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| # Auto detect text files and perform LF normalization | ||
| * text=auto |
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| # phosphoRS-cli | ||
| A command line interface of phosphoRS (version 3.1). | ||
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| ## Denpendency | ||
| Download the phosphoRS library (`IMP.PhosphoRS.dll`) from Research Institute of Molecular Pathology (IMP): | ||
| https://ms.imp.ac.at/index.php?action=phosphors. | ||
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| Place the DLL file in the `src/lib` directory (source code), and in the same directory as the executable file (released binary). | ||
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| ## Usage | ||
| ``` | ||
| phosphoRS: | ||
| PhosphoRS Commandline Tool | ||
| Usage: | ||
| phosphoRS [options] | ||
| Options: | ||
| -i, --input <INPUT> Input file (.XML). This option will be used first. | ||
| -o, --output <OUTPUT> Output path (.XML, .JSON or .CSV). | ||
| -p, --peptide <PEPTIDE> Peptide identification result file (.PepXML). This option will be ignored if --input is given. | ||
| -s, --spectra <SPECTRA> MS2 Spectra file (.MGF). This option will be ignored if --input is given. | ||
| -a, --activation <ACTIVATION> Activation type (CID, HCD, ECD or ETD). Default CID. This option will be ignored if --input is given. | ||
| -t, --tolerance <TOLERANCE> Mass tolerance. Default 0.02. This option will be ignored if --input is given. | ||
| -I, --max-isoform <MAX-ISOFORM> Maximun number of isoforms. Default 200. This option will be ignored if --input is given. | ||
| -P, --max-ptm <MAX-PTM> Maximun number of PTMs. Default 20. This option will be ignored if --input is given. | ||
| -n, --neutral-loss <NEUTRAL-LOSS> Score neutral loss. Default on. This option will be ignored if --input is given. | ||
| --version Display version information | ||
| ``` | ||
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| Example input and output files are provided in the `data` directory. | ||
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| ## Accessories | ||
| R scripts are provided in the `scripts` directory to generate an input XML file from a PSM list file and MGF files. | ||
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| ## License | ||
| phosphoRS-cli is distributed under a MIT license. See the LICENSE file for details. | ||
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| The phosphoRS library (`IMP.PhosphoRS.dll`) is provided as freeware by its copyright owner, Research Institute of Molecular Pathology (IMP), under their license. |
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| Spectrum.ID,Spectrum.Name,Spectrum.PrecursorCharge,Spectrum.ActivationType,Peptide.ID,Peptide.Sequence,Peptide.SitePrediction,Isoform.ID,Isoform.Sites,Isoform.Score,Isoform.Probability | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",9,"S4 S5",392.754005072161,0.999999999066859 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",6,"S3 S5",302.397053342907,9.21095852282221E-10 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",2,"S1 S5",280.521623440042,5.98083520897E-12 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",5,"S3 S4",280.521623440042,5.98083520897E-12 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",0,"S1 S3",258.958320603989,4.17283827033656E-14 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",1,"S1 S4",258.958320603989,4.17283827033656E-14 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",10,"S4 S8",237.723547110095,3.14017754282338E-16 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",12,"S5 S8",196.317442760866,2.2716622886442E-20 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",7,"S3 S8",156.491972688571,2.3648127663106E-24 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",11,"S4 T11",156.491972688571,2.3648127663106E-24 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",3,"S1 S8",137.250075295303,2.81583382727202E-26 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",13,"S5 T11",118.510058924983,3.76361668224792E-28 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",14,"S8 T11",118.510058924983,3.76361668224792E-28 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",8,"S3 T11",82.7620269536716,1.00184881249549E-31 | ||
| 1,,2,HCD,1,SGSSSPDSEITELK,"S1(0) S3(0) S4(1) S5(1) S8(0) T11(0)",4,"S1 T11",65.9091945557713,2.06784959874149E-33 | ||
| 2,,2,HCD,2,LPSGSGAASPTGSAVDIR,"S3(0) S5(0) S9(0) T11(0.004) S13(0.996)",19,S13,579.22843820125,0.996047014031657 | ||
| 2,,2,HCD,2,LPSGSGAASPTGSAVDIR,"S3(0) S5(0) S9(0) T11(0.004) S13(0.996)",18,T11,555.214813596436,0.00395291410469091 | ||
| 2,,2,HCD,2,LPSGSGAASPTGSAVDIR,"S3(0) S5(0) S9(0) T11(0.004) S13(0.996)",17,S9,507.810732683006,7.18636524044619E-08 | ||
| 2,,2,HCD,2,LPSGSGAASPTGSAVDIR,"S3(0) S5(0) S9(0) T11(0.004) S13(0.996)",16,S5,243.380094522614,2.59086909156132E-34 | ||
| 2,,2,HCD,2,LPSGSGAASPTGSAVDIR,"S3(0) S5(0) S9(0) T11(0.004) S13(0.996)",15,S3,164.783478028759,3.57918231292123E-42 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",20,"S4 T5",399.131001144813,0.495133709035036 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",21,"S4 S6",399.131001144813,0.495133709035036 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",22,"S4 S8",379.0112406066,0.00481666498312469 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",27,"T5 S6",379.0112406066,0.00481666498312469 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",23,"S4 T12",359.094384297048,4.90976617555566E-05 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",28,"T5 S8",359.094384297048,4.90976617555566E-05 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",29,"T5 T12",339.38780588696,5.25294639080144E-07 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",33,"S6 S8",339.38780588696,5.25294639080144E-07 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",34,"S6 T12",319.899548167704,5.90986005148112E-09 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",24,"S4 T15",300.638415825034,7.00590045775085E-11 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",38,"S8 T12",300.638415825034,7.00590045775085E-11 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",30,"T5 T15",281.614086243079,8.77063432348358E-13 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",25,"S4 Y16",262.837242936226,1.16237610489763E-14 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",35,"S6 T15",262.837242936226,1.16237610489763E-14 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",42,"T12 T15",262.837242936226,1.16237610489763E-14 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",31,"T5 Y16",244.319737687871,1.63529514998421E-16 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",39,"S8 T15",244.319737687871,1.63529514998421E-16 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",26,"S4 T17",226.074789544064,2.44963475065072E-18 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",36,"S6 Y16",226.074789544064,2.44963475065072E-18 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",43,"T12 Y16",226.074789544064,2.44963475065072E-18 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",45,"T15 Y16",226.074789544064,2.44963475065072E-18 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",32,"T5 T17",208.117231749231,3.92053698177584E-20 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",40,"S8 Y16",208.117231749231,3.92053698177584E-20 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",37,"S6 T17",190.463821964802,6.72983747841857E-22 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",44,"T12 T17",190.463821964802,6.72983747841857E-22 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",46,"T15 T17",190.463821964802,6.72983747841857E-22 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",47,"Y16 T17",190.463821964802,6.72983747841857E-22 | ||
| 3,,3,HCD,3,RAPSTSPSFEGTQETYTVAHEENVR,"S4(0.995) T5(0.5) S6(0.5) S8(0.005) T12(0) T15(0) Y16(0) T17(0)",41,"S8 T17",173.133637396762,1.24447483670051E-23 |
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