.ac.uk/pride-archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool5_HCDOT_rep1.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	5
-Sample 5	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	5	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 10	proteomic profiling by mass spectrometry	2	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool5_HCDOT_rep2.raw	https://ftp.ebi.ac.uk/pride-archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool5_HCDOT_rep2.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	5
+Sample 1	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	1	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 1	proteomic profiling by mass spectrometry	1	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool1_HCDOT_rep1.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool1_HCDOT_rep1.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	1
+Sample 1	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	1	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 2	proteomic profiling by mass spectrometry	2	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool1_HCDOT_rep2.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool1_HCDOT_rep2.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	1
+Sample 2	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	2	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 3	proteomic profiling by mass spectrometry	1	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool2_HCDOT_rep1.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool2_HCDOT_rep1.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	2
+Sample 2	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	2	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 4	proteomic profiling by mass spectrometry	2	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool2_HCDOT_rep2.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool2_HCDOT_rep2.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	2
+Sample 3	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	3	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 5	proteomic profiling by mass spectrometry	1	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool3_HCDOT_rep1.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool3_HCDOT_rep1.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	3
+Sample 3	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	3	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 6	proteomic profiling by mass spectrometry	2	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool3_HCDOT_rep2.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool3_HCDOT_rep2.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	3
+Sample 4	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	4	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 7	proteomic profiling by mass spectrometry	1	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool4_HCDOT_rep1.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool4_HCDOT_rep1.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	4
+Sample 4	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	4	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 8	proteomic profiling by mass spectrometry	2	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool4_HCDOT_rep2.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool4_HCDOT_rep2.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	4
+Sample 5	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	5	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 9	proteomic profiling by mass spectrometry	1	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool5_HCDOT_rep1.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool5_HCDOT_rep1.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	5
+Sample 5	Homo sapiens	Epithelial cell	Epithelial cell	Bone osteosarcoma	5	enrichment of phosphorylated Protein	not available	not available	not available	1	not available	run 10	proteomic profiling by mass spectrometry	2	1	AC=MS:1002038;NT=label free sample	SF_200217_pPeptideLibrary_pool5_HCDOT_rep2.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/09/PXD007058/SF_200217_pPeptideLibrary_pool5_HCDOT_rep2.raw	NT=Orbitrap Fusion ETD;AC=MS:1002417	NT=Trypsin;AC=MS:1001251	NT=Phospho;TA=S,T,Y;AC=UNIMOD:21;MT=variable	NT=Oxidation;TA=M;AC=UNIMOD:35;MT=variable	NT=Carbamidomethyl;TA=C;AC=UNIMOD:4;MT=fixed	NT=pyrophospho;TA=S,T;AC=UNIMOD:898;MT=variable	NT=Deamidated;TA=N,Q;AC=UNIMOD:7;MT=variable	NT=Acetyl;TA=N-term;AC=UNIMOD:1;MT=variable	0.6 Da	10 ppm	5