From 2b1e40e61c21e052ece036aba1d61482dc2c89ee Mon Sep 17 00:00:00 2001 From: trishorts Date: Tue, 14 Jan 2025 15:38:28 -0600 Subject: [PATCH 1/9] supposedToBeDifferent --- mzLib/Test/DatabaseTests/05.xml | 2654 ++++++++++++++++++++++++++++ mzLib/Test/DatabaseTests/06.xml | 2654 ++++++++++++++++++++++++++++ mzLib/Test/Test.csproj | 6 + mzLib/Test/TestProteinDigestion.cs | 32 + 4 files changed, 5346 insertions(+) create mode 100644 mzLib/Test/DatabaseTests/05.xml create mode 100644 mzLib/Test/DatabaseTests/06.xml diff --git a/mzLib/Test/DatabaseTests/05.xml b/mzLib/Test/DatabaseTests/05.xml new file mode 100644 index 000000000..472cef3c6 --- /dev/null +++ b/mzLib/Test/DatabaseTests/05.xml @@ -0,0 +1,2654 @@ + + + ID (3R)-3-hydroxyasparagine on N +AC PTM-0369 +MT UniProt +FT MOD_RES +TG N +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00035 +DR RESID; AA0026 +TR Eukaryota; taxId:40674 (Mammalia) +KW Hydroxylation + +// + ID (3R)-3-hydroxyaspartate on D +AC PTM-0371 +MT UniProt +FT MOD_RES +TG D +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00036 +DR RESID; AA0027 +TR Bacteria; taxId:68215 (Streptomyces griseoverticillatus) +TR Eukaryota; taxId:40674 (Mammalia) +KW Hydroxylation + +// + ID (3S)-3-hydroxyasparagine on N +AC PTM-0370 +MT UniProt +FT MOD_RES +TG N +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:01401 +DR RESID; AA0478 +TR Eukaryota; taxId:7742 (Vertebrata) +KW Hydroxylation + +// + ID (3S)-3-hydroxyaspartate on D +AC PTM-0473 +MT UniProt +FT MOD_RES +TG D +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:01919 +TR Eukaryota; taxId:33208 (Metazoa) +KW Hydroxylation + +// + ID (3S)-3-hydroxyhistidine on H +AC PTM-0477 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:01920 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hydroxylation + +// + ID (4R)-5-hydroxyleucine on L +AC PTM-0491 +MT UniProt +FT MOD_RES +TG L +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:01373 +DR RESID; AA0443 +TR Eukaryota; taxId:33208 (Metazoa) +KW Hydroxylation + +// + ID (4R)-5-oxoleucine on L +AC PTM-0492 +MT UniProt +FT MOD_RES +TG L +PP Anywhere. +CF H-2O +MM 13.979265 +DR PSI-MOD; MOD:01374 +DR RESID; AA0444 +TR Eukaryota; taxId:33208 (Metazoa) +KW Oxidation + +// + ID 2',4',5'-topaquinone on Y +AC PTM-0009 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF H-2O2 +MM 29.974179 +DR PSI-MOD; MOD:00156 +DR RESID; AA0147 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW TPQ + +// + ID 3-hydroxyasparagine on N +AC PTM-0028 +MT UniProt +FT MOD_RES +TG N +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00035 +DR RESID; AA0026 +TR Eukaryota; taxId:7742 (Vertebrata) +KW Hydroxylation + +// + ID 3-hydroxyproline on P +AC PTM-0030 +MT UniProt +FT MOD_RES +TG P +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00038 +DR RESID; AA0029 +TR Eukaryota; taxId:33208 (Metazoa) +KW Hydroxylation + +// + ID 3-oxoalanine (Cys) on C +AC PTM-0033 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF H-2OS-1 +MM -17.992806 +DR PSI-MOD; MOD:00193 +DR RESID; AA0185 +TR Bacteria; taxId:1224 (Proteobacteria), taxId:1239 (Firmicutes) +TR Eukaryota; taxId:3041 (Chlorophyta), taxId:33208 (Metazoa) + +// + ID 3'-nitrotyrosine on Y +AC PTM-0434 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF H-1NO2 +MM 44.985078 +DR PSI-MOD; MOD:01786 +DR RESID; AA0537 +TR Eukaryota; taxId:40674 (Mammalia) +KW Nitration + +// + ID 4-carboxyglutamate on E +AC PTM-0039 +MT UniProt +FT MOD_RES +TG E +PP Anywhere. +CF CO2 +MM 43.989829 +DR PSI-MOD; MOD:00041 +DR RESID; AA0032 +TR Eukaryota; taxId:6447 (Mollusca), taxId:7742 (Vertebrata) +KW Gamma-carboxyglutamic acid + +// + ID 4-hydroxyproline on P +AC PTM-0043 +MT UniProt +FT MOD_RES +TG P +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00039 +DR RESID; AA0030 +TR Bacteria; taxId:415003 (Microbispora sp. (strain 107891)) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hydroxylation + +// + ID 5-glutamyl glutamate on E +AC PTM-0479 +MT UniProt +FT MOD_RES +TG E +PP Anywhere. +CF C5H7NO3 +MM 129.042593 +DR PSI-MOD; MOD:01970 +DR RESID; AA0612 +TR Archaea; taxId:2267 (Thermoproteaceae) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Isopeptide bond + +// + ID 5-glutamyl glycerylphosphorylethanolamine on E +AC PTM-0403 +MT UniProt +FT MOD_RES +TG E +PP Anywhere. +CF C5H12NO5P +MM 197.045309 +DR PSI-MOD; MOD:00179 +DR RESID; AA0170 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Phosphoprotein + +// + ID 5-hydroxylysine on K +AC PTM-0044 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00037 +DR RESID; AA0028 +TR Eukaryota; taxId:33208 (Metazoa) +KW Hydroxylation + +// + ID Acetylation on K +MT Common Biological +TG K +PP Anywhere. +CF C2H2O +MM 42.010564684 +DR Unimod; 1 +NL ETD:45.0204 +DI HCD:125.084063979 + +// + ID Acetylation on S +MT Less Common +TG S +PP Anywhere. +CF C2H2O +MM 42.010564684 +DR Unimod; 1 + +// + ID Acetylation on T +MT Less Common +TG T +PP Anywhere. +CF C2H2O +MM 42.010564684 +DR Unimod; 1 + +// + ID Acetylation on X +MT Common Biological +TG X +PP N-terminal. +CF C2H2O +MM 42.010564684 +DR Unimod; 1 + +// + ID ADP-ribosyl glutamic acid on E +AC PTM-0646 +MT UniProt +FT MOD_RES +TG E +PP Anywhere. +CF C15H21N5O13P2 +MM 541.061109 +TR Eukaryota; taxId:40674 (Mammalia) +KW ADP-ribosylation + +// + ID ADP-ribosylarginine on R +AC PTM-0053 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF C15H21N5O13P2 +MM 541.061109 +DR PSI-MOD; MOD:00177 +DR RESID; AA0168 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW ADP-ribosylation + +// + ID ADP-ribosylcysteine on C +AC PTM-0055 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF C15H21N5O13P2 +MM 541.061109 +DR PSI-MOD; MOD:00178 +DR RESID; AA0169 +TR Eukaryota; taxId:40674 (Mammalia) +KW ADP-ribosylation + +// + ID ADP-ribosylserine on S +AC PTM-0056 +MT UniProt +FT MOD_RES +TG S +PP Anywhere. +CF C15H21N5O13P2 +MM 541.061109 +DR PSI-MOD; MOD:00242 +DR RESID; AA0237 +TR Eukaryota; taxId:9606 (Homo sapiens) +KW ADP-ribosylation + +// + ID Allysine on K +AC PTM-0059 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF H-3N-1O +MM -1.031634 +DR PSI-MOD; MOD:00130 +DR RESID; AA0121 +TR Eukaryota; taxId:6052 (Ephydatia muelleri), taxId:7742 (Vertebrata) + +// + ID Amidation on X +MT Less Common +TG X +PP Peptide C-terminal. +CF HNO-1 +MM -0.984015583 +DR Unimod; 2 + +// + ID Ammonia loss on C +MT Common Artifact +TG C +PP Peptide N-terminal. +CF H-3N-1 +MM -17.026549101 +DR Unimod; 385 + +// + ID Ammonia loss on N +MT Common Artifact +TG N +PP Anywhere. +CF H-3N-1 +MM -17.026549101 +DR Unimod; 385 + +// + ID Asymmetric dimethylarginine on R +AC PTM-0066 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF C2H4 +MM 28.0313 +DR PSI-MOD; MOD:00077 +DR RESID; AA0068 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID Calcium on D +MT Metal +TG D +PP Anywhere. +CF H-2Ca +MM 37.946940799 +DR Unimod; 951 + +// + ID Calcium on E +MT Metal +TG E +PP Anywhere. +CF H-2Ca +MM 37.946940799 +DR Unimod; 951 + +// + ID Carbamidomethyl on D +MT Less Common +TG D +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on E +MT Less Common +TG E +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on H +MT Less Common +TG H +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on K +MT Less Common +TG K +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on S +MT Less Common +TG S +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on T +MT Less Common +TG T +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on X +MT Less Common +TG X +PP Peptide N-terminal. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on Y +MT Less Common +TG Y +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamyl on C +MT Common Artifact +TG C +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on K +MT Common Artifact +TG K +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on M +MT Common Artifact +TG M +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on R +MT Common Artifact +TG R +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on X +MT Common Artifact +TG X +PP Peptide N-terminal. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carboxylation on D +MT Common Biological +TG D +PP Anywhere. +CF CO2 +MM 43.989829239 +DR Unimod; 299 + +// + ID Carboxylation on E +MT Common Biological +TG E +PP Anywhere. +CF CO2 +MM 43.989829239 +DR Unimod; 299 + +// + ID Carboxylation on K +MT Common Biological +TG K +PP Anywhere. +CF CO2 +MM 43.989829239 +DR Unimod; 299 + +// + ID Carboxymethylation on K +MT Less Common +TG K +PP Anywhere. +CF C2H2O2 +MM 58.005479304 +DR Unimod; 6 + +// + ID Carboxymethylation on W +MT Less Common +TG W +PP Anywhere. +CF C2H2O2 +MM 58.005479304 +DR Unimod; 6 + +// + ID Carboxymethylation on X +MT Less Common +TG X +PP Peptide N-terminal. +CF C2H2O2 +MM 58.005479304 +DR Unimod; 6 + +// + ID Citrullination on R +MT Common Biological +TG R +PP Anywhere. +CF H-1N-1O +MM 0.984015583 +DR Unimod; 7 +NL HCD:43.0058 +DI HCD:129.090223533 + +// + ID Citrulline on R +AC PTM-0092 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF H-1N-1O +MM 0.984016 +DR PSI-MOD; MOD:00219 +DR RESID; AA0214 +TR Eukaryota; taxId:7742 (Vertebrata) +KW Citrullination + +// + ID Crotonylation on K +MT Common Biological +TG K +PP Anywhere. +CF C4H4O +MM 68.026214748 +DR Unimod; 1363 +DI HCD:151.099723533 + +// + ID Cu[I] on D +MT Metal +TG D +PP Anywhere. +CF H-1Cu +MM 61.921772688 +DR Unimod; 531 + +// + ID Cu[I] on E +MT Metal +TG E +PP Anywhere. +CF H-1Cu +MM 61.921772688 +DR Unimod; 531 + +// + ID Cysteine methyl ester on C +AC PTM-0105 +MT UniProt +FT MOD_RES +TG C +PP C-terminal. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00114 +DR RESID; AA0105 +TR Bacteria; taxId:201174 (Actinobacteria) +TR Eukaryota; taxId:4751 (Fungi), taxId:33208 (Metazoa) +KW Methylation + +// + ID Cysteine persulfide on C +AC PTM-0106 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF S +MM 31.972071 +DR PSI-MOD; MOD:00274 +DR RESID; AA0269 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID Cysteine sulfenic acid (-SOH) on C +AC PTM-0107 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00210 +DR RESID; AA0205 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:40674 (Mammalia) +KW Oxidation + +// + ID Cysteine sulfinic acid (-SO2H) on C +AC PTM-0108 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF O2 +MM 31.989829 +DR PSI-MOD; MOD:00267 +DR RESID; AA0262 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:40674 (Mammalia) +KW Oxidation + +// + ID Cysteine sulfonic acid (-SO3H) on C +AC PTM-0634 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF O3 +MM 47.984744 +DR PSI-MOD; MOD:00460 +DR RESID; AA0556 +TR Eukaryota; taxId:40674 (Mammalia) +KW Oxidation + +// + ID Deamidated asparagine on N +AC PTM-0116 +MT UniProt +FT MOD_RES +TG N +PP Anywhere. +CF H-1N-1O +MM 0.984016 +DR PSI-MOD; MOD:00684 +DR RESID; AA0004 +TR Eukaryota; taxId:3702 (Arabidopsis thaliana), taxId:7742 (Vertebrata) + +// + ID Deamidated glutamine on Q +AC PTM-0117 +MT UniProt +FT MOD_RES +TG Q +PP Anywhere. +CF H-1N-1O +MM 0.984016 +DR PSI-MOD; MOD:00685 +DR RESID; AA0006 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:7742 (Vertebrata) + +// + ID Deamidation on N +MT Common Artifact +TG N +PP Anywhere. +CF H-1N-1O +MM 0.984015583 +DR Unimod; 7 + +// + ID Deamidation on Q +MT Common Artifact +TG Q +PP Anywhere. +CF H-1N-1O +MM 0.984015583 +DR Unimod; 7 + +// + ID Decarboxylation on D +MT Less Common +TG D +PP Anywhere. +CF C-1H-2O-1 +MM -30.010564684 +DR Unimod; 914 + +// + ID Decarboxylation on E +MT Less Common +TG E +PP Anywhere. +CF C-1H-2O-1 +MM -30.010564684 +DR Unimod; 914 + +// + ID Dehydroalanine on S +MT Less Common +TG S +PP Anywhere. +CF H-2O-1 +MM -18.010564684 + +// + ID Dehydrobutyrine on T +MT Less Common +TG T +PP Anywhere. +CF H-2O-1 +MM -18.010564684 + +// + ID Didehydro on Y +MT Less Common +TG Y +PP Anywhere. +CF H-2 +MM -2.015650064 +DR Unimod; 401 + +// + ID Dimethylated arginine on R +AC PTM-0341 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF C2H4 +MM 28.0313 +DR PSI-MOD; MOD:00783 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID Dimethylation