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@marekmosna marekmosna released this 31 Aug 12:46
· 31 commits to develop since this release
v0.2.0
8112e83

v0.2.0

1. Intersect_mz similarity function

Added similarity function based on spectrum intersection implemented in matchms.

2. Array support

Added array support for spectrum parameters such as PEPMASS.

Example:

select * from pgms.load_from_mgf(:LASTOID) as (
    ...
    "PEPMASS" float4[],
    ...
);

3. PrecursorMzMatch similarity

Added similarity function based on precursor_mz match implemented in matchms

4. Precursor_mz correction function

Correction function implemented for precursor_mz with parameters of typesfloat4 and float4[]

5. Support json as literal

Added json specification of a spectrum such as

[{
    "spectrum_id": "CCMSLIB00000001547",
    "source_file": "130618_Ger_Jenia_WT-3-Des-MCLR_MH981.4-qb.1.1..mgf",
    "task": "47daa4396adb426eaa5fa54b6ce7dd5f",
    "scan": "-1",
    "ms_level": "2",
    "library_membership": "GNPS-LIBRARY",
    "spectrum_status": "1",
    "splash": "splash10-0w2a-0001282259-0001282259",
    "submit_user": "mwang87",
    "compound_name": "3-Des-Microcystein_LR",
    "ion_source": "LC-ESI",
    "compound_source": "Isolated",
    "instrument": "qTof",
    "pi": "Gerwick",
    "data_collector": "Jenia",
    "adduct": "M+H",
    "precursor_mz": 981.54,
    "exactmass": "0.0",
    "charge": 1,
    "cas_number": "N/A",
    "pubmed_id": "N/A",
    "smiles": "CC(C)CC1NC(=O)C(C)NC(=O)C(=C)N(C)C(=O)CCC(NC(=O)C(C)C(NC(=O)C(CCCNC(N)=N)NC(=O)C(C)C(NC1=O)C(O)=O)\\C=C\\C(\\C)=C\\C(C)C(O)Cc1ccccc1)C(O)=O",
    "inchi": "InChI=1S/C48H72N10O12/c1-25(2)22-36-45(66)57-39(47(69)70)29(6)41(62)54-34(16-13-21-51-48(49)50)44(65)53-33(18-17-26(3)23-27(4)37(59)24-32-14-11-10-12-15-32)28(5)40(61)55-35(46(67)68)19-20-38(60)58(9)31(8)43(64)52-30(7)42(63)56-36/h10-12,14-15,17-18,23,25,27-30,33-37,39,59H,8,13,16,19-22,24H2,1-7,9H3,(H,52,64)(H,53,65)(H,54,62)(H,55,61)(H,56,63)(H,57,66)(H,67,68)(H,69,70)(H4,49,50,51)/b18-17+,26-23+",
    "inchiaux": "N/A",
    "library_class": "1",
    "spectrumid": "CCMSLIB00000001547",
    "ionmode": "positive",
    "create_time": "2019-10-30 21:18:25.0",
    "task_id": "aa87bf9cd0784df9956753f435c32434",
    "user_id": "null",
    "inchikey_smiles": "IYDKWWDUBYWQGF-NNAZGLEUSA-N",
    "inchikey_inchi": "",
    "formula_smiles": "C48H72N10O12",
    "formula_inchi": "",
    "url": "https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00000001547",
    "parent_mass": 980.5327235480092,
    "inchikey": "IYDKWWDUBYWQGF-NNAZGLEUSA-N",
    "annotation_history": [{"Compound_Name": "3-Des-Microcystein_LR", "Ion_Source": "LC-ESI", "Compound_Source": "Isolated", "Instrument": "Ger", "PI": "Gerwick", "Data_Collector": "Jenia", "Adduct": "M+H", "Scan": "-1", "Precursor_MZ": "981.4", "ExactMass": "0.0", "Charge": "0", "CAS_Number": "N/A", "Pubmed_ID": "N/A", "Smiles": "N/A", "INCHI": "N/A", "INCHI_AUX": "N/A", "Library_Class": "1", "SpectrumID": "CCMSLIB00000001547", "Ion_Mode": "Positive", "create_time": "2014-02-04 17:56:43.0", "task_id": "47daa4396adb426eaa5fa54b6ce7dd5f", "user_id": "mwang87"}, {"Compound_Name": "3-Des-Microcystein_LR", "Ion_Source": "LC-ESI", "Compound_Source": "Isolated", "Instrument": "qTof", "PI": "Gerwick", "Data_Collector": "Jenia", "Adduct": "M+H", "Scan": "-1", "Precursor_MZ": "981.54", "ExactMass": "0.0", "Charge": "0", "CAS_Number": "N/A", "Pubmed_ID": "N/A", "Smiles": "CC(C)CC1NC(=O)C(C)NC(=O)C(=C)N(C)C(=O)CCC(NC(=O)C(C)C(NC(=O)C(CCCNC(N)=N)NC(=O)C(C)C(NC1=O)C(O)=O)\\C=C\\C(\\C)=C\\C(C)C(O)Cc1ccccc1)C(O)=O", "INCHI": "N/A", "INCHI_AUX": "N/A", "Library_Class": "1", "SpectrumID": "CCMSLIB00000001547", "Ion_Mode": "Positive", "create_time": "2019-10-30 21:18:25.0", "task_id": "aa87bf9cd0784df9956753f435c32434", "user_id": "lfnothias"}],
    "peaks_json": [
        [
            289.286377,
            8068.0
        ],
        [
            295.545288,
            22507.0
        ],
        [
            298.489624,
