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Plasmodium annotations
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ypriverol authored Nov 10, 2023
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2 changes: 1 addition & 1 deletion README.md
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## Final PSI specification

The final HUPO-PSI specification is: [SDRF HUPO-PSI](psi-document/SDRF_Proteomics_Specification_Final.pdf)
The final HUPO-PSI specification is: [SDRF HUPO-PSI](psi-document/SDRF_Proteomics_Specification_20230524_Final.pdf)

## How to contribute

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7 changes: 7 additions & 0 deletions annotated-projects/PXD000070/PXD000070.sdrf.tsv
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source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[biological replicate] assay name comment[plasmodium strain] comment[proteomexchange accession number] comment[data file] comment[file uri] comment[fraction identifier] comment[technical replicate] comment[label] comment[instrument] comment[dissociation method] comment[cleavage agent details] comment[modification parameters] comment[modification parameters] comment[modification parameters] comment[modification parameters] comment[modification parameters] comment[modification parameters] comment[modification parameters] comment[modification parameters] comment[precursor mass tolerance] comment[fragment mass tolerance]
Sample 1 plasmodium falciparum human erythrocytes schizont not applicable 1 run 1 3D7 PXD000070 OTPf-IMACDT2010Mar11-02.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2014/04/PXD000070/OTPf-IMACDT2010Mar11-02.raw 1 1 label free sample AC=MS:1001742;NT=LTQ Orbitrap Velos ETD AC=MS:1001251;NT=Trypsin NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed "NT=Oxidation;AC=UNIMOD:35;TA=M,W,H;MT=Variable" NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable NT=Acetyl;AC=UNIMOD:1;TA=K;MT=Variable "NT=Ammonia-loss;AC=UNIMOD:385;TA=Q,C;MT=Variable" NT=Glu->pyro-Glu;AC=UNIMOD:27;TA=E;MT=Variable NT=Deamidated;AC=UNIMOD:7;PP=Protein N-term;MT=Variable "NT=Phospho;AC=UNIMOD:21;TA=S,T,Y,A;MT=Variable" 20 ppm 1.0005 Da
Sample 2 plasmodium falciparum human erythrocytes schizont not applicable 2 run 2 3D7 PXD000070 OTPf-IMACDT2010Mar11-01.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2014/04/PXD000070/OTPf-IMACDT2010Mar11-01.raw 2 1 label free sample AC=MS:1001742;NT=LTQ Orbitrap Velos ETD AC=MS:1001251;NT=Trypsin NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed "NT=Oxidation;AC=UNIMOD:35;TA=M,W,H;MT=Variable" NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable NT=Acetyl;AC=UNIMOD:1;TA=K;MT=Variable "NT=Ammonia-loss;AC=UNIMOD:385;TA=Q,C;MT=Variable" NT=Glu->pyro-Glu;AC=UNIMOD:27;TA=E;MT=Variable NT=Deamidated;AC=UNIMOD:7;PP=Protein N-term;MT=Variable "NT=Phospho;AC=UNIMOD:21;TA=S,T,Y,A;MT=Variable" 20 ppm 1.0005 Da
Sample 3 plasmodium falciparum human erythrocytes schizont not applicable 3 run 3 3D7 PXD000070 OTPf-IMACDT2010Mar10-01.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2014/04/PXD000070/OTPf-IMACDT2010Mar10-01.raw 3 1 label free sample AC=MS:1001742;NT=LTQ Orbitrap Velos ETD AC=MS:1001251;NT=Trypsin NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed "NT=Oxidation;AC=UNIMOD:35;TA=M,W,H;MT=Variable" NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable NT=Acetyl;AC=UNIMOD:1;TA=K;MT=Variable "NT=Ammonia-loss;AC=UNIMOD:385;TA=Q,C;MT=Variable" NT=Glu->pyro-Glu;AC=UNIMOD:27;TA=E;MT=Variable NT=Deamidated;AC=UNIMOD:7;PP=Protein N-term;MT=Variable "NT=Phospho;AC=UNIMOD:21;TA=S,T,Y,A;MT=Variable" 20 ppm 1.0005 Da
Sample 4 plasmodium falciparum human erythrocytes schizont not applicable 1 run 1 3D7 PXD000070 OTPf-IMACDDNL_2010Mar9-02.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2014/04/PXD000070/OTPf-IMACDDNL_2010Mar9-02.raw 1 1 label free sample AC=MS:1001742;NT=LTQ Orbitrap Velos CID AC=MS:1001251;NT=Trypsin NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed "NT=Oxidation;AC=UNIMOD:35;TA=M,W,H;MT=Variable" NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable NT=Acetyl;AC=UNIMOD:1;TA=K;MT=Variable "NT=Ammonia-loss;AC=UNIMOD:385;TA=Q,C;MT=Variable" NT=Glu->pyro-Glu;AC=UNIMOD:27;TA=E;MT=Variable NT=Deamidated;AC=UNIMOD:7;PP=Protein N-term;MT=Variable "NT=Phospho;AC=UNIMOD:21;TA=S,T,Y,A;MT=Variable" 20 ppm 1.0005 Da
Sample 5 plasmodium falciparum human erythrocytes schizont not applicable 2 run 2 3D7 PXD000070 OTPf-IMACDDNL_2010Mar9-01.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2014/04/PXD000070/OTPf-IMACDDNL_2010Mar9-01.raw 2 1 label free sample AC=MS:1001742;NT=LTQ Orbitrap Velos CID AC=MS:1001251;NT=Trypsin NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed "NT=Oxidation;AC=UNIMOD:35;TA=M,W,H;MT=Variable" NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable NT=Acetyl;AC=UNIMOD:1;TA=K;MT=Variable "NT=Ammonia-loss;AC=UNIMOD:385;TA=Q,C;MT=Variable" NT=Glu->pyro-Glu;AC=UNIMOD:27;TA=E;MT=Variable NT=Deamidated;AC=UNIMOD:7;PP=Protein N-term;MT=Variable "NT=Phospho;AC=UNIMOD:21;TA=S,T,Y,A;MT=Variable" 20 ppm 1.0005 Da
Sample 6 plasmodium falciparum human erythrocytes schizont not applicable 3 run 3 3D7 PXD000070 OTPf-IMACDDNL_2010Mar06-02.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2014/04/PXD000070/OTPf-IMACDDNL_2010Mar06-02.raw 3 1 label free sample AC=MS:1001742;NT=LTQ Orbitrap Velos CID AC=MS:1001251;NT=Trypsin NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed "NT=Oxidation;AC=UNIMOD:35;TA=M,W,H;MT=Variable" NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable NT=Acetyl;AC=UNIMOD:1;TA=K;MT=Variable "NT=Ammonia-loss;AC=UNIMOD:385;TA=Q,C;MT=Variable" NT=Glu->pyro-Glu;AC=UNIMOD:27;TA=E;MT=Variable NT=Deamidated;AC=UNIMOD:7;PP=Protein N-term;MT=Variable "NT=Phospho;AC=UNIMOD:21;TA=S,T,Y,A;MT=Variable" 20 ppm 1.0005 Da
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