on N +MT Less Common +TG N +PP Anywhere. +CF C2H4 +MM 28.031300129 +DR Unimod; 36 + +// + ID Dimethylation on R +MT Common Biological +TG R +PP Anywhere. +CF C2H4 +MM 28.031300129 +DR Unimod; 36 +NL ETD:31.0422 or ETD:45.0579 + +// + ID Dioxidation on C +MT Less Common +TG C +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on F +MT Less Common +TG F +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on K +MT Less Common +TG K +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on M +MT Less Common +TG M +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on P +MT Less Common +TG P +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on R +MT Less Common +TG R +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on W +MT Less Common +TG W +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on Y +MT Less Common +TG Y +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Diphthamide on H +AC PTM-0118 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF C7H14N2O +MM 142.110613533 +DR PSI-MOD; MOD:00049 +DR RESID; AA0040 +TR Archaea; taxId:2157 (Archaea) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID Ethylation on D +MT Less Common +TG D +PP Anywhere. +CF C2H4 +MM 28.031300129 +DR Unimod; 280 + +// + ID Ethylation on X +MT Less Common +TG X +PP Peptide N-terminal. +CF C2H4 +MM 28.031300129 +DR Unimod; 280 + +// + ID Formylation on K +MT Common Biological +TG K +PP Anywhere. +CF CO +MM 27.99491462 +DR Unimod; 122 +DI HCD:111.068423533 + +// + ID Formylation on S +MT Less Common +TG S +PP Anywhere. +CF CO +MM 27.99491462 +DR Unimod; 122 + +// + ID Formylation on T +MT Less Common +TG T +PP Anywhere. +CF CO +MM 27.99491462 +DR Unimod; 122 + +// + ID Formylation on X +MT Less Common +TG X +PP Peptide N-terminal. +CF CO +MM 27.99491462 +DR Unimod; 122 + +// + ID Glycyl adenylate on G +AC PTM-0409 +MT UniProt +FT MOD_RES +TG G +PP C-terminal. +CF C10H12N5O6P +MM 329.05252 +DR PSI-MOD; MOD:01614 +DR RESID; AA0511 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Nucleotide-binding or Phosphoprotein + +// + ID Hydroxylation on K +MT Common Biological +TG K +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Hydroxylation on N +MT Common Biological +TG N +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Hydroxylation on P +MT Common Biological +TG P +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 +DI HCD:170.069143 + +// + ID Hydroxyproline on P +AC PTM-0149 +MT UniProt +FT MOD_RES +TG P +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00678 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hydroxylation + +// + ID Hypusine on K +AC PTM-0150 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H9NO +MM 87.068414 +DR PSI-MOD; MOD:00125 +DR RESID; AA0116 +TR Archaea; taxId:2157 (Archaea) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hypusine + +// + ID Leucine methyl ester on L +AC PTM-0167 +MT UniProt +FT MOD_RES +TG L +PP C-terminal. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00304 +DR RESID; AA0299 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID Magnesium on D +MT Metal +TG D +PP Anywhere. +CF H-2Mg +MM 21.969391633 +DR Unimod; 956 + +// + ID Magnesium on E +MT Metal +TG E +PP Anywhere. +CF H-2Mg +MM 21.969391633 +DR Unimod; 956 + +// + ID Methionine (R)-sulfoxide on M +AC PTM-0480 +MT UniProt +FT MOD_RES +TG M +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00720 +DR RESID; AA0581 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Oxidation + +// + ID Methionine sulfoxide on M +AC PTM-0469 +MT UniProt +FT MOD_RES +TG M +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00719 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Oxidation + +// + ID Methylation on C +MT Less Common +TG C +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on D +MT Less Common +TG D +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on E +MT Less Common +TG E +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on H +MT Less Common +TG H +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on I +MT Less Common +TG I +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on K +MT Common Biological +TG K +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on L +MT Less Common +TG L +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on N +MT Less Common +TG N +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on Q +MT Less Common +TG Q +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on R +MT Common Biological +TG R +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on S +MT Less Common +TG S +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on T +MT Less Common +TG T +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylhistidine on H +AC PTM-0176 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00661 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Eukaryota; taxId:5791 (Physarum polycephalum), taxId:7742 (Vertebrata) +KW Methylation + +// + ID N-acetylalanine on A +AC PTM-0199 +MT UniProt +FT MOD_RES +TG A +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00050 +DR RESID; AA0041 +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylaspartate on D +AC PTM-0200 +MT UniProt +FT MOD_RES +TG D +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00051 +DR RESID; AA0042 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylcysteine on C +AC PTM-0201 +MT UniProt +FT MOD_RES +TG C +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00052 +DR RESID; AA0043 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Eukaryota; taxId:7742 (Vertebrata) +KW Acetylation + +// + ID N-acetylglutamate on E +AC PTM-0202 +MT UniProt +FT MOD_RES +TG E +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00053 +DR RESID; AA0044 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylglycine on G +AC PTM-0203 +MT UniProt +FT MOD_RES +TG G +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00055 +DR RESID; AA0046 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylmethionine on M +AC PTM-0205 +MT UniProt +FT MOD_RES +TG M +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00058 +DR RESID; AA0049 +TR Archaea; taxId:2287 (Sulfolobus solfataricus) +TR Bacteria; taxId:1270 (Micrococcus luteus) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylproline on P +AC PTM-0206 +MT UniProt +FT MOD_RES +TG P +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00059 +DR RESID; AA0050 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:33090 (Viridiplantae), taxId:40674 (Mammalia) +KW Acetylation + +// + ID N-acetylserine on S +AC PTM-0207 +MT UniProt +FT MOD_RES +TG S +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00060 +DR RESID; AA0051 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylthreonine on T +AC PTM-0208 +MT UniProt +FT MOD_RES +TG T +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00061 +DR RESID; AA0052 +TR Bacteria; taxId:90370 (Salmonella typhi) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylvaline on V +AC PTM-0210 +MT UniProt +FT MOD_RES +TG V +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00063 +DR RESID; AA0054 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:3055 (Chlamydomonas reinhardtii), taxId:33208 (Metazoa) +KW Acetylation + +// + ID N-methylproline on P +AC PTM-0219 +MT UniProt +FT MOD_RES +TG P +PP N-terminal. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00830 +DR RESID; AA0419 +TR Eukaryota; taxId:7227 (Drosophila melanogaster) +KW Methylation + +// + ID N,N-dimethylproline on P +AC PTM-0179 +MT UniProt +FT MOD_RES +TG P +PP N-terminal. +CF C2H4 +MM 28.031300533 +DR PSI-MOD; MOD:00075 +DR RESID; AA0066 +TR Eukaryota; taxId:6446 (Sipunculus nudus), taxId:7586 (Echinodermata), taxId:33682 (Euglenozoa) +KW Methylation + +// + ID N,N,N-trimethylalanine on A +AC PTM-0177 +MT UniProt +FT MOD_RES +TG A +PP N-terminal. +CF C3H6 +MM 42.046950533 +DR PSI-MOD; MOD:00071 +DR RESID; AA0062 +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:5908 (Tetrahymena pyriformis), taxId:9986 (Oryctolagus cuniculus) +KW Methylation + +// + ID N,N,N-trimethylglycine on G +AC PTM-0485 +MT UniProt +FT MOD_RES +TG G +PP N-terminal. +CF C3H7 +MM 43.054775 +DR PSI-MOD; MOD:01982 +DR RESID; AA0619 +TR Eukaryota; taxId:40674 (Mammalia) +KW Methylation + +// + ID N5-methylglutamine on Q +AC PTM-0185 +MT UniProt +FT MOD_RES +TG Q +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00080 +DR RESID; AA0071 +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:4932 (Saccharomyces cerevisiae) +KW Methylation + +// + ID N6-(2-hydroxyisobutyryl)lysine on K +AC PTM-0638 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H6O2 +MM 86.03678 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hydroxylation + +// + ID N6-(ADP-ribosyl)lysine on K +AC PTM-0355 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C15H21N5O13P2 +MM 541.061109 +DR PSI-MOD; MOD:01399 +DR RESID; AA0476 +TR Eukaryota; taxId:10090 (Mus musculus) +KW ADP-ribosylation + +// + ID N6-(beta-hydroxybutyryl)lysine on K +AC PTM-0499 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H7O2 +MM 87.044604 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hydroxylation + +// + ID N6-(pyridoxal phosphate)lysine on K +AC PTM-0387 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C8H8NO5P +MM 229.014009 +DR PSI-MOD; MOD:00128 +DR RESID; AA0119 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Pyridoxal phosphate + +// + ID N6-(retinylidene)lysine on K +AC PTM-0388 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C20H26 +MM 266.203451 +DR PSI-MOD; MOD:00129 +DR RESID; AA0120 +TR Archaea; taxId:28890 (Euryarchaeota), taxId:2236 (Halobacteriaceae) +TR Bacteria; taxId:1236 (Gammaproteobacteria) +TR Eukaryota; taxId:33154 (Opisthokonta) +KW Retinal protein + +// + ID N6-acetyllysine on K +AC PTM-0190 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00064 +DR RESID; AA0055 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N6-biotinyllysine on K +AC PTM-0382 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C10H14N2O2S +MM 226.077599 +DR PSI-MOD; MOD:00126 +DR RESID; AA0117 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Biotin + +// + ID N6-butyryllysine on K +AC PTM-0637 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H6O +MM 70.041865 +DR PSI-MOD; MOD:01781 +DR RESID; AA0532 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID N6-carboxylysine on K +AC PTM-0191 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF CO2 +MM 43.989829 +DR PSI-MOD; MOD:00123 +DR RESID; AA0114 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2763 (Rhodophyta), taxId:2830 (Haptophyceae), taxId:3027 (Cryptophyta), taxId:33090 (Viridiplantae), taxId:33634 (Stramenopiles), taxId:33682 (Euglenozoa), taxId:38254 (Glaucocystophyceae) + +// + ID N6-crotonyllysine on K +AC PTM-0475 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H4O +MM 68.026215 +DR PSI-MOD; MOD:01892 +DR RESID; AA0567 +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID N6-glutaryllysine on K +AC PTM-0487 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C5H6O3 +MM 114.031694 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID N6-lipoyllysine on K +AC PTM-0383 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C8H12OS2 +MM 188.032957 +DR PSI-MOD; MOD:00127 +DR RESID; AA0118 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Lipoyl + +// + ID N6-malonyllysine on K +AC PTM-0467 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C3H2O3 +MM 86.000394 +DR PSI-MOD; MOD:01893 +DR RESID; AA0568 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID N6-methyllysine on K +AC PTM-0194 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00085 +DR RESID; AA0076 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID N6-propionyllysine on K +AC PTM-0642 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C3H4O +MM 56.026215 +DR PSI-MOD; MOD:01398 +DR RESID; AA0475 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:40674 (Mammalia) + +// + ID N6-succinyllysine on K +AC PTM-0438 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H4O3 +MM 100.016044 +DR PSI-MOD; MOD:01819 +DR RESID; AA0545 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID N6,N6-dimethyllysine on K +AC PTM-0188 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C2H4 +MM 28.0313 +DR PSI-MOD; MOD:00084 +DR RESID; AA0075 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID N6,N6,N6-trimethyllysine on K +AC PTM-0187 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C3H6 +MM 42.046950533 +DR PSI-MOD; MOD:00083 +DR RESID; AA0074 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID Nitrated tyrosine on Y +AC PTM-0213 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF H-1NO2 +MM 44.985078 +DR PSI-MOD; MOD:01352 +TR Eukaryota; taxId:40674 (Mammalia) +KW Nitration + +// + ID O-(2-cholinephosphoryl)serine on S +AC PTM-0400 +MT UniProt +FT MOD_RES +TG S +PP Anywhere. +CF C5H12NO3P +MM 165.055479533 +DR PSI-MOD; MOD:01588 +DR RESID; AA0498 +TR Bacteria; taxId:206351 (Neisseriales) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Phosphoprotein + +// + ID O-(pantetheine 4'-phosphoryl)serine on S +AC PTM-0391 +MT UniProt +FT MOD_RES +TG S +PP Anywhere. +CF C11H21N2O6PS +MM 340.085794 +DR PSI-MOD; MOD:00159 +DR RESID; AA0150 +TR Bacteria; taxId:638 (Arsenophonus nasoniae), taxId:112 (Planctomycetales) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Phosphopantetheine or Phosphoprotein + +// + ID O-acetylserine on S +AC PTM-0232 +MT UniProt +FT MOD_RES +TG S +PP Anywhere. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00369 +DR RESID; AA0364 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID Omega-N-methylarginine on R +AC PTM-0237 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00078 +DR RESID; AA0069 +TR Eukaryota; taxId:5661 (Leishmania donovani), taxId:40674 (Mammalia) +KW Methylation + +// + ID Oxidation on C +MT Less Common +TG C +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on D +MT Less Common +TG D +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on E +MT Less Common +TG E +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on F +MT Less Common +TG F +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on H +MT Less Common +TG H +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on I +MT Less Common +TG I +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on L +MT Less Common +TG L +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on Q +MT Less Common +TG Q +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on R +MT Less Common +TG R +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on S +MT Less Common +TG S +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on T +MT Less Common +TG T +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on V +MT Less Common +TG V +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on W +MT Less Common +TG W +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on Y +MT Less Common +TG Y +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation to Kynurenine on W +MT Less Common +TG W +PP Anywhere. +CF C-1O +MM 3.99491462 +DR Unimod; 351 +DI HCD:194.06914219 + +// + ID Phosphoarginine on R +AC PTM-0250 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF HO3P +MM 79.966331 +DR PSI-MOD; MOD:00227 +DR RESID; AA0222 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:40674 (Mammalia) +KW Phosphoprotein + +// + ID Phosphohistidine on H +AC PTM-0252 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF HO3P +MM 79.966331 +DR PSI-MOD; MOD:00890 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Phosphoprotein + +// + ID Phosphorylation on S +MT Common Biological +TG S +PP Anywhere. +CF HO3P +MM 79.966330889 +DR Unimod; 21 +NL HCD:0 or HCD:97.976895573 + +// + ID Phosphorylation on T +MT Common Biological +TG T +PP Anywhere. +CF HO3P +MM 79.966330889 +DR Unimod; 21 +NL HCD:0 or HCD:97.976895573 + +// + ID Phosphorylation on Y +MT Common Biological +TG Y +PP Anywhere. +CF HO3P +MM 79.966330889 +DR Unimod; 21 +NL HCD:0 or HCD:97.976895573 +DI HCD:215.034744803 + +// + ID Phosphoserine on S +AC PTM-0253 +MT UniProt +FT MOD_RES +TG S +PP Anywhere. +CF HO3P +MM 79.966331 +DR PSI-MOD; MOD:00046 +DR RESID; AA0037 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +TR Viruses; taxId:10239 (Viruses) +KW Phosphoprotein + +// + ID Phosphothreonine on T +AC PTM-0254 +MT UniProt +FT MOD_RES +TG T +PP Anywhere. +CF HO3P +MM 79.966331 +DR PSI-MOD; MOD:00047 +DR RESID; AA0038 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +TR Viruses; taxId:10239 (Viruses) +KW Phosphoprotein + +// + ID Phosphotyrosine on Y +AC PTM-0255 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF HO3P +MM 79.966331 +DR PSI-MOD; MOD:00048 +DR RESID; AA0039 +TR Archaea; taxId:2287 (Sulfolobus solfataricus) +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +TR Viruses; taxId:10239 (Viruses) +KW Phosphoprotein + +// + ID Potassium on D +MT Metal +TG D +PP Anywhere. +CF H-1K +MM 37.955881454 +DR Unimod; 530 + +// + ID Potassium on E +MT Metal +TG E +PP Anywhere. +CF H-1K +MM 37.955881454 +DR Unimod; 530 + +// + ID Proline pyrrole to pyrrolidine six member ring on P +MT Less Common +TG P +PP Anywhere. +CF C +MM 12 + +// + ID Propionamidation on C +MT Less Common +TG C +PP Anywhere. +CF C3H5NO +MM 71.037113785 +DR Unimod; 24 + +// + ID Propionamidation on K +MT Less Common +TG K +PP Anywhere. +CF C3H5NO +MM 71.037113785 +DR Unimod; 24 + +// + ID Propionamidation on X +MT Less Common +TG X +PP Peptide N-terminal. +CF C3H5NO +MM 71.037113785 +DR Unimod; 24 + +// + ID Propionylation on K +MT Less Common +TG K +PP Anywhere. +CF C3H4O +MM 56.026214748 +DR Unimod; 58 +DI HCD:139.099823533 + +// + ID Pros-8alpha-FAD histidine on H +AC PTM-0258 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF C27H31N9O15P2 +MM 783.141485 +DR PSI-MOD; MOD:00153 +DR RESID; AA0144 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW FAD + +// + ID Pros-methylhistidine on H +AC PTM-0259 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00082 +DR RESID; AA0073 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Eukaryota; taxId:7742 (Vertebrata) +KW Methylation + +// + ID Pyrrolidinone on P +MT Less Common +TG P +PP Anywhere. +CF C-1H-2O-1 +MM -30.010564684 +DR Unimod; 360 + +// + ID Pyrrolidone carboxylic acid on Q +AC PTM-0261 +MT UniProt +FT MOD_RES +TG Q +PP N-terminal. +CF H-3N-1 +MM -17.026549 +DR PSI-MOD; MOD:00040 +DR RESID; AA0031 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Pyrrolidone carboxylic acid + +// + ID Reduction on D +MT Less Common +TG D +PP Anywhere. +CF O-1 +MM -15.99491462 +DR Unimod; 447 + +// + ID Reduction on S +MT Less Common +TG S +PP Anywhere. +CF O-1 +MM -15.99491462 +DR Unimod; 447 + +// + ID Reduction on T +MT Less Common +TG T +PP Anywhere. +CF O-1 +MM -15.99491462 +DR Unimod; 447 + +// + ID S-(dipyrrolylmethanemethyl)cysteine on C +AC PTM-0421 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF C20H22N2O8 +MM 418.137616 +DR PSI-MOD; MOD:00257 +DR RESID; AA0252 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID S-8alpha-FAD cysteine on C +AC PTM-0272 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF C27H31N9O15P2 +MM 783.141485 +DR PSI-MOD; MOD:00152 +DR RESID; AA0143 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW FAD + +// + ID S-cysteinyl cysteine on C +AC PTM-0415 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF C3H5NO2S +MM 119.004099 +DR PSI-MOD; MOD:00765 +DR RESID; AA0025 +TR Bacteria; taxId:91347 (Enterobacterales) +TR Eukaryota; taxId:40674 (Mammalia) + +// + ID S-glutathionyl cysteine on C +AC PTM-0311 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF C10H15N3O6S +MM 305.068156 +DR PSI-MOD; MOD:00234 +DR RESID; AA0229 +TR Bacteria; taxId:83333 (Escherichia coli (strain K12)) +TR Eukaryota; taxId:3981 (Hevea brasiliensis), taxId:7742 (Vertebrata) +KW Glutathionylation + +// + ID S-methylcysteine on C +AC PTM-0279 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00239 +DR RESID; AA0234 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Bacteria; taxId:1421 (Lysinibacillus sphaericus) +TR Eukaryota; taxId:3055 (Chlamydomonas reinhardtii) +KW Methylation + +// + ID S-nitrosocysteine on C +AC PTM-0280 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF H-1NO +MM 28.990164 +DR PSI-MOD; MOD:00235 +DR RESID; AA0230 +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:40674 (Mammalia) +KW S-nitrosylation + +// + ID Sodium on D +MT Metal +TG D +PP Anywhere. +CF H-1Na +MM 21.98194425 +DR Unimod; 30 + +// + ID Sodium on E +MT Metal +TG E +PP Anywhere. +CF H-1Na +MM 21.98194425 +DR Unimod; 30 + +// + ID Sulfonation on S +MT Less Common +TG S +PP Anywhere. +CF O3S +MM 79.956815033 +DR Unimod; 40 +NL AnyActivationType:79.956815033 + +// + ID Sulfonation on T +MT Less Common +TG T +PP Anywhere. +CF O3S +MM 79.956815033 +DR Unimod; 40 +NL AnyActivationType:79.956815033 + +// + ID Sulfonation on Y +MT Common Biological +TG Y +PP Anywhere. +CF O3S +MM 79.956815033 +DR Unimod; 40 +NL AnyActivationType:79.956815033 + +// + ID Sulfotyrosine on Y +AC PTM-0286 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF O3S +MM 79.956815 +DR PSI-MOD; MOD:00181 +DR RESID; AA0172 +TR Eukaryota; taxId:33208 (Metazoa), taxId:33090 (Viridiplantae) +KW Sulfation + +// + ID Symmetric dimethylarginine on R +AC PTM-0287 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF C2H4 +MM 28.0313 +DR PSI-MOD; MOD:00076 +DR RESID; AA0067 +TR Eukaryota; taxId:7742 (Vertebrata) +KW Methylation + +// + ID Tele-8alpha-FAD histidine on H +AC PTM-0288 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF C27H31N9O15P2 +MM 783.141485 +DR PSI-MOD; MOD:00226 +DR RESID; AA0221 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW FAD + +// + ID Tele-methylhistidine on H +AC PTM-0290 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00322 +DR RESID; AA0317 +TR Eukaryota; taxId:5791 (Physarum polycephalum), taxId:7742 (Vertebrata) +KW Methylation + +// + ID Thyroxine on Y +AC PTM-0294 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF C6I4O +MM 595.612805 +DR PSI-MOD; MOD:00187 +DR RESID; AA0178 +TR Eukaryota; taxId:40674 (Mammalia) +KW Iodination + +// + ID Triiodothyronine on Y +AC PTM-0295 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF C6HI3O +MM 469.716158 +DR PSI-MOD; MOD:00186 +DR RESID; AA0177 +TR Eukaryota; taxId:40674 (Mammalia) +KW Iodination + +// + ID Trioxidation on C +MT Less Common +TG C +PP Anywhere. +CF O3 +MM 47.984743859 +DR Unimod; 345 + +// + ID Water loss on D +MT Less Common +TG D +PP Anywhere. +CF H-2O-1 +MM -18.010564684 +DR Unimod; 23 + +// + ID Water Loss on E +MT Common Artifact +TG E +PP Peptide N-terminal. +CF H-2O-1 +MM -18.010564684 +DR Unimod; 23 + +// + ID Zinc on D +MT Metal +TG D +PP Anywhere. +CF H-2Zn +MM 61.913491946 +DR Unimod; 954 + +// + ID Zinc on E +MT Metal +TG E +PP Anywhere. +CF H-2Zn +MM 61.913491946 +DR Unimod; 954 + +// + + P63250 + KCNJ3_MOUSE + + + G protein-activated inward rectifier potassium channel 1 + + + + Kcnj3 + Girk1 + + + Mus musculus + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MSALRRKFGDDYQVVTTSSSGSGLQPQGPGQGPQQQLVPKKKRQRFVDKNGRCNVQHGNLGSETSRYLSDLFTTLVDLKWRWNLFIFILTYTVAWLFMASMWWVIAYTRGDLNKAHVGNYTPCVANVYNFPSAFLFFIETEATIGYGYRYITDKCPEGIILFLFQSILGSIVDAFLIGCMFIKMSQPKKRAETLMFSEHAVISMRDGKLTLMFRVGNLRNSHMVSAQIRCKLLKSRQTPEGEFLPLDQLELDVGFSTGADQLFLVSPLTICHVIDAKSPFYDLSQRSMQTEQFEVVVILEGIVETTGMTCQARTSYTEDEVLWGHRFFPVISLEEGFFKVDYSQFHATFEVPTPPYSVKEQEEMLLMSSPLIAPAITNSKERHNSVECLDGLDDISTKLPSKLQKITGREDFPKKLLRMSSTTSEKAYSLGDLPMKLQRISSVPGNSEEKLVSKTTKMLSDPMSQSVADLPPKLQKMAGGPTRMEGNLPAKLRKMNSDRFT + + \ No newline at end of file diff --git a/mzLib/Test/DatabaseTests/06.xml b/mzLib/Test/DatabaseTests/06.xml new file mode 100644 index 000000000..1a7030e7d --- /dev/null +++ b/mzLib/Test/DatabaseTests/06.xml @@ -0,0 +1,2654 @@ + + + ID (3R)-3-hydroxyasparagine on N +AC PTM-0369 +MT UniProt +FT MOD_RES +TG N +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00035 +DR RESID; AA0026 +TR Eukaryota; taxId:40674 (Mammalia) +KW Hydroxylation + +// + ID (3R)-3-hydroxyaspartate on D +AC PTM-0371 +MT UniProt +FT MOD_RES +TG D +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00036 +DR RESID; AA0027 +TR Bacteria; taxId:68215 (Streptomyces griseoverticillatus) +TR Eukaryota; taxId:40674 (Mammalia) +KW Hydroxylation + +// + ID (3S)-3-hydroxyasparagine on N +AC PTM-0370 +MT UniProt +FT MOD_RES +TG N +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:01401 +DR RESID; AA0478 +TR Eukaryota; taxId:7742 (Vertebrata) +KW Hydroxylation + +// + ID (3S)-3-hydroxyaspartate on D +AC PTM-0473 +MT UniProt +FT MOD_RES +TG D +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:01919 +TR Eukaryota; taxId:33208 (Metazoa) +KW Hydroxylation + +// + ID (3S)-3-hydroxyhistidine on H +AC PTM-0477 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:01920 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hydroxylation + +// + ID (4R)-5-hydroxyleucine on L +AC PTM-0491 +MT UniProt +FT MOD_RES +TG L +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:01373 +DR RESID; AA0443 +TR Eukaryota; taxId:33208 (Metazoa) +KW Hydroxylation + +// + ID (4R)-5-oxoleucine on L +AC PTM-0492 +MT UniProt +FT MOD_RES +TG L +PP Anywhere. +CF H-2O +MM 13.979265 +DR PSI-MOD; MOD:01374 +DR RESID; AA0444 +TR Eukaryota; taxId:33208 (Metazoa) +KW Oxidation + +// + ID 2',4',5'-topaquinone on Y +AC PTM-0009 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF H-2O2 +MM 29.974179 +DR PSI-MOD; MOD:00156 +DR RESID; AA0147 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW TPQ + +// + ID 3-hydroxyasparagine on N +AC PTM-0028 +MT UniProt +FT MOD_RES +TG N +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00035 +DR RESID; AA0026 +TR Eukaryota; taxId:7742 (Vertebrata) +KW Hydroxylation + +// + ID 3-hydroxyproline on P +AC PTM-0030 +MT UniProt +FT MOD_RES +TG P +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00038 +DR RESID; AA0029 +TR Eukaryota; taxId:33208 (Metazoa) +KW Hydroxylation + +// + ID 3-oxoalanine (Cys) on C +AC PTM-0033 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF H-2OS-1 +MM -17.992806 +DR PSI-MOD; MOD:00193 +DR RESID; AA0185 +TR Bacteria; taxId:1224 (Proteobacteria), taxId:1239 (Firmicutes) +TR Eukaryota; taxId:3041 (Chlorophyta), taxId:33208 (Metazoa) + +// + ID 3'-nitrotyrosine on Y +AC PTM-0434 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF H-1NO2 +MM 44.985078 +DR PSI-MOD; MOD:01786 +DR RESID; AA0537 +TR Eukaryota; taxId:40674 (Mammalia) +KW Nitration + +// + ID 4-carboxyglutamate on E +AC PTM-0039 +MT UniProt +FT MOD_RES +TG E +PP Anywhere. +CF CO2 +MM 43.989829 +DR PSI-MOD; MOD:00041 +DR RESID; AA0032 +TR Eukaryota; taxId:6447 (Mollusca), taxId:7742 (Vertebrata) +KW Gamma-carboxyglutamic acid + +// + ID 4-hydroxyproline on P +AC PTM-0043 +MT UniProt +FT MOD_RES +TG P +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00039 +DR RESID; AA0030 +TR Bacteria; taxId:415003 (Microbispora sp. (strain 107891)) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hydroxylation + +// + ID 5-glutamyl glutamate on E +AC PTM-0479 +MT UniProt +FT MOD_RES +TG E +PP Anywhere. +CF C5H7NO3 +MM 129.042593 +DR PSI-MOD; MOD:01970 +DR RESID; AA0612 +TR Archaea; taxId:2267 (Thermoproteaceae) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Isopeptide bond + +// + ID 5-glutamyl glycerylphosphorylethanolamine on E +AC PTM-0403 +MT UniProt +FT MOD_RES +TG E +PP Anywhere. +CF C5H12NO5P +MM 197.045309 +DR PSI-MOD; MOD:00179 +DR RESID; AA0170 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Phosphoprotein + +// + ID 5-hydroxylysine on K +AC PTM-0044 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00037 +DR RESID; AA0028 +TR Eukaryota; taxId:33208 (Metazoa) +KW Hydroxylation + +// + ID Acetylation on K +MT Common Biological +TG K +PP Anywhere. +CF C2H2O +MM 42.010564684 +DR Unimod; 1 +NL ETD:45.0204 +DI HCD:125.084063979 + +// + ID Acetylation on S +MT Less Common +TG S +PP Anywhere. +CF C2H2O +MM 42.010564684 +DR Unimod; 1 + +// + ID Acetylation on T +MT Less Common +TG T +PP Anywhere. +CF C2H2O +MM 42.010564684 +DR Unimod; 1 + +// + ID Acetylation on X +MT Common Biological +TG X +PP N-terminal. +CF C2H2O +MM 42.010564684 +DR Unimod; 1 + +// + ID ADP-ribosyl glutamic acid on E +AC PTM-0646 +MT UniProt +FT MOD_RES +TG E +PP Anywhere. +CF C15H21N5O13P2 +MM 541.061109 +TR Eukaryota; taxId:40674 (Mammalia) +KW ADP-ribosylation + +// + ID ADP-ribosylarginine on R +AC PTM-0053 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF C15H21N5O13P2 +MM 541.061109 +DR PSI-MOD; MOD:00177 +DR RESID; AA0168 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW ADP-ribosylation + +// + ID ADP-ribosylcysteine on C +AC PTM-0055 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF C15H21N5O13P2 +MM 541.061109 +DR PSI-MOD; MOD:00178 +DR RESID; AA0169 +TR Eukaryota; taxId:40674 (Mammalia) +KW ADP-ribosylation + +// + ID ADP-ribosylserine on S +AC PTM-0056 +MT UniProt +FT MOD_RES +TG S +PP Anywhere. +CF C15H21N5O13P2 +MM 541.061109 +DR PSI-MOD; MOD:00242 +DR RESID; AA0237 +TR Eukaryota; taxId:9606 (Homo sapiens) +KW ADP-ribosylation + +// + ID Allysine on K +AC PTM-0059 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF H-3N-1O +MM -1.031634 +DR PSI-MOD; MOD:00130 +DR RESID; AA0121 +TR Eukaryota; taxId:6052 (Ephydatia muelleri), taxId:7742 (Vertebrata) + +// + ID Amidation on X +MT Less Common +TG X +PP Peptide C-terminal. +CF HNO-1 +MM -0.984015583 +DR Unimod; 2 + +// + ID Ammonia loss on C +MT Common Artifact +TG C +PP Peptide N-terminal. +CF H-3N-1 +MM -17.026549101 +DR Unimod; 385 + +// + ID Ammonia loss on N +MT Common Artifact +TG N +PP Anywhere. +CF H-3N-1 +MM -17.026549101 +DR Unimod; 385 + +// + ID Asymmetric dimethylarginine on R +AC PTM-0066 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF C2H4 +MM 28.0313 +DR PSI-MOD; MOD:00077 +DR RESID; AA0068 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID Calcium on D +MT Metal +TG D +PP Anywhere. +CF H-2Ca +MM 37.946940799 +DR Unimod; 951 + +// + ID Calcium on E +MT Metal +TG E +PP Anywhere. +CF H-2Ca +MM 37.946940799 +DR Unimod; 951 + +// + ID Carbamidomethyl on D +MT Less Common +TG D +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on E +MT Less Common +TG E +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on H +MT Less Common +TG H +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on K +MT Less Common +TG K +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on S +MT Less Common +TG S +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on T +MT Less Common +TG T +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on X +MT Less Common +TG X +PP Peptide N-terminal. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamidomethyl on Y +MT Less Common +TG Y +PP Anywhere. +CF C2H3NO +MM 57.021463721 +DR Unimod; 4 + +// + ID Carbamyl on C +MT Common Artifact +TG C +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on K +MT Common Artifact +TG K +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on M +MT Common Artifact +TG M +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on R +MT Common Artifact +TG R +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on X +MT Common Artifact +TG X +PP Peptide N-terminal. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carboxylation on D +MT Common Biological +TG D +PP Anywhere. +CF CO2 +MM 43.989829239 +DR Unimod; 299 + +// + ID Carboxylation on E +MT Common Biological +TG E +PP Anywhere. +CF CO2 +MM 43.989829239 +DR Unimod; 299 + +// + ID Carboxylation on K +MT Common Biological +TG K +PP Anywhere. +CF CO2 +MM 43.989829239 +DR Unimod; 299 + +// + ID Carboxymethylation on K +MT Less Common +TG K +PP Anywhere. +CF C2H2O2 +MM 58.005479304 +DR Unimod; 6 + +// + ID Carboxymethylation on W +MT Less Common +TG W +PP Anywhere. +CF C2H2O2 +MM 58.005479304 +DR Unimod; 6 + +// + ID Carboxymethylation on X +MT Less Common +TG X +PP Peptide N-terminal. +CF C2H2O2 +MM 58.005479304 +DR Unimod; 6 + +// + ID Citrullination on R +MT Common Biological +TG R +PP Anywhere. +CF H-1N-1O +MM 0.984015583 +DR Unimod; 7 +NL HCD:43.0058 +DI HCD:129.090223533 + +// + ID Citrulline on R +AC PTM-0092 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF H-1N-1O +MM 0.984016 +DR PSI-MOD; MOD:00219 +DR RESID; AA0214 +TR Eukaryota; taxId:7742 (Vertebrata) +KW Citrullination + +// + ID Crotonylation on K +MT Common Biological +TG K +PP Anywhere. +CF C4H4O +MM 68.026214748 +DR Unimod; 1363 +DI HCD:151.099723533 + +// + ID Cu[I] on D +MT Metal +TG D +PP Anywhere. +CF H-1Cu +MM 61.921772688 +DR Unimod; 531 + +// + ID Cu[I] on E +MT Metal +TG E +PP Anywhere. +CF H-1Cu +MM 61.921772688 +DR Unimod; 531 + +// + ID Cysteine methyl ester on C +AC PTM-0105 +MT UniProt +FT MOD_RES +TG C +PP C-terminal. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00114 +DR RESID; AA0105 +TR Bacteria; taxId:201174 (Actinobacteria) +TR Eukaryota; taxId:4751 (Fungi), taxId:33208 (Metazoa) +KW Methylation + +// + ID Cysteine persulfide on C +AC PTM-0106 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF S +MM 31.972071 +DR PSI-MOD; MOD:00274 +DR RESID; AA0269 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID Cysteine sulfenic acid (-SOH) on C +AC PTM-0107 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00210 +DR RESID; AA0205 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:40674 (Mammalia) +KW Oxidation + +// + ID Cysteine sulfinic acid (-SO2H) on C +AC PTM-0108 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF O2 +MM 31.989829 +DR PSI-MOD; MOD:00267 +DR RESID; AA0262 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:40674 (Mammalia) +KW Oxidation + +// + ID Cysteine sulfonic acid (-SO3H) on C +AC PTM-0634 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF O3 +MM 47.984744 +DR PSI-MOD; MOD:00460 +DR RESID; AA0556 +TR Eukaryota; taxId:40674 (Mammalia) +KW Oxidation + +// + ID Deamidated asparagine on N +AC PTM-0116 +MT UniProt +FT MOD_RES +TG N +PP Anywhere. +CF H-1N-1O +MM 0.984016 +DR PSI-MOD; MOD:00684 +DR RESID; AA0004 +TR Eukaryota; taxId:3702 (Arabidopsis thaliana), taxId:7742 (Vertebrata) + +// + ID Deamidated glutamine on Q +AC PTM-0117 +MT UniProt +FT MOD_RES +TG Q +PP Anywhere. +CF H-1N-1O +MM 0.984016 +DR PSI-MOD; MOD:00685 +DR RESID; AA0006 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:7742 (Vertebrata) + +// + ID Deamidation on N +MT Common Artifact +TG N +PP Anywhere. +CF H-1N-1O +MM 0.984015583 +DR Unimod; 7 + +// + ID Deamidation on Q +MT Common Artifact +TG Q +PP Anywhere. +CF H-1N-1O +MM 0.984015583 +DR Unimod; 7 + +// + ID Decarboxylation on D +MT Less Common +TG D +PP Anywhere. +CF C-1H-2O-1 +MM -30.010564684 +DR Unimod; 914 + +// + ID Decarboxylation on E +MT Less Common +TG E +PP Anywhere. +CF C-1H-2O-1 +MM -30.010564684 +DR Unimod; 914 + +// + ID Dehydroalanine on S +MT Less Common +TG S +PP Anywhere. +CF H-2O-1 +MM -18.010564684 + +// + ID Dehydrobutyrine on T +MT Less Common +TG T +PP Anywhere. +CF H-2O-1 +MM -18.010564684 + +// + ID Didehydro on Y +MT Less Common +TG Y +PP Anywhere. +CF H-2 +MM -2.015650064 +DR Unimod; 401 + +// + ID Dimethylated arginine on R +AC PTM-0341 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF C2H4 +MM 28.0313 +DR PSI-MOD; MOD:00783 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID Dimethylation on N +MT Less Common +TG N +PP Anywhere. +CF C2H4 +MM 28.031300129 +DR Unimod; 36 + +// + ID Dimethylation on R +MT Common Biological +TG R +PP Anywhere. +CF C2H4 +MM 28.031300129 +DR Unimod; 36 +NL ETD:31.0422 or ETD:45.0579 + +// + ID Dioxidation on C +MT Less Common +TG C +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on F +MT Less Common +TG F +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on K +MT Less Common +TG K +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on M +MT Less Common +TG M +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on P +MT Less Common +TG P +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on R +MT Less Common +TG R +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on W +MT Less Common +TG W +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Dioxidation on Y +MT Less Common +TG Y +PP Anywhere. +CF O2 +MM 31.989829239 +DR Unimod; 425 + +// + ID Diphthamide on H +AC PTM-0118 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF C7H14N2O +MM 142.110613533 +DR PSI-MOD; MOD:00049 +DR RESID; AA0040 +TR Archaea; taxId:2157 (Archaea) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID Ethylation on D +MT Less Common +TG D +PP Anywhere. +CF C2H4 +MM 28.031300129 +DR Unimod; 280 + +// + ID Ethylation on X +MT Less Common +TG X +PP Peptide N-terminal. +CF C2H4 +MM 28.031300129 +DR Unimod; 280 + +// + ID Formylation on K +MT Common Biological +TG K +PP Anywhere. +CF CO +MM 27.99491462 +DR Unimod; 122 +DI HCD:111.068423533 + +// + ID Formylation on S +MT Less Common +TG S +PP Anywhere. +CF CO +MM 27.99491462 +DR Unimod; 122 + +// + ID Formylation on T +MT Less Common +TG T +PP Anywhere. +CF CO +MM 27.99491462 +DR Unimod; 122 + +// + ID Formylation on X +MT Less Common +TG X +PP Peptide N-terminal. +CF CO +MM 27.99491462 +DR Unimod; 122 + +// + ID Glycyl adenylate on G +AC PTM-0409 +MT UniProt +FT MOD_RES +TG G +PP C-terminal. +CF C10H12N5O6P +MM 329.05252 +DR PSI-MOD; MOD:01614 +DR RESID; AA0511 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Nucleotide-binding or Phosphoprotein + +// + ID Hydroxylation on K +MT Common Biological +TG K +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Hydroxylation on N +MT Common Biological +TG N +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Hydroxylation on P +MT Common Biological +TG P +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 +DI HCD:170.069143 + +// + ID Hydroxyproline on P +AC PTM-0149 +MT UniProt +FT MOD_RES +TG P +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00678 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hydroxylation + +// + ID Hypusine on K +AC PTM-0150 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H9NO +MM 87.068414 +DR PSI-MOD; MOD:00125 +DR RESID; AA0116 +TR Archaea; taxId:2157 (Archaea) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hypusine + +// + ID Leucine methyl ester on L +AC PTM-0167 +MT UniProt +FT MOD_RES +TG L +PP C-terminal. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00304 +DR RESID; AA0299 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID Magnesium on D +MT Metal +TG D +PP Anywhere. +CF H-2Mg +MM 21.969391633 +DR Unimod; 956 + +// + ID Magnesium on E +MT Metal +TG E +PP Anywhere. +CF H-2Mg +MM 21.969391633 +DR Unimod; 956 + +// + ID Methionine (R)-sulfoxide on M +AC PTM-0480 +MT UniProt +FT MOD_RES +TG M +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00720 +DR RESID; AA0581 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Oxidation + +// + ID Methionine sulfoxide on M +AC PTM-0469 +MT UniProt +FT MOD_RES +TG M +PP Anywhere. +CF O +MM 15.994915 +DR PSI-MOD; MOD:00719 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Oxidation + +// + ID Methylation on C +MT Less Common +TG C +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on D +MT Less Common +TG D +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on E +MT Less Common +TG E +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on H +MT Less Common +TG H +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on I +MT Less Common +TG I +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on K +MT Common Biological +TG K +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on L +MT Less Common +TG L +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on N +MT Less Common +TG N +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on Q +MT Less Common +TG Q +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on R +MT Common Biological +TG R +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on S +MT Less Common +TG S +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on T +MT Less Common +TG T +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylhistidine on H +AC PTM-0176 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00661 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Eukaryota; taxId:5791 (Physarum polycephalum), taxId:7742 (Vertebrata) +KW Methylation + +// + ID N-acetylalanine on A +AC PTM-0199 +MT UniProt +FT MOD_RES +TG A +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00050 +DR RESID; AA0041 +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylaspartate on D +AC PTM-0200 +MT UniProt +FT MOD_RES +TG D +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00051 +DR RESID; AA0042 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylcysteine on C +AC PTM-0201 +MT UniProt +FT MOD_RES +TG C +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00052 +DR RESID; AA0043 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Eukaryota; taxId:7742 (Vertebrata) +KW Acetylation + +// + ID N-acetylglutamate on E +AC PTM-0202 +MT UniProt +FT MOD_RES +TG E +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00053 +DR RESID; AA0044 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylglycine on G +AC PTM-0203 +MT UniProt +FT MOD_RES +TG G +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00055 +DR RESID; AA0046 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylmethionine on M +AC PTM-0205 +MT UniProt +FT MOD_RES +TG M +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00058 +DR RESID; AA0049 +TR Archaea; taxId:2287 (Sulfolobus solfataricus) +TR Bacteria; taxId:1270 (Micrococcus luteus) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylproline on P +AC PTM-0206 +MT UniProt +FT MOD_RES +TG P +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00059 +DR RESID; AA0050 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:33090 (Viridiplantae), taxId:40674 (Mammalia) +KW Acetylation + +// + ID N-acetylserine on S +AC PTM-0207 +MT UniProt +FT MOD_RES +TG S +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00060 +DR RESID; AA0051 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylthreonine on T +AC PTM-0208 +MT UniProt +FT MOD_RES +TG T +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00061 +DR RESID; AA0052 +TR Bacteria; taxId:90370 (Salmonella typhi) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N-acetylvaline on V +AC PTM-0210 +MT UniProt +FT MOD_RES +TG V +PP N-terminal. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00063 +DR RESID; AA0054 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:3055 (Chlamydomonas reinhardtii), taxId:33208 (Metazoa) +KW Acetylation + +// + ID N-methylproline on P +AC PTM-0219 +MT UniProt +FT MOD_RES +TG P +PP N-terminal. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00830 +DR RESID; AA0419 +TR Eukaryota; taxId:7227 (Drosophila melanogaster) +KW Methylation + +// + ID N,N-dimethylproline on P +AC PTM-0179 +MT UniProt +FT MOD_RES +TG P +PP N-terminal. +CF C2H4 +MM 28.031300533 +DR PSI-MOD; MOD:00075 +DR RESID; AA0066 +TR Eukaryota; taxId:6446 (Sipunculus nudus), taxId:7586 (Echinodermata), taxId:33682 (Euglenozoa) +KW Methylation + +// + ID N,N,N-trimethylalanine on A +AC PTM-0177 +MT UniProt +FT MOD_RES +TG A +PP N-terminal. +CF C3H6 +MM 42.046950533 +DR PSI-MOD; MOD:00071 +DR RESID; AA0062 +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:5908 (Tetrahymena pyriformis), taxId:9986 (Oryctolagus cuniculus) +KW Methylation + +// + ID N,N,N-trimethylglycine on G +AC PTM-0485 +MT UniProt +FT MOD_RES +TG G +PP N-terminal. +CF C3H7 +MM 43.054775 +DR PSI-MOD; MOD:01982 +DR RESID; AA0619 +TR Eukaryota; taxId:40674 (Mammalia) +KW Methylation + +// + ID N5-methylglutamine on Q +AC PTM-0185 +MT UniProt +FT MOD_RES +TG Q +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00080 +DR RESID; AA0071 +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:4932 (Saccharomyces cerevisiae) +KW Methylation + +// + ID N6-(2-hydroxyisobutyryl)lysine on K +AC PTM-0638 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H6O2 +MM 86.03678 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hydroxylation + +// + ID N6-(ADP-ribosyl)lysine on K +AC PTM-0355 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C15H21N5O13P2 +MM 541.061109 +DR PSI-MOD; MOD:01399 +DR RESID; AA0476 +TR Eukaryota; taxId:10090 (Mus musculus) +KW ADP-ribosylation + +// + ID N6-(beta-hydroxybutyryl)lysine on K +AC PTM-0499 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H7O2 +MM 87.044604 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Hydroxylation + +// + ID N6-(pyridoxal phosphate)lysine on K +AC PTM-0387 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C8H8NO5P +MM 229.014009 +DR PSI-MOD; MOD:00128 +DR RESID; AA0119 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Pyridoxal phosphate + +// + ID N6-(retinylidene)lysine on K +AC PTM-0388 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C20H26 +MM 266.203451 +DR PSI-MOD; MOD:00129 +DR RESID; AA0120 +TR Archaea; taxId:28890 (Euryarchaeota), taxId:2236 (Halobacteriaceae) +TR Bacteria; taxId:1236 (Gammaproteobacteria) +TR Eukaryota; taxId:33154 (Opisthokonta) +KW Retinal protein + +// + ID N6-acetyllysine on K +AC PTM-0190 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00064 +DR RESID; AA0055 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID N6-biotinyllysine on K +AC PTM-0382 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C10H14N2O2S +MM 226.077599 +DR PSI-MOD; MOD:00126 +DR RESID; AA0117 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Biotin + +// + ID N6-butyryllysine on K +AC PTM-0637 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H6O +MM 70.041865 +DR PSI-MOD; MOD:01781 +DR RESID; AA0532 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID N6-carboxylysine on K +AC PTM-0191 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF CO2 +MM 43.989829 +DR PSI-MOD; MOD:00123 +DR RESID; AA0114 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2763 (Rhodophyta), taxId:2830 (Haptophyceae), taxId:3027 (Cryptophyta), taxId:33090 (Viridiplantae), taxId:33634 (Stramenopiles), taxId:33682 (Euglenozoa), taxId:38254 (Glaucocystophyceae) + +// + ID N6-crotonyllysine on K +AC PTM-0475 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H4O +MM 68.026215 +DR PSI-MOD; MOD:01892 +DR RESID; AA0567 +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID N6-glutaryllysine on K +AC PTM-0487 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C5H6O3 +MM 114.031694 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID N6-lipoyllysine on K +AC PTM-0383 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C8H12OS2 +MM 188.032957 +DR PSI-MOD; MOD:00127 +DR RESID; AA0118 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Lipoyl + +// + ID N6-malonyllysine on K +AC PTM-0467 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C3H2O3 +MM 86.000394 +DR PSI-MOD; MOD:01893 +DR RESID; AA0568 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID N6-methyllysine on K +AC PTM-0194 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00085 +DR RESID; AA0076 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID N6-propionyllysine on K +AC PTM-0642 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C3H4O +MM 56.026215 +DR PSI-MOD; MOD:01398 +DR RESID; AA0475 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:40674 (Mammalia) + +// + ID N6-succinyllysine on K +AC PTM-0438 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C4H4O3 +MM 100.016044 +DR PSI-MOD; MOD:01819 +DR RESID; AA0545 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID N6,N6-dimethyllysine on K +AC PTM-0188 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C2H4 +MM 28.0313 +DR PSI-MOD; MOD:00084 +DR RESID; AA0075 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID N6,N6,N6-trimethyllysine on K +AC PTM-0187 +MT UniProt +FT MOD_RES +TG K +PP Anywhere. +CF C3H6 +MM 42.046950533 +DR PSI-MOD; MOD:00083 +DR RESID; AA0074 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Methylation + +// + ID Nitrated tyrosine on Y +AC PTM-0213 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF H-1NO2 +MM 44.985078 +DR PSI-MOD; MOD:01352 +TR Eukaryota; taxId:40674 (Mammalia) +KW Nitration + +// + ID O-(2-cholinephosphoryl)serine on S +AC PTM-0400 +MT UniProt +FT MOD_RES +TG S +PP Anywhere. +CF C5H12NO3P +MM 165.055479533 +DR PSI-MOD; MOD:01588 +DR RESID; AA0498 +TR Bacteria; taxId:206351 (Neisseriales) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Phosphoprotein + +// + ID O-(pantetheine 4'-phosphoryl)serine on S +AC PTM-0391 +MT UniProt +FT MOD_RES +TG S +PP Anywhere. +CF C11H21N2O6PS +MM 340.085794 +DR PSI-MOD; MOD:00159 +DR RESID; AA0150 +TR Bacteria; taxId:638 (Arsenophonus