diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 90ca75f..304c21a 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -22,12 +22,12 @@ jobs: - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names - flake8 implementations/python --count --select=E9,F63,F7,F82 --show-source --statistics + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 implementations/python --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Install python package run: | - pip install --editable implementations/python[test] + pip install --editable .[test] - name: Test with pytest run: | pytest -r a \ No newline at end of file diff --git a/.gitignore b/.gitignore index 4786091..21ce63d 100644 --- a/.gitignore +++ b/.gitignore @@ -4,4 +4,6 @@ __pycache__ *.ipynb examples/*splindex .coverage -htmlcov/ \ No newline at end of file +htmlcov/ +dist/ +build/ \ No newline at end of file diff --git a/examples/chinese_hamster_hcd_selected_head.mzlb.txt b/examples/chinese_hamster_hcd_selected_head.mzlb.txt index 4991bc3..c9278c5 100644 --- a/examples/chinese_hamster_hcd_selected_head.mzlb.txt +++ b/examples/chinese_hamster_hcd_selected_head.mzlb.txt @@ -1,4 +1,5 @@ +MS:1003186|library format version=1.0 MS:1003188|library name=examples/chinese_hamster_hcd_selected_head @@ -6,7 +7,6 @@ MS:1003188|library name=examples/chinese_hamster_hcd_selected_head MS:1003061|library spectrum name=AAAACALTPGPLADLAAR/2_1(4,C,CAM)_46eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=855.4538 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=46 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -30,6 +30,7 @@ MS:1003059|number of peaks=87 MS:1000224|molecular mass=1710.9076 MS:1000888|stripped peptide sequence=AAAACALTPGPLADLAAR MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=855.4538 [1]MS:1001975|delta m/z=1.4 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=855.455 @@ -39,7 +40,7 @@ MS:1001117|theoretical mass=1708.89303961159 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=R [2]MS:1001113|c-terminal flanking residue=L -[2]MS:1000885|protein accession="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.2848 MS:1003080|top 20 peak unassigned intensity fraction=0.1879 @@ -137,7 +138,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=4 MS:1003061|library spectrum name=AAAACALTPGPLADLAAR/2_1(4,C,CAM)_53eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=855.4538 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=53 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -161,6 +161,7 @@ MS:1003059|number of peaks=204 MS:1000224|molecular mass=1710.9076 MS:1000888|stripped peptide sequence=AAAACALTPGPLADLAAR MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=855.4538 [1]MS:1001975|delta m/z=4.2 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=855.4574 @@ -170,7 +171,7 @@ MS:1001117|theoretical mass=1708.89303961159 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=R [2]MS:1001113|c-terminal flanking residue=L -[2]MS:1000885|protein accession="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.3165 MS:1003080|top 20 peak unassigned intensity fraction=0.142 @@ -385,7 +386,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=5 MS:1003061|library spectrum name=AAAAGQTGTVPPGAPGALPLPGMAIVK/2_0_76eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=1207.1672 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=76 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -409,6 +409,7 @@ MS:1003059|number of peaks=122 MS:1000224|molecular mass=2414.3344 MS:1000888|stripped peptide sequence=AAAAGQTGTVPPGAPGALPLPGMAIVK MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=1207.1672 [1]MS:1001975|delta m/z=-0.9 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=1207.1661 @@ -418,7 +419,7 @@ MS:1001117|theoretical mass=2412.319901150229 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=A [2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3I2Q7|G3I2Q7_CRIGR Transcription intermediary factor 1-beta OS=Cricetulus griseus GN=I79_017700 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3I2Q7|G3I2Q7_CRIGR Transcription intermediary factor 1-beta OS=Cricetulus griseus GN=I79_017700 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.2591 MS:1003080|top 20 peak unassigned intensity fraction=0.0 @@ -551,7 +552,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=0 