            3925.0
        ],
        [
            317.324951,
            18742.0
        ]
    ]
},
{
    "spectrum_id": "CCMSLIB00000001548",
    "source_file": "130618_Ger_Jenia_WT-3-Des-MCLR_MH981.4-qb.1.1..mgf",
    "task": "47daa4396adb426eaa5fa54b6ce7dd5f",
    "scan": "-1",
    "ms_level": "2",
    "library_membership": "GNPS-LIBRARY",
    "spectrum_status": "1",
    "splash": "splash10-0w2a-0001282259-0001282259",
    "submit_user": "mwang87",
    "compound_name": "3-Des-Microcystein_LR",
    "ion_source": "LC-ESI",
    "compound_source": "Isolated",
    "instrument": "qTof",
    "pi": "Gerwick",
    "data_collector": "Jenia",
    "adduct": "M+H",
    "precursor_mz": 981.54,
    "exactmass": "0.0",
    "charge": 1,
    "cas_number": "N/A",
    "pubmed_id": "N/A",
    "smiles": "CC(C)CC1NC(=O)C(C)NC(=O)C(=C)N(C)C(=O)CCC(NC(=O)C(C)C(NC(=O)C(CCCNC(N)=N)NC(=O)C(C)C(NC1=O)C(O)=O)\\C=C\\C(\\C)=C\\C(C)C(O)Cc1ccccc1)C(O)=O",
    "inchi": "InChI=1S/C48H72N10O12/c1-25(2)22-36-45(66)57-39(47(69)70)29(6)41(62)54-34(16-13-21-51-48(49)50)44(65)53-33(18-17-26(3)23-27(4)37(59)24-32-14-11-10-12-15-32)28(5)40(61)55-35(46(67)68)19-20-38(60)58(9)31(8)43(64)52-30(7)42(63)56-36/h10-12,14-15,17-18,23,25,27-30,33-37,39,59H,8,13,16,19-22,24H2,1-7,9H3,(H,52,64)(H,53,65)(H,54,62)(H,55,61)(H,56,63)(H,57,66)(H,67,68)(H,69,70)(H4,49,50,51)/b18-17+,26-23+",
    "inchiaux": "N/A",
    "library_class": "1",
    "spectrumid": "CCMSLIB00000001547",
    "ionmode": "positive",
    "create_time": "2019-10-30 21:18:25.0",
    "task_id": "aa87bf9cd0784df9956753f435c32434",
    "user_id": "null",
    "inchikey_smiles": "IYDKWWDUBYWQGF-NNAZGLEUSA-N",
    "inchikey_inchi": "",
    "formula_smiles": "C48H72N10O12",
    "formula_inchi": "",
    "url": "https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00000001547",
    "parent_mass": 980.5327235480092,
    "inchikey": "IYDKWWDUBYWQGF-NNAZGLEUSA-N",
    "annotation_history": [{"Compound_Name": "3-Des-Microcystein_LR", "Ion_Source": "LC-ESI", "Compound_Source": "Isolated", "Instrument": "Ger", "PI": "Gerwick", "Data_Collector": "Jenia", "Adduct": "M+H", "Scan": "-1", "Precursor_MZ": "981.4", "ExactMass": "0.0", "Charge": "0", "CAS_Number": "N/A", "Pubmed_ID": "N/A", "Smiles": "N/A", "INCHI": "N/A", "INCHI_AUX": "N/A", "Library_Class": "1", "SpectrumID": "CCMSLIB00000001547", "Ion_Mode": "Positive", "create_time": "2014-02-04 17:56:43.0", "task_id": "47daa4396adb426eaa5fa54b6ce7dd5f", "user_id": "mwang87"}, {"Compound_Name": "3-Des-Microcystein_LR", "Ion_Source": "LC-ESI", "Compound_Source": "Isolated", "Instrument": "qTof", "PI": "Gerwick", "Data_Collector": "Jenia", "Adduct": "M+H", "Scan": "-1", "Precursor_MZ": "981.54", "ExactMass": "0.0", "Charge": "0", "CAS_Number": "N/A", "Pubmed_ID": "N/A", "Smiles": "CC(C)CC1NC(=O)C(C)NC(=O)C(=C)N(C)C(=O)CCC(NC(=O)C(C)C(NC(=O)C(CCCNC(N)=N)NC(=O)C(C)C(NC1=O)C(O)=O)\\C=C\\C(\\C)=C\\C(C)C(O)Cc1ccccc1)C(O)=O", "INCHI": "N/A", "INCHI_AUX": "N/A", "Library_Class": "1", "SpectrumID": "CCMSLIB00000001547", "Ion_Mode": "Positive", "create_time": "2019-10-30 21:18:25.0", "task_id": "aa87bf9cd0784df9956753f435c32434", "user_id": "lfnothias"}],
    "peaks_json": [
        [
            289.286377,
            8068.0
        ],
        [
            295.545288,
            22507.0
        ],
        [
            298.489624,
            3925.0
        ],
        [
            317.3249511231221321465465,
            18742.0
        ]
    ]
}]

6. Modified cosine similarity function

Added similarity function based on modified cosine algorithm implemented in matchms

7. Wrong value of missing parameter

In case of any of a spectrum parameter is not defined in *.mgf there is bug that leads to place incorrect value instead. In v0.2.0 this issue is fixed.

8. Standardize versioning

Move from two-component versioning to major.minor.patch

9. Add extension API documentation

Enjoy the API documentation how to use the functions in PosgreSQL

Assets 2
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