nasoniae), taxId:112 (Planctomycetales) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Phosphopantetheine or Phosphoprotein + +// + ID O-acetylserine on S +AC PTM-0232 +MT UniProt +FT MOD_RES +TG S +PP Anywhere. +CF C2H2O +MM 42.010565 +DR PSI-MOD; MOD:00369 +DR RESID; AA0364 +TR Eukaryota; taxId:2759 (Eukaryota) +KW Acetylation + +// + ID Omega-N-methylarginine on R +AC PTM-0237 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00078 +DR RESID; AA0069 +TR Eukaryota; taxId:5661 (Leishmania donovani), taxId:40674 (Mammalia) +KW Methylation + +// + ID Oxidation on C +MT Less Common +TG C +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on D +MT Less Common +TG D +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on E +MT Less Common +TG E +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on F +MT Less Common +TG F +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on H +MT Less Common +TG H +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on I +MT Less Common +TG I +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on L +MT Less Common +TG L +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on Q +MT Less Common +TG Q +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on R +MT Less Common +TG R +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on S +MT Less Common +TG S +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on T +MT Less Common +TG T +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on V +MT Less Common +TG V +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on W +MT Less Common +TG W +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation on Y +MT Less Common +TG Y +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Oxidation to Kynurenine on W +MT Less Common +TG W +PP Anywhere. +CF C-1O +MM 3.99491462 +DR Unimod; 351 +DI HCD:194.06914219 + +// + ID Phosphoarginine on R +AC PTM-0250 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF HO3P +MM 79.966331 +DR PSI-MOD; MOD:00227 +DR RESID; AA0222 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:40674 (Mammalia) +KW Phosphoprotein + +// + ID Phosphohistidine on H +AC PTM-0252 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF HO3P +MM 79.966331 +DR PSI-MOD; MOD:00890 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Phosphoprotein + +// + ID Phosphorylation on S +MT Common Biological +TG S +PP Anywhere. +CF HO3P +MM 79.966330889 +DR Unimod; 21 +NL HCD:0 or HCD:97.976895573 + +// + ID Phosphorylation on T +MT Common Biological +TG T +PP Anywhere. +CF HO3P +MM 79.966330889 +DR Unimod; 21 +NL HCD:0 or HCD:97.976895573 + +// + ID Phosphorylation on Y +MT Common Biological +TG Y +PP Anywhere. +CF HO3P +MM 79.966330889 +DR Unimod; 21 +NL HCD:0 or HCD:97.976895573 +DI HCD:215.034744803 + +// + ID Phosphoserine on S +AC PTM-0253 +MT UniProt +FT MOD_RES +TG S +PP Anywhere. +CF HO3P +MM 79.966331 +DR PSI-MOD; MOD:00046 +DR RESID; AA0037 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +TR Viruses; taxId:10239 (Viruses) +KW Phosphoprotein + +// + ID Phosphothreonine on T +AC PTM-0254 +MT UniProt +FT MOD_RES +TG T +PP Anywhere. +CF HO3P +MM 79.966331 +DR PSI-MOD; MOD:00047 +DR RESID; AA0038 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +TR Viruses; taxId:10239 (Viruses) +KW Phosphoprotein + +// + ID Phosphotyrosine on Y +AC PTM-0255 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF HO3P +MM 79.966331 +DR PSI-MOD; MOD:00048 +DR RESID; AA0039 +TR Archaea; taxId:2287 (Sulfolobus solfataricus) +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +TR Viruses; taxId:10239 (Viruses) +KW Phosphoprotein + +// + ID Potassium on D +MT Metal +TG D +PP Anywhere. +CF H-1K +MM 37.955881454 +DR Unimod; 530 + +// + ID Potassium on E +MT Metal +TG E +PP Anywhere. +CF H-1K +MM 37.955881454 +DR Unimod; 530 + +// + ID Proline pyrrole to pyrrolidine six member ring on P +MT Less Common +TG P +PP Anywhere. +CF C +MM 12 + +// + ID Propionamidation on C +MT Less Common +TG C +PP Anywhere. +CF C3H5NO +MM 71.037113785 +DR Unimod; 24 + +// + ID Propionamidation on K +MT Less Common +TG K +PP Anywhere. +CF C3H5NO +MM 71.037113785 +DR Unimod; 24 + +// + ID Propionamidation on X +MT Less Common +TG X +PP Peptide N-terminal. +CF C3H5NO +MM 71.037113785 +DR Unimod; 24 + +// + ID Propionylation on K +MT Less Common +TG K +PP Anywhere. +CF C3H4O +MM 56.026214748 +DR Unimod; 58 +DI HCD:139.099823533 + +// + ID Pros-8alpha-FAD histidine on H +AC PTM-0258 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF C27H31N9O15P2 +MM 783.141485 +DR PSI-MOD; MOD:00153 +DR RESID; AA0144 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW FAD + +// + ID Pros-methylhistidine on H +AC PTM-0259 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00082 +DR RESID; AA0073 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Eukaryota; taxId:7742 (Vertebrata) +KW Methylation + +// + ID Pyrrolidinone on P +MT Less Common +TG P +PP Anywhere. +CF C-1H-2O-1 +MM -30.010564684 +DR Unimod; 360 + +// + ID Pyrrolidone carboxylic acid on Q +AC PTM-0261 +MT UniProt +FT MOD_RES +TG Q +PP N-terminal. +CF H-3N-1 +MM -17.026549 +DR PSI-MOD; MOD:00040 +DR RESID; AA0031 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW Pyrrolidone carboxylic acid + +// + ID Reduction on D +MT Less Common +TG D +PP Anywhere. +CF O-1 +MM -15.99491462 +DR Unimod; 447 + +// + ID Reduction on S +MT Less Common +TG S +PP Anywhere. +CF O-1 +MM -15.99491462 +DR Unimod; 447 + +// + ID Reduction on T +MT Less Common +TG T +PP Anywhere. +CF O-1 +MM -15.99491462 +DR Unimod; 447 + +// + ID S-(dipyrrolylmethanemethyl)cysteine on C +AC PTM-0421 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF C20H22N2O8 +MM 418.137616 +DR PSI-MOD; MOD:00257 +DR RESID; AA0252 +TR Archaea; taxId:2157 (Archaea) +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) + +// + ID S-8alpha-FAD cysteine on C +AC PTM-0272 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF C27H31N9O15P2 +MM 783.141485 +DR PSI-MOD; MOD:00152 +DR RESID; AA0143 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW FAD + +// + ID S-cysteinyl cysteine on C +AC PTM-0415 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF C3H5NO2S +MM 119.004099 +DR PSI-MOD; MOD:00765 +DR RESID; AA0025 +TR Bacteria; taxId:91347 (Enterobacterales) +TR Eukaryota; taxId:40674 (Mammalia) + +// + ID S-glutathionyl cysteine on C +AC PTM-0311 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF C10H15N3O6S +MM 305.068156 +DR PSI-MOD; MOD:00234 +DR RESID; AA0229 +TR Bacteria; taxId:83333 (Escherichia coli (strain K12)) +TR Eukaryota; taxId:3981 (Hevea brasiliensis), taxId:7742 (Vertebrata) +KW Glutathionylation + +// + ID S-methylcysteine on C +AC PTM-0279 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00239 +DR RESID; AA0234 +TR Archaea; taxId:28890 (Euryarchaeota) +TR Bacteria; taxId:1421 (Lysinibacillus sphaericus) +TR Eukaryota; taxId:3055 (Chlamydomonas reinhardtii) +KW Methylation + +// + ID S-nitrosocysteine on C +AC PTM-0280 +MT UniProt +FT MOD_RES +TG C +PP Anywhere. +CF H-1NO +MM 28.990164 +DR PSI-MOD; MOD:00235 +DR RESID; AA0230 +TR Bacteria; taxId:1224 (Proteobacteria) +TR Eukaryota; taxId:40674 (Mammalia) +KW S-nitrosylation + +// + ID Sodium on D +MT Metal +TG D +PP Anywhere. +CF H-1Na +MM 21.98194425 +DR Unimod; 30 + +// + ID Sodium on E +MT Metal +TG E +PP Anywhere. +CF H-1Na +MM 21.98194425 +DR Unimod; 30 + +// + ID Sulfonation on S +MT Less Common +TG S +PP Anywhere. +CF O3S +MM 79.956815033 +DR Unimod; 40 +NL AnyActivationType:79.956815033 + +// + ID Sulfonation on T +MT Less Common +TG T +PP Anywhere. +CF O3S +MM 79.956815033 +DR Unimod; 40 +NL AnyActivationType:79.956815033 + +// + ID Sulfonation on Y +MT Common Biological +TG Y +PP Anywhere. +CF O3S +MM 79.956815033 +DR Unimod; 40 +NL AnyActivationType:79.956815033 + +// + ID Sulfotyrosine on Y +AC PTM-0286 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF O3S +MM 79.956815 +DR PSI-MOD; MOD:00181 +DR RESID; AA0172 +TR Eukaryota; taxId:33208 (Metazoa), taxId:33090 (Viridiplantae) +KW Sulfation + +// + ID Symmetric dimethylarginine on R +AC PTM-0287 +MT UniProt +FT MOD_RES +TG R +PP Anywhere. +CF C2H4 +MM 28.0313 +DR PSI-MOD; MOD:00076 +DR RESID; AA0067 +TR Eukaryota; taxId:7742 (Vertebrata) +KW Methylation + +// + ID Tele-8alpha-FAD histidine on H +AC PTM-0288 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF C27H31N9O15P2 +MM 783.141485 +DR PSI-MOD; MOD:00226 +DR RESID; AA0221 +TR Bacteria; taxId:2 (Bacteria) +TR Eukaryota; taxId:2759 (Eukaryota) +KW FAD + +// + ID Tele-methylhistidine on H +AC PTM-0290 +MT UniProt +FT MOD_RES +TG H +PP Anywhere. +CF CH2 +MM 14.01565 +DR PSI-MOD; MOD:00322 +DR RESID; AA0317 +TR Eukaryota; taxId:5791 (Physarum polycephalum), taxId:7742 (Vertebrata) +KW Methylation + +// + ID Thyroxine on Y +AC PTM-0294 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF C6I4O +MM 595.612805 +DR PSI-MOD; MOD:00187 +DR RESID; AA0178 +TR Eukaryota; taxId:40674 (Mammalia) +KW Iodination + +// + ID Triiodothyronine on Y +AC PTM-0295 +MT UniProt +FT MOD_RES +TG Y +PP Anywhere. +CF C6HI3O +MM 469.716158 +DR PSI-MOD; MOD:00186 +DR RESID; AA0177 +TR Eukaryota; taxId:40674 (Mammalia) +KW Iodination + +// + ID Trioxidation on C +MT Less Common +TG C +PP Anywhere. +CF O3 +MM 47.984743859 +DR Unimod; 345 + +// + ID Water loss on D +MT Less Common +TG D +PP Anywhere. +CF H-2O-1 +MM -18.010564684 +DR Unimod; 23 + +// + ID Water Loss on E +MT Common Artifact +TG E +PP Peptide N-terminal. +CF H-2O-1 +MM -18.010564684 +DR Unimod; 23 + +// + ID Zinc on D +MT Metal +TG D +PP Anywhere. +CF H-2Zn +MM 61.913491946 +DR Unimod; 954 + +// + ID Zinc on E +MT Metal +TG E +PP Anywhere. +CF H-2Zn +MM 61.913491946 +DR Unimod; 954 + +// + + P63250_A + KCNJ3_MOUSE + + + G protein-activated inward rectifier potassium channel 1 + + + + Kcnj3 + Girk1 + + + Mus musculus + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MSALRRKFGDDYQVVTTSSSGSGLQPQGPGQGPQQQLVPKKKRQRFVDKNGRCNVQHGNLGSETSRYLSDLFTTLVDLKWRWNLFIFILTYTVAWLFMASMWWVIAYTRGDLNKAHVGNYTPCVANVYNFPSAFLFFIETEATIGYGYRYITDKCPEGIILFLFQSILGSIVDAFLIGCMFIKMSQPKKRAETLMFSEHAVISMRDGKLTLMFRVGNLRNSHMVSAQIRCKLLKSRQTPEGEFLPLDQLELDVGFSTGADQLFLVSPLTICHVIDAKSPFYDLSQRSMQTEQFEVVVILEGIVETTGMTCQARTSYTEDEVLWGHRFFPVISLEEGFFKVDYSQFHATFEVPTPPYSVKEQEEMLLMSSPLIAPAITNSKERHNSVECLDGLDDISTKLPSKLQKITGREDFPKKLLRMSSTTSEKAYSLGDLPMKLQRISSVPGNSEEKLVSKTTKMLSDPMSQSVADLPPKLQKMAGGPTRMEGNLPAKLRKMNSDRFT + + \ No newline at end of file diff --git a/mzLib/Test/Test.csproj b/mzLib/Test/Test.csproj index d87c4245b..4a2f6cb38 100644 --- a/mzLib/Test/Test.csproj +++ b/mzLib/Test/Test.csproj @@ -39,6 +39,12 @@ + + Always + + + Always + Always diff --git a/mzLib/Test/TestProteinDigestion.cs b/mzLib/Test/TestProteinDigestion.cs index 02cc3aed5..900583ce0 100644 --- a/mzLib/Test/TestProteinDigestion.cs +++ b/mzLib/Test/TestProteinDigestion.cs @@ -361,6 +361,38 @@ public static void Test_ProteinDigest() Assert.AreEqual("MED[mt:mod1 on D]EEK", pep2.FullSequence); } + /// + /// We want to have protein digestion yield the same set of peptides regardless of the order their modifications are encoded in the XML. + /// + [Test] + public static void TestDigestionOfSameProteinFromDifferentXmls() + { + DigestionParams digestionParams = new DigestionParams("trypsin", maxMissedCleavages: 2, minPeptideLength: 7, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain); + ModificationMotif.TryGetMotif("C", out ModificationMotif motif); + Modification carbamidomethylOnC = new Modification(_originalId: "Carbamidomethyl on C", _modificationType: "Common Fixed", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("C2H3NO")); + var fixedModifications = new List { carbamidomethylOnC }; + ModificationMotif.TryGetMotif("M", out ModificationMotif motifM); + Modification oxidationOnM = new Modification(_originalId: "Oxidation on M", _modificationType: "Common Variable", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("O")); + + // Load in proteins + var dbFive = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "05.xml"); + var dbSix = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "05.xml"); + DecoyType decoyType = DecoyType.Reverse; + List proteins5 = null; + List proteins6 = null; + + proteins5 = ProteinDbLoader.LoadProteinXML(dbFive, true, decoyType, null, false, null, out var unknownModificationsFive); + proteins6 = ProteinDbLoader.LoadProteinXML(dbSix, true, decoyType, null, false, null, out var unknownModificationsSix); + + unknownModificationsFive.Add("", oxidationOnM); + unknownModificationsSix.Add("", oxidationOnM); + + var peptides5 = proteins5.First().Digest(digestionParams, fixedModifications, unknownModificationsFive.Values.Distinct().ToList()).ToList(); + var peptides6 = proteins6.First().Digest(digestionParams, fixedModifications, unknownModificationsSix.Values.Distinct().ToList()).ToList(); + Assert.AreEqual(peptides5.Count, peptides6.Count); + CollectionAssert.AreEquivalent(peptides5, peptides6); + } + [Test] [TestCase("cRAP_databaseGPTMD.xml")] [TestCase("uniprot_aifm1.fasta")] From 7de7d9c3ed48a4704677b83f442375c457533780 Mon Sep 17 00:00:00 2001 From: trishorts Date: Tue, 14 Jan 2025 15:49:00 -0600 Subject: [PATCH 2/9] dunno --- mzLib/Test/TestProteinDigestion.cs | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/mzLib/Test/TestProteinDigestion.cs b/mzLib/Test/TestProteinDigestion.cs index 900583ce0..db89a7497 100644 --- a/mzLib/Test/TestProteinDigestion.cs +++ b/mzLib/Test/TestProteinDigestion.cs @@ -377,15 +377,18 @@ public static void TestDigestionOfSameProteinFromDifferentXmls() // Load in proteins var dbFive = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "05.xml"); var dbSix = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "05.xml"); - DecoyType decoyType = DecoyType.Reverse; + DecoyType decoyType = DecoyType.None; List proteins5 = null; List proteins6 = null; proteins5 = ProteinDbLoader.LoadProteinXML(dbFive, true, decoyType, null, false, null, out var unknownModificationsFive); proteins6 = ProteinDbLoader.LoadProteinXML(dbSix, true, decoyType, null, false, null, out var unknownModificationsSix); - unknownModificationsFive.Add("", oxidationOnM); - unknownModificationsSix.Add("", oxidationOnM); + var fiveMods = ProteinDbLoader.GetPtmListFromProteinXml(dbFive); + var sixMods = ProteinDbLoader.GetPtmListFromProteinXml(dbSix); + + Assert.AreEqual(fiveMods.Count, sixMods.Count); + CollectionAssert.AreEquivalent(fiveMods, sixMods); var peptides5 = proteins5.First().Digest(digestionParams, fixedModifications, unknownModificationsFive.Values.Distinct().ToList()).ToList(); var peptides6 = proteins6.First().Digest(digestionParams, fixedModifications, unknownModificationsSix.Values.Distinct().ToList()).ToList(); From 088e2b1481f2fd09422eab6b22fc5714a2450255 Mon Sep 17 00:00:00 2001 From: trishorts Date: Wed, 15 Jan 2025 09:44:27 -0600 Subject: [PATCH 3/9] correct protein accession now --- mzLib/Test/DatabaseTests/05.xml | 1265 ++++++++++++++++++++++++---- mzLib/Test/DatabaseTests/06.xml | 1399 ++++++++++++++++++++++++++----- 2 files changed, 2295 insertions(+), 369 deletions(-) diff --git a/mzLib/Test/DatabaseTests/05.xml b/mzLib/Test/DatabaseTests/05.xml index 472cef3c6..3b7232bd4 100644 --- a/mzLib/Test/DatabaseTests/05.xml +++ b/mzLib/Test/DatabaseTests/05.xml @@ -2434,221 +2434,1184 @@ DR Unimod; 954 // - P63250 - KCNJ3_MOUSE + P63260 + ACTG_MOUSE - G protein-activated inward rectifier potassium channel 1 + Actin, cytoplasmic 2 - Kcnj3 - Girk1 + Actg1 + Actg Mus musculus - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + - + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - + + + - + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + - - + + - + - - + + - - - + + + + + + + + - - - - + + + + - - + + - - + + - - + + + + - - + + - - + + - - + + - - + + + - - + + - - + + + + + - - + + + - - + + + - - + + - - - - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - MSALRRKFGDDYQVVTTSSSGSGLQPQGPGQGPQQQLVPKKKRQRFVDKNGRCNVQHGNLGSETSRYLSDLFTTLVDLKWRWNLFIFILTYTVAWLFMASMWWVIAYTRGDLNKAHVGNYTPCVANVYNFPSAFLFFIETEATIGYGYRYITDKCPEGIILFLFQSILGSIVDAFLIGCMFIKMSQPKKRAETLMFSEHAVISMRDGKLTLMFRVGNLRNSHMVSAQIRCKLLKSRQTPEGEFLPLDQLELDVGFSTGADQLFLVSPLTICHVIDAKSPFYDLSQRSMQTEQFEVVVILEGIVETTGMTCQARTSYTEDEVLWGHRFFPVISLEEGFFKVDYSQFHATFEVPTPPYSVKEQEEMLLMSSPLIAPAITNSKERHNSVECLDGLDDISTKLPSKLQKITGREDFPKKLLRMSSTTSEKAYSLGDLPMKLQRISSVPGNSEEKLVSKTTKMLSDPMSQSVADLPPKLQKMAGGPTRMEGNLPAKLRKMNSDRFT + MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF \ No newline at end of file diff --git a/mzLib/Test/DatabaseTests/06.xml b/mzLib/Test/DatabaseTests/06.xml index 1a7030e7d..1bd37acd1 100644 --- a/mzLib/Test/DatabaseTests/06.xml +++ b/mzLib/Test/DatabaseTests/06.xml @@ -2433,222 +2433,1185 @@ MM 61.913491946 DR Unimod; 954 // - - P63250_A - KCNJ3_MOUSE - - - G protein-activated inward rectifier potassium channel 1 - - - - Kcnj3 - Girk1 - - - Mus musculus - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MSALRRKFGDDYQVVTTSSSGSGLQPQGPGQGPQQQLVPKKKRQRFVDKNGRCNVQHGNLGSETSRYLSDLFTTLVDLKWRWNLFIFILTYTVAWLFMASMWWVIAYTRGDLNKAHVGNYTPCVANVYNFPSAFLFFIETEATIGYGYRYITDKCPEGIILFLFQSILGSIVDAFLIGCMFIKMSQPKKRAETLMFSEHAVISMRDGKLTLMFRVGNLRNSHMVSAQIRCKLLKSRQTPEGEFLPLDQLELDVGFSTGADQLFLVSPLTICHVIDAKSPFYDLSQRSMQTEQFEVVVILEGIVETTGMTCQARTSYTEDEVLWGHRFFPVISLEEGFFKVDYSQFHATFEVPTPPYSVKEQEEMLLMSSPLIAPAITNSKERHNSVECLDGLDDISTKLPSKLQKITGREDFPKKLLRMSSTTSEKAYSLGDLPMKLQRISSVPGNSEEKLVSKTTKMLSDPMSQSVADLPPKLQKMAGGPTRMEGNLPAKLRKMNSDRFT - + + P63260 + ACTG_MOUSE + + + Actin, cytoplasmic 2 + + + + Actg1 + Actg + + + Mus musculus + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF + \ No newline at end of file From 00d87f05bdf691242ff97cc08af013951167f629 Mon Sep 17 00:00:00 2001 From: trishorts Date: Wed, 15 Jan 2025 09:58:52 -0600 Subject: [PATCH 4/9] j --- mzLib/Test/TestProteinDigestion.cs | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/mzLib/Test/TestProteinDigestion.cs b/mzLib/Test/TestProteinDigestion.cs index db89a7497..deb8a829e 100644 --- a/mzLib/Test/TestProteinDigestion.cs +++ b/mzLib/Test/TestProteinDigestion.cs @@ -363,6 +363,7 @@ public static void Test_ProteinDigest() /// /// We want to have protein digestion yield the same set of peptides regardless of the order their modifications are encoded in the XML. + /// While all of the positions of the modifications are the same, the order of the modifications in the XML is different. /// [Test] public static void TestDigestionOfSameProteinFromDifferentXmls() @@ -373,7 +374,7 @@ public static void TestDigestionOfSameProteinFromDifferentXmls() var fixedModifications = new List { carbamidomethylOnC }; ModificationMotif.TryGetMotif("M", out ModificationMotif motifM); Modification oxidationOnM = new Modification(_originalId: "Oxidation on M", _modificationType: "Common Variable", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("O")); - + var variableModifications = new List { oxidationOnM }; // Load in proteins var dbFive = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "05.xml"); var dbSix = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "05.xml"); @@ -390,8 +391,8 @@ public static void TestDigestionOfSameProteinFromDifferentXmls() Assert.AreEqual(fiveMods.Count, sixMods.Count); CollectionAssert.AreEquivalent(fiveMods, sixMods); - var peptides5 = proteins5.First().Digest(digestionParams, fixedModifications, unknownModificationsFive.Values.Distinct().ToList()).ToList(); - var peptides6 = proteins6.First().Digest(digestionParams, fixedModifications, unknownModificationsSix.Values.Distinct().ToList()).ToList(); + var peptides5 = proteins5.First().Digest(digestionParams, fixedModifications, variableModifications).ToList(); + var peptides6 = proteins6.First().Digest(digestionParams, fixedModifications, variableModifications).ToList(); Assert.AreEqual(peptides5.Count, peptides6.Count); CollectionAssert.AreEquivalent(peptides5, peptides6); } From 7ccefd18e5803bf6c130f50603828a55c6fcb93f Mon Sep 17 00:00:00 2001 From: trishorts Date: Wed, 15 Jan 2025 15:10:45 -0600 Subject: [PATCH 5/9] k --- mzLib/Omics/Digestion/DigestionProduct.cs | 10 ++++++++++ mzLib/Proteomics/Protein/Protein.cs | 2 ++ mzLib/Test/TestProteinDigestion.cs | 6 ++++-- 3 files changed, 16 insertions(+), 2 deletions(-) diff --git a/mzLib/Omics/Digestion/DigestionProduct.cs b/mzLib/Omics/Digestion/DigestionProduct.cs index 55aed3255..9a78aa378 100644 --- a/mzLib/Omics/Digestion/DigestionProduct.cs +++ b/mzLib/Omics/Digestion/DigestionProduct.cs @@ -1,6 +1,7 @@ using System; using System.Collections.Generic; using System.ComponentModel; +using System.IO; using System.Linq; using System.Text; using System.Threading.Tasks; @@ -186,6 +187,15 @@ private static Dictionary GetNewVariableModificationPattern(i } } + using (StreamWriter sw = File.AppendText(@"C:\Users\trish\Downloads\pattern.txt")) + { + foreach (var kvp in modification_pattern) + { + sw.WriteLine(kvp.Key + " " + kvp.Value); + } + sw.WriteLine("-------------------------------------------------------------------------------------------------------"); + } + return modification_pattern; } diff --git a/mzLib/Proteomics/Protein/Protein.cs b/mzLib/Proteomics/Protein/Protein.cs index 0053a20d7..6a13896c4 100644 --- a/mzLib/Proteomics/Protein/Protein.cs +++ b/mzLib/Proteomics/Protein/Protein.cs @@ -265,6 +265,8 @@ public IEnumerable Digest(IDigestionParams digestionPara unmodifiedPeptides = GetGlycoPeptides(unmodifiedPeptides, digestionParameters.KeepNGlycopeptide, digestionParameters.KeepOGlycopeptide); } + unmodifiedPeptides = unmodifiedPeptides.Where(p => p.BaseSequence == "EKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNER"); + IEnumerable modifiedPeptides = unmodifiedPeptides.SelectMany(peptide => peptide.GetModifiedPeptides(allKnownFixedModifications, digestionParameters, variableModifications)); diff --git a/mzLib/Test/TestProteinDigestion.cs b/mzLib/Test/TestProteinDigestion.cs index deb8a829e..95f1ce239 100644 --- a/mzLib/Test/TestProteinDigestion.cs +++ b/mzLib/Test/TestProteinDigestion.cs @@ -368,7 +368,7 @@ public static void Test_ProteinDigest() [Test] public static void TestDigestionOfSameProteinFromDifferentXmls() { - DigestionParams digestionParams = new DigestionParams("trypsin", maxMissedCleavages: 2, minPeptideLength: 7, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain); + DigestionParams digestionParams = new DigestionParams("trypsin", maxMissedCleavages: 2, minPeptideLength: 7, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain, maxModificationIsoforms: int.MaxValue); ModificationMotif.TryGetMotif("C", out ModificationMotif motif); Modification carbamidomethylOnC = new Modification(_originalId: "Carbamidomethyl on C", _modificationType: "Common Fixed", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("C2H3NO")); var fixedModifications = new List { carbamidomethylOnC }; @@ -377,7 +377,7 @@ public static void TestDigestionOfSameProteinFromDifferentXmls() var variableModifications = new List { oxidationOnM }; // Load in proteins var dbFive = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "05.xml"); - var dbSix = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "05.xml"); + var dbSix = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "06.xml"); DecoyType decoyType = DecoyType.None; List proteins5 = null; List proteins6 = null; @@ -393,6 +393,8 @@ public static void TestDigestionOfSameProteinFromDifferentXmls() var peptides5 = proteins5.First().Digest(digestionParams, fixedModifications, variableModifications).ToList(); var peptides6 = proteins6.First().Digest(digestionParams, fixedModifications, variableModifications).ToList(); + File.WriteAllLines(@"C:\Users\trish\Downloads\peptides5.txt", peptides5.OrderBy(p => p.FullSequence).Select(p => p.FullSequence)); + File.WriteAllLines(@"C:\Users\trish\Downloads\peptides6.txt", peptides6.OrderBy(p => p.FullSequence).Select(p => p.FullSequence)); Assert.AreEqual(peptides5.Count, peptides6.Count); CollectionAssert.AreEquivalent(peptides5, peptides6); } From a15c4f8c52d87cd2a7378355cc15d8204c4ac7be Mon Sep 17 00:00:00 2001 From: trishorts Date: Thu, 16 Jan 2025 10:34:14 -0600 Subject: [PATCH 6/9] added sort feature to GetModifiedPeptide4s using IComparable for Modification --- mzLib/Omics/Modifications/Modification.cs | 14 ++++- .../ProteolyticPeptide.cs | 59 ++++++++++--------- 2 files changed, 