MS:1003061|library spectrum name=AAAAGSTSVKPIFSR/2_0_44eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=731.9043 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=44 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -575,6 +575,7 @@ MS:1003059|number of peaks=111 MS:1000224|molecular mass=1463.8086 MS:1000888|stripped peptide sequence=AAAAGSTSVKPIFSR MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=731.9043 [1]MS:1001975|delta m/z=-2.7 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=731.9023 @@ -584,7 +585,7 @@ MS:1001117|theoretical mass=1461.7939769138902 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=Q [2]MS:1001113|c-terminal flanking residue=D -[2]MS:1000885|protein accession="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.1681 MS:1003080|top 20 peak unassigned intensity fraction=0.0217 @@ -706,7 +707,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=1 MS:1003061|library spectrum name=AAAAGSTSVKPIFSR/3_0_28eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=488.2719 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=28 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -730,6 +730,7 @@ MS:1003059|number of peaks=161 MS:1000224|molecular mass=1464.8157 MS:1000888|stripped peptide sequence=AAAAGSTSVKPIFSR MS:1000041|charge state=3 +MS:1003208|experimental precursor monoisotopic m/z=488.2719 [1]MS:1001975|delta m/z=3.8 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=488.2738 @@ -739,7 +740,7 @@ MS:1001117|theoretical mass=1461.7939769138902 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=Q [2]MS:1001113|c-terminal flanking residue=D -[2]MS:1000885|protein accession="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.1804 MS:1003080|top 20 peak unassigned intensity fraction=0.0 @@ -911,7 +912,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=0 MS:1003061|library spectrum name=AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_50eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=830.8834 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=50 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -935,6 +935,7 @@ MS:1003059|number of peaks=68 MS:1000224|molecular mass=1661.7668 MS:1000888|stripped peptide sequence=AAAALGSHGSCSSEVEK MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=830.8834 [1]MS:1001975|delta m/z=4.1 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=830.8868 @@ -944,7 +945,7 @@ MS:1001117|theoretical mass=1659.7522486039798 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=K [2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.4368 MS:1003080|top 20 peak unassigned intensity fraction=0.184 @@ -1023,7 +1024,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=6 MS:1003061|library spectrum name=AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_52eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=830.8834 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=52 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -1047,6 +1047,7 @@ MS:1003059|number of peaks=402 MS:1000224|molecular mass=1661.7668 MS:1000888|stripped peptide sequence=AAAALGSHGSCSSEVEK MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=830.8834 [1]MS:1001975|delta m/z=-2.0 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=830.8817 @@ -1056,7 +1057,7 @@ MS:1001117|theoretical mass=1659.7522486039798 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=K [2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.339 MS:1003080|top 20 peak unassigned intensity fraction=0.0816 diff --git a/mzlib/validate/rules/base.json b/mzlib/validate/rules/base.json index d22733c..0db1bbf 100644 --- a/mzlib/validate/rules/base.json +++ b/mzlib/validate/rules/base.json @@ -112,7 +112,7 @@ ], "combination_logic": "OR", "id": "Spectrum_has_precursor_mz", - "level": "SHOULD", + "level": "MAY", "path": "/Library/Spectrum" }, { diff --git a/mzlib/validate/validator.py b/mzlib/validate/validator.py index 4a58e86..2db65b9 100644 --- a/mzlib/validate/validator.py +++ b/mzlib/validate/validator.py @@ -2,6 +2,8 @@ import logging import warnings import re +import numbers + from dataclasses import dataclass, field from typing import Any, Callable, Deque, Dict, Iterator, List, Optional, Sequence, Tuple, Union @@ -78,7 +80,11 @@ def _warning_iterator(iterator: Iterator[Spectrum]) -> Iterator[Spectrum]: def _is_of_type(attrib, relation) -> bool: if isinstance(relation.value_type.type_definition, type): - return isinstance(attrib.value, relation.value_type.type_definition) + if relation.value_type.type_definition is float: + tp = numbers.Number + else: + tp = relation.value_type.type_definition + return isinstance(attrib.value, tp) else: return _try_convert(attrib.value, relation.value_type.type_definition) diff --git a/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.json b/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.json index bc6d6ba..e6ecb07 100644 --- a/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.json +++ b/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.json @@ -39,6 +39,11 @@ "name": "charge state", "value": 2 }, + { + "accession": "MS:1003208", + "name": "experimental precursor monoisotopic m/z", + "value": 855.4538 + }, { "accession": "MS:1001975", "cv_param_group": "1", @@ -96,7 +101,8 @@ "accession": "MS:1000885", "cv_param_group": "2", "name": "protein accession", - "value": "\"tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1\"" + "value": "G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1", + "value_accession": "tr" } ], "id": "1" @@ -119,11 +125,6 @@ "value": "singleton spectrum", "value_accession": "MS:1003066" }, - { - "accession": "MS:1003208", - "name": "experimental precursor monoisotopic m/z", - "value": 855.4538 - }, { "accession": "MS:1000044", "name": "dissociation method", @@ -546,6 +547,11 @@ "name": "charge state", "value": 2 }, + { + "accession": "MS:1003208", + "name": "experimental precursor monoisotopic m/z", + "value": 855.4538 + }, { "accession": "MS:1001975", "cv_param_group": "1", @@ -603,7 +609,8 @@ "accession": "MS:1000885", "cv_param_group": "2", "name": "protein accession", - "value": "\"tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1\"" + "value": "G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1", + "value_accession": "tr" } ], "id": "1" @@ -626,11 +633,6 @@ "value": "singleton spectrum", "value_accession": "MS:1003066" }, - { - "accession": "MS:1003208", - "name": "experimental precursor monoisotopic m/z", - "value": 855.4538 - }, { "accession": "MS:1000044", "name": "dissociation method", @@ -1404,6 +1406,11 @@ "name": "charge state", "value": 2 }, + { + "accession": "MS:1003208", + "name": "experimental precursor monoisotopic m/z", + "value": 1207.1672 + }, { "accession": "MS:1001975", "cv_param_group": "1", @@ -1461,7 +1468,8 @@ "accession": "MS:1000885", "cv_param_group": "2", "name": "protein accession", - "value": "\"tr|G3I2Q7|G3I2Q7_CRIGR Transcription intermediary factor 1-beta OS=Cricetulus griseus GN=I79_017700 PE=4 SV=1\"" + "value": "G3I2Q7|G3I2Q7_CRIGR Transcription intermediary factor 1-beta OS=Cricetulus griseus GN=I79_017700 PE=4 SV=1", + "value_accession": "tr" } ], "id": "1" @@ -1484,11 +1492,6 @@ "value": "singleton spectrum", "value_accession": "MS:1003066" }, - { - "accession": "MS:1003208", - "name": "experimental precursor monoisotopic m/z", - "value": 1207.1672 - }, { "accession": "MS:1000044", "name": "dissociation method", @@ -2016,6 +2019,11 @@ "name": "charge state", "value": 2 }, + { + "accession": "MS:1003208", + "name": "experimental precursor monoisotopic m/z", + "value": 731.9043 + }, { "accession": "MS:1001975", "cv_param_group": "1", @@ -2073,7 +2081,8 @@ "accession": "MS:1000885", "cv_param_group": "2", "name": "protein accession", - "value": "\"tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1\"" + "value": "G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1", + "value_accession": "tr" } ], "id": "1" @@ -2096,11 +2105,6 @@ "value": "singleton spectrum", "value_accession": "MS:1003066" }, - { - "accession": "MS:1003208", - "name": "experimental precursor monoisotopic m/z", - "value": 731.9043 - }, { "accession": "MS:1000044", "name": "dissociation method", @@ -2595,6 +2599,11 @@ "name": "charge state", "value": 3 }, + { + "accession": "MS:1003208", + "name": "experimental precursor monoisotopic m/z", + "value": 488.2719 + }, { "accession": "MS:1001975", "cv_param_group": "1", @@ -2652,7 +2661,8 @@ "accession": "MS:1000885", "cv_param_group": "2", "name": "protein accession", - "value": "\"tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1\"" + "value": "G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1", + "value_accession": "tr" } ], "id": "1" @@ -2675,11 +2685,6 @@ "value": "singleton spectrum", "value_accession": "MS:1003066" }, - { - "accession": "MS:1003208", - "name": "experimental precursor monoisotopic m/z", - "value": 488.2719 - }, { "accession": "MS:1000044", "name": "dissociation method", @@ -3324,6 +3329,11 @@ "name": "charge state", "value": 2 }, + { + "accession": "MS:1003208", + "name": "experimental precursor monoisotopic m/z", + "value": 830.8834 + }, { "accession": "MS:1001975", "cv_param_group": "1", @@ -3381,7 +3391,8 @@ "accession": "MS:1000885", "cv_param_group": "2", "name": "protein accession", - "value": "\"tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1\"" + "value": "G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1", + "value_accession": "tr" } ], "id": "1" @@ -3404,11 +3415,6 @@ "value": "singleton spectrum", "value_accession": "MS:1003066" }, - { - "accession": "MS:1003208", - "name": "experimental precursor monoisotopic m/z", - "value": 830.8834 - }, { "accession": "MS:1000044", "name": "dissociation method", @@ -3774,6 +3780,11 @@ "name": "charge state", "value": 2 }, + { + "accession": "MS:1003208", + "name": "experimental precursor monoisotopic m/z", + "value": 830.8834 + }, { "accession": "MS:1001975", "cv_param_group": "1", @@ -3831,7 +3842,8 @@ "accession": "MS:1000885", "cv_param_group": "2", "name": "protein accession", - "value": "\"tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1\"" + "value": "G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1", + "value_accession": "tr" } ], "id": "1" @@ -3854,11 +3866,6 @@ "value": "singleton spectrum", "value_accession": "MS:1003066" }, - { - "accession": "MS:1003208", - "name": "experimental precursor monoisotopic m/z", - "value": 830.8834 - }, { "accession": "MS:1000044", "name": "dissociation method", diff --git a/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt b/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt index 226cdf8..b6c8631 100644 --- a/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt +++ b/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt @@ -1,4 +1,5 @@ +MS:1003186|library format version=1.0 MS:1003188|library name=tests/test_data/chinese_hamster_hcd_selected_head @@ -6,7 +7,6 @@ MS:1003188|library name=tests/test_data/chinese_hamster_hcd_selected_head MS:1003061|library spectrum name=AAAACALTPGPLADLAAR/2_1(4,C,CAM)_46eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=855.4538 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=46 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -30,6 +30,7 @@ MS:1003059|number of peaks=87 MS:1000224|molecular mass=1710.9076 MS:1000888|stripped peptide sequence=AAAACALTPGPLADLAAR MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=855.4538 [1]MS:1001975|delta m/z=1.4 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=855.455 @@ -39,7 +40,7 @@ MS:1001117|theoretical mass=1708.89303961159 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=R [2]MS:1001113|c-terminal flanking residue=L -[2]MS:1000885|protein accession="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.2848 MS:1003080|top 20 peak unassigned intensity fraction=0.1879 @@ -137,7 +138,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=4 MS:1003061|library spectrum name=AAAACALTPGPLADLAAR/2_1(4,C,CAM)_53eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=855.4538 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=53 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -161,6 +161,7 @@ MS:1003059|number of peaks=204 MS:1000224|molecular mass=1710.9076 MS:1000888|stripped peptide sequence=AAAACALTPGPLADLAAR MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=855.4538 [1]MS:1001975|delta m/z=4.2 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=855.4574 @@ -170,7 +171,7 @@ MS:1001117|theoretical mass=1708.89303961159 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=R [2]MS:1001113|c-terminal flanking residue=L -[2]MS:1000885|protein accession="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.3165 MS:1003080|top 20 peak unassigned intensity fraction=0.142 @@ -385,7 +386,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=5 MS:1003061|library spectrum name=AAAAGQTGTVPPGAPGALPLPGMAIVK/2_0_76eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=1207.1672 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=76 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -409,6 +409,7 @@ MS:1003059|number of peaks=122 MS:1000224|molecular mass=2414.3344 MS:1000888|stripped peptide sequence=AAAAGQTGTVPPGAPGALPLPGMAIVK MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=1207.1672 [1]MS:1001975|delta m/z=-0.9 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=1207.1661 @@ -418,7 +419,7 @@ MS:1001117|theoretical mass=2412.319901150229 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=A [2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3I2Q7|G3I2Q7_CRIGR Transcription intermediary factor 1-beta OS=Cricetulus griseus GN=I79_017700 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3I2Q7|G3I2Q7_CRIGR Transcription intermediary factor 1-beta OS=Cricetulus griseus GN=I79_017700 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.2591 MS:1003080|top 20 peak unassigned intensity fraction=0.0 @@ -551,7 +552,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=0 MS:1003061|library spectrum name=AAAAGSTSVKPIFSR/2_0_44eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=731.9043 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=44 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -575,6 +575,7 @@ MS:1003059|number of peaks=111 MS:1000224|molecular mass=1463.8086 MS:1000888|stripped peptide sequence=AAAAGSTSVKPIFSR MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=731.9043 [1]MS:1001975|delta m/z=-2.7 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=731.9023 @@ -584,7 +585,7 @@ MS:1001117|theoretical mass=1461.7939769138902 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=Q [2]MS:1001113|c-terminal flanking residue=D -[2]MS:1000885|protein accession="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.1681 MS:1003080|top 20 peak unassigned intensity fraction=0.0217 @@ -706,7 +707,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=1 MS:1003061|library spectrum name=AAAAGSTSVKPIFSR/3_0_28eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=488.2719 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=28 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -730,6 +730,7 @@ MS:1003059|number of peaks=161 MS:1000224|molecular mass=1464.8157 MS:1000888|stripped peptide sequence=AAAAGSTSVKPIFSR MS:1000041|charge state=3 +MS:1003208|experimental precursor monoisotopic m/z=488.2719 [1]MS:1001975|delta m/z=3.8 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=488.2738 @@ -739,7 +740,7 @@ MS:1001117|theoretical mass=1461.7939769138902 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=Q [2]MS:1001113|c-terminal flanking residue=D -[2]MS:1000885|protein accession="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.1804 MS:1003080|top 20 peak unassigned intensity fraction=0.0 @@ -911,7 +912,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=0 MS:1003061|library spectrum name=AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_50eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=830.8834 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=50 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -935,6 +935,7 @@ MS:1003059|number of peaks=68 MS:1000224|molecular mass=1661.7668 MS:1000888|stripped peptide sequence=AAAALGSHGSCSSEVEK MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=830.8834 [1]MS:1001975|delta m/z=4.1 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=830.8868 @@ -944,7 +945,7 @@ MS:1001117|theoretical mass=1659.7522486039798 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=K [2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.4368 MS:1003080|top 20 peak unassigned intensity fraction=0.184 @@ -1023,7 +1024,6 @@ MS:1003290|number of unassigned peaks among top 20 peaks=6 MS:1003061|library spectrum name=AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_52eV MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=830.8834 MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation [1]MS:1000045|collision energy=52 [1]UO:0000000|unit=UO:0000266|electronvolt @@ -1047,6 +1047,7 @@ MS:1003059|number of peaks=402 MS:1000224|molecular mass=1661.7668 MS:1000888|stripped peptide sequence=AAAALGSHGSCSSEVEK MS:1000041|charge state=2 +MS:1003208|experimental precursor monoisotopic m/z=830.8834 [1]MS:1001975|delta m/z=-2.0 [1]UO:0000000|unit=UO:0000169|parts per million MS:1003208|experimental precursor monoisotopic m/z=830.8817 @@ -1056,7 +1057,7 @@ MS:1001117