Skip to content

fix(metamorpheus): Fix input file from metamorpheus #115

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
tonywu1999 wants to merge 1 commit into from
Closed

fix(metamorpheus): Fix input file from metamorpheus #115

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
File Name Base Sequence Full Sequence Protein Group Peptide Monoisotopic Mass MS2 Retention Time Precursor Charge Theoretical MZ Peak intensity Peak RT Start Peak RT Apex Peak RT End Peak MZ Peak Charge Num Charge States Observed Peak Detection Type MBR Score PSMs Mapped Base Sequences Mapped Full Sequences Mapped Peak Split Valley RT Peak Apex Mass Error (ppm)
File Name Base Sequence Full Sequence Protein Group Peptide Monoisotopic Mass MS2 Retention Time Precursor Charge Theoretical MZ Peak intensity Peak RT Start Peak RT Apex Peak RT End Peak MZ Peak Charge Num Charge States Observed Peak Detection Type PIP Q-Value PSMs Mapped Base Sequences Mapped Full Sequences Mapped Peak Split Valley RT Peak Apex Mass Error (ppm)
180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib SQSPAASDCSSSSSSASLPSSGR SQS[UniProt:Phosphoserine on S]PAASDC[Common Fixed:Carbamidomethyl on C]SSSSSSASLPSSGR O95817 2278.900914 50.397666666666666 2 1140.4577332313788 5707.40135 50.252475 50.42875166666666 50.510398333333335 1140.9592170625633 2 2 MSMS 1 1 1 0 0.087875825
180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib SSTPLHSPSPIR SST[UniProt:Phosphothreonine on T]PLHS[UniProt:Phosphoserine on S]PSPIR O95817 1437.605461 2 719.810007 5707.40135 54.139628333333334 54.50228833333333 54.78205 719.8097832775803 2 1 MBR 1.7336595330500857 1 1 1 0 -0.311308359
180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib SQSPAASDCSSSSSSASLPSSGR SQS[UniProt:Phosphoserine on S]PAASDC[Common Fixed:Carbamidomethyl on C]SSSSSSASLPSSGR O95817 2278.900914 2 1140.4577332313788 5742.40502 50.199040000000004 50.302225 50.42404833333333 1140.9595414912699 2 1 MBR 9.237016638440622 4 1 1 0 0.37247443285717907
Expand Down Expand Up @@ -290,4 +290,4 @@ File Name Base Sequence Full Sequence Protein Group Peptide Monoisotopic Mass MS
180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib IGEGTYGVVYK IGEGTY[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1264.57407 61.50265666666667 2 633.2943116 133865.9758500041 61.426230000000004 61.50793 61.607135 633.2942515188375 2 1 MSMS 1 1 1 0 -0.095043134
180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 64.64144166666667 2 673.2774771133791 130513.20674378073 64.42739833333333 64.60346166666668 64.75379833333332 673.2768593517005 2 1 MSMS 1 1 1 0 -0.918918729
180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IGEGTYGVVYK IGEGTY[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1264.57407 2 633.2943116 143669.64531045672 61.92338 62.068884999999995 62.1854 633.2943373625029 2 1 MBR 7.936988119061599 3 1 1 0 0.040723789135849814
180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 2 673.2774771133791 119183.79826575483 64.96146999999999 65.14224 65.257965 673.2777346890584 2 1 MBR 2.7541674040199124 1 1 1 0 0.3831430861023523
180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 2 673.2774771133791 119183.79826575483 64.96146999999999 65.14224 65.257965 673.2777346890584 2 1 MBR 2.7541674040199124 1 1 1 0 0.3831430861023523
4 changes: 2 additions & 2 deletions inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaksGlobalProteome.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
File Name Base Sequence Full Sequence Protein Group Peptide Monoisotopic Mass MS2 Retention Time Precursor Charge Theoretical MZ Peak intensity Peak RT Start Peak RT Apex Peak RT End Peak MZ Peak Charge Num Charge States Observed Peak Detection Type MBR Score PSMs Mapped Base Sequences Mapped Full Sequences Mapped Peak Split Valley RT Peak Apex Mass Error (ppm)
File Name Base Sequence Full Sequence Protein Group Peptide Monoisotopic Mass MS2 Retention Time Precursor Charge Theoretical MZ Peak intensity Peak RT Start Peak RT Apex Peak RT End Peak MZ Peak Charge Num Charge States Observed Peak Detection Type PIP Q-Value PSMs Mapped Base Sequences Mapped Full Sequences Mapped Peak Split Valley RT Peak Apex Mass Error (ppm)
180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib SQSPAASDCSSSSSSASLPSSGR SQS[UniProt:Phosphoserine on S]PAASDCSSSSSSASLPSSGR O95817 2278.900914 50.397666666666666 2 1140.4577332313788 514664.0859 50.252475 50.42875166666666 50.510398333333335 1140.9592170625633 2 2 MSMS 1 1 1 0 0.087875825
180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib SSTPLHSPSPIR SST[UniProt:Phosphothreonine on T]PLHS[UniProt:Phosphoserine on S]PSPIR O95817 1437.605461 2 719.810007 514664.0859 54.139628333333334 54.50228833333333 54.78205 719.8097832775803 2 1 MBR 1.7336595330500857 1 1 1 0 -0.311308359
180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib SQSPAASDCSSSSSSASLPSSGR SQS[UniProt:Phosphoserine on S]PAASDCSSSSSSASLPSSGR O95817 2278.900914 2 1140.4577332313788 496019.547 50.199040000000004 50.302225 50.42404833333333 1140.9595414912699 2 1 MBR 9.237016638440622 4 1 1 0 0.37247443285717907
Expand Down Expand Up @@ -290,4 +290,4 @@ File Name Base Sequence Full Sequence Protein Group Peptide Monoisotopic Mass MS
180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib IGEGTYGVVYK IGEGTY[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1264.57407 61.50265666666667 2 633.2943116 133865.9758500041 61.426230000000004 61.50793 61.607135 633.2942515188375 2 1 MSMS 1 1 1 0 -0.095043134
180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 64.64144166666667 2 673.2774771133791 130513.20674378073 64.42739833333333 64.60346166666668 64.75379833333332 673.2768593517005 2 1 MSMS 1 1 1 0 -0.918918729
180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IGEGTYGVVYK IGEGTY[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1264.57407 2 633.2943116 143669.64531045672 61.92338 62.068884999999995 62.1854 633.2943373625029 2 1 MBR 7.936988119061599 3 1 1 0 0.040723789135849814
180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 2 673.2774771133791 119183.79826575483 64.96146999999999 65.14224 65.257965 673.2777346890584 2 1 MBR 2.7541674040199124 1 1 1 0 0.3831430861023523
180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 2 673.2774771133791 119183.79826575483 64.96146999999999 65.14224 65.257965 673.2777346890584 2 1 MBR 2.7541674040199124 1 1 1 0 0.3831430861023523
Loading