44 insertions(+), 29 deletions(-) diff --git a/mzLib/Omics/Modifications/Modification.cs b/mzLib/Omics/Modifications/Modification.cs index 5b2beaa81..0e78a14ac 100644 --- a/mzLib/Omics/Modifications/Modification.cs +++ b/mzLib/Omics/Modifications/Modification.cs @@ -13,7 +13,7 @@ namespace Omics.Modifications /// Represents a modification /// Mods.txt format was taken from https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ptmlist.txt /// - public class Modification + public class Modification : IComparable { public string IdWithMotif { get; private set; } public string OriginalId { get; private set; } @@ -299,5 +299,17 @@ public string ModificationErrorsToString() //reports errors in required fields. return sb.ToString(); } + public int CompareTo(Modification other) + { + if (other == null) return 1; + + int idComparison = string.Compare(this.IdWithMotif, other.IdWithMotif, StringComparison.Ordinal); + if (idComparison != 0) + { + return idComparison; + } + + return Nullable.Compare(this.MonoisotopicMass, other.MonoisotopicMass); + } } } \ No newline at end of file diff --git a/mzLib/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs b/mzLib/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs index 954ce449a..a613aa620 100644 --- a/mzLib/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs +++ b/mzLib/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs @@ -97,48 +97,51 @@ internal IEnumerable GetModifiedPeptides(IEnumerabl } // LOCALIZED MODS - foreach (var kvp in Protein.OneBasedPossibleLocalizedModifications) + var localizedModsOrderedByPositionThenByModification = Protein.OneBasedPossibleLocalizedModifications + .SelectMany(kvp => kvp.Value.Select(value => (kvp.Key, value))) + .OrderBy(tuple => tuple.Key) + .ThenBy(tuple => tuple.value) + .ToList(); + foreach (var localizedMod in localizedModsOrderedByPositionThenByModification) { - bool inBounds = kvp.Key >= OneBasedStartResidue && kvp.Key <= OneBasedEndResidue; + bool inBounds = localizedMod.Key >= OneBasedStartResidue && localizedMod.Key <= OneBasedEndResidue; if (!inBounds) { continue; } - int locInPeptide = kvp.Key - OneBasedStartResidueInProtein + 1; - foreach (Modification modWithMass in kvp.Value) + int locInPeptide = localizedMod.Key - OneBasedStartResidueInProtein + 1; + + if (localizedMod.value is Modification variableModification) { - if (modWithMass is Modification variableModification) + // Check if can be a n-term mod + if (locInPeptide == 1 && CanBeNTerminalMod(variableModification, peptideLength) && !Protein.IsDecoy) { - // Check if can be a n-term mod - if (locInPeptide == 1 && CanBeNTerminalMod(variableModification, peptideLength) && !Protein.IsDecoy) - { - pepNTermVariableMods.Add(variableModification); - } + pepNTermVariableMods.Add(variableModification); + } - int r = locInPeptide - 1; - if (r >= 0 && r < peptideLength - && (Protein.IsDecoy || - (ModificationLocalization.ModFits(variableModification, Protein.BaseSequence, r + 1, peptideLength, OneBasedStartResidueInProtein + r) - && variableModification.LocationRestriction == "Anywhere."))) + int r = locInPeptide - 1; + if (r >= 0 && r < peptideLength + && (Protein.IsDecoy || + (ModificationLocalization.ModFits(variableModification, Protein.BaseSequence, r + 1, peptideLength, OneBasedStartResidueInProtein + r) + && variableModification.LocationRestriction == "Anywhere."))) + { + if (!twoBasedPossibleVariableAndLocalizeableModifications.TryGetValue(r + 2, out List residueVariableMods)) { - if (!twoBasedPossibleVariableAndLocalizeableModifications.TryGetValue(r + 2, out List residueVariableMods)) - { - residueVariableMods = new List { variableModification }; - twoBasedPossibleVariableAndLocalizeableModifications.Add(r + 2, residueVariableMods); - } - else - { - residueVariableMods.Add(variableModification); - } + residueVariableMods = new List { variableModification }; + twoBasedPossibleVariableAndLocalizeableModifications.Add(r + 2, residueVariableMods); } - - // Check if can be a c-term mod - if (locInPeptide == peptideLength && CanBeCTerminalMod(variableModification, peptideLength) && !Protein.IsDecoy) + else { - pepCTermVariableMods.Add(variableModification); + residueVariableMods.Add(variableModification); } } + + // Check if can be a c-term mod + if (locInPeptide == peptideLength && CanBeCTerminalMod(variableModification, peptideLength) && !Protein.IsDecoy) + { + pepCTermVariableMods.Add(variableModification); + } } } From c61cffe709a2a37f3988df9adca3826c1c2ff9cf Mon Sep 17 00:00:00 2001 From: trishorts Date: Thu, 16 Jan 2025 10:44:27 -0600 Subject: [PATCH 7/9] eliminate unused code --- mzLib/Omics/Digestion/DigestionProduct.cs | 20 +------------------- mzLib/Proteomics/Protein/Protein.cs | 2 +- mzLib/Test/TestProteinDigestion.cs | 6 +++--- 3 files changed, 5 insertions(+), 23 deletions(-) diff --git a/mzLib/Omics/Digestion/DigestionProduct.cs b/mzLib/Omics/Digestion/DigestionProduct.cs index 9a78aa378..6e4e82b79 100644 --- a/mzLib/Omics/Digestion/DigestionProduct.cs +++ b/mzLib/Omics/Digestion/DigestionProduct.cs @@ -1,11 +1,4 @@ -using System; -using System.Collections.Generic; -using System.ComponentModel; -using System.IO; -using System.Linq; -using System.Text; -using System.Threading.Tasks; -using Omics.Modifications; +using Omics.Modifications; namespace Omics.Digestion { @@ -187,18 +180,7 @@ private static Dictionary GetNewVariableModificationPattern(i } } - using (StreamWriter sw = File.AppendText(@"C:\Users\trish\Downloads\pattern.txt")) - { - foreach (var kvp in modification_pattern) - { - sw.WriteLine(kvp.Key + " " + kvp.Value); - } - sw.WriteLine("-------------------------------------------------------------------------------------------------------"); - } - return modification_pattern; } - - } } diff --git a/mzLib/Proteomics/Protein/Protein.cs b/mzLib/Proteomics/Protein/Protein.cs index 6a13896c4..46a9a6fc5 100644 --- a/mzLib/Proteomics/Protein/Protein.cs +++ b/mzLib/Proteomics/Protein/Protein.cs @@ -265,7 +265,7 @@ public IEnumerable Digest(IDigestionParams digestionPara unmodifiedPeptides = GetGlycoPeptides(unmodifiedPeptides, digestionParameters.KeepNGlycopeptide, digestionParameters.KeepOGlycopeptide); } - unmodifiedPeptides = unmodifiedPeptides.Where(p => p.BaseSequence == "EKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNER"); + //unmodifiedPeptides = unmodifiedPeptides.Where(p => p.BaseSequence == "EKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNER"); IEnumerable modifiedPeptides = unmodifiedPeptides.SelectMany(peptide => peptide.GetModifiedPeptides(allKnownFixedModifications, digestionParameters, variableModifications)); diff --git a/mzLib/Test/TestProteinDigestion.cs b/mzLib/Test/TestProteinDigestion.cs index 95f1ce239..81368534b 100644 --- a/mzLib/Test/TestProteinDigestion.cs +++ b/mzLib/Test/TestProteinDigestion.cs @@ -364,11 +364,12 @@ public static void Test_ProteinDigest() /// /// We want to have protein digestion yield the same set of peptides regardless of the order their modifications are encoded in the XML. /// While all of the positions of the modifications are the same, the order of the modifications in the XML is different. + /// The issue is that we are running into the cap of max modified forms of 1024 and depending on which mod you use first, you cut off some other modified forms /// [Test] public static void TestDigestionOfSameProteinFromDifferentXmls() { - DigestionParams digestionParams = new DigestionParams("trypsin", maxMissedCleavages: 2, minPeptideLength: 7, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain, maxModificationIsoforms: int.MaxValue); + DigestionParams digestionParams = new DigestionParams("trypsin", maxMissedCleavages: 2, minPeptideLength: 7, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain); ModificationMotif.TryGetMotif("C", out ModificationMotif motif); Modification carbamidomethylOnC = new Modification(_originalId: "Carbamidomethyl on C", _modificationType: "Common Fixed", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("C2H3NO")); var fixedModifications = new List { carbamidomethylOnC }; @@ -393,8 +394,7 @@ public static void TestDigestionOfSameProteinFromDifferentXmls() var peptides5 = proteins5.First().Digest(digestionParams, fixedModifications, variableModifications).ToList(); var peptides6 = proteins6.First().Digest(digestionParams, fixedModifications, variableModifications).ToList(); - File.WriteAllLines(@"C:\Users\trish\Downloads\peptides5.txt", peptides5.OrderBy(p => p.FullSequence).Select(p => p.FullSequence)); - File.WriteAllLines(@"C:\Users\trish\Downloads\peptides6.txt", peptides6.OrderBy(p => p.FullSequence).Select(p => p.FullSequence)); + Assert.AreEqual(peptides5.Count, peptides6.Count); CollectionAssert.AreEquivalent(peptides5, peptides6); } From 20b2bc585c69639154c037628b3895e299f381fd Mon Sep 17 00:00:00 2001 From: trishorts Date: Thu, 16 Jan 2025 11:16:57 -0600 Subject: [PATCH 8/9] eliminate unused codfe --- mzLib/Proteomics/Protein/Protein.cs | 2 -- 1 file changed, 2 deletions(-) diff --git a/mzLib/Proteomics/Protein/Protein.cs b/mzLib/Proteomics/Protein/Protein.cs index 46a9a6fc5..0053a20d7 100644 --- a/mzLib/Proteomics/Protein/Protein.cs +++ b/mzLib/Proteomics/Protein/Protein.cs @@ -265,8 +265,6 @@ public IEnumerable Digest(IDigestionParams digestionPara unmodifiedPeptides = GetGlycoPeptides(unmodifiedPeptides, digestionParameters.KeepNGlycopeptide, digestionParameters.KeepOGlycopeptide); } - //unmodifiedPeptides = unmodifiedPeptides.Where(p => p.BaseSequence == "EKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNER"); - IEnumerable modifiedPeptides = unmodifiedPeptides.SelectMany(peptide => peptide.GetModifiedPeptides(allKnownFixedModifications, digestionParameters, variableModifications)); From 91515ccd01c5c633a6e008c8c0e422c7122eec58 Mon Sep 17 00:00:00 2001 From: trishorts Date: Thu, 16 Jan 2025 12:01:23 -0600 Subject: [PATCH 9/9] eliminate icomparable and swtich to linq --- mzLib/Omics/Modifications/Modification.cs | 14 +------------- .../ProteolyticDigestion/ProteolyticPeptide.cs | 6 ++---- 2 files changed, 3 insertions(+), 17 deletions(-) diff --git a/mzLib/Omics/Modifications/Modification.cs b/mzLib/Omics/Modifications/Modification.cs index 0e78a14ac..5b2beaa81 100644 --- a/mzLib/Omics/Modifications/Modification.cs +++ b/mzLib/Omics/Modifications/Modification.cs @@ -13,7 +13,7 @@ namespace Omics.Modifications /// Represents a modification /// Mods.txt format was taken from https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ptmlist.txt /// - public class Modification : IComparable + public class Modification { public string IdWithMotif { get; private set; } public string OriginalId { get; private set; } @@ -299,17 +299,5 @@ public string ModificationErrorsToString() //reports errors in required fields. return sb.ToString(); } - public int CompareTo(Modification other) - { - if (other == null) return 1; - - int idComparison = string.Compare(this.IdWithMotif, other.IdWithMotif, StringComparison.Ordinal); - if (idComparison != 0) - { - return idComparison; - } - - return Nullable.Compare(this.MonoisotopicMass, other.MonoisotopicMass); - } } } \ No newline at end of file diff --git a/mzLib/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs b/mzLib/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs index a613aa620..b63aaa153 100644 --- a/mzLib/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs +++ b/mzLib/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs @@ -97,12 +97,10 @@ internal IEnumerable GetModifiedPeptides(IEnumerabl } // LOCALIZED MODS - var localizedModsOrderedByPositionThenByModification = Protein.OneBasedPossibleLocalizedModifications + foreach (var localizedMod in Protein.OneBasedPossibleLocalizedModifications .SelectMany(kvp => kvp.Value.Select(value => (kvp.Key, value))) .OrderBy(tuple => tuple.Key) - .ThenBy(tuple => tuple.value) - .ToList(); - foreach (var localizedMod in localizedModsOrderedByPositionThenByModification) + .ThenBy(tuple => tuple.value.IdWithMotif)) { bool inBounds = localizedMod.Key >= OneBasedStartResidue && localizedMod.Key <= OneBasedEndResidue; if (!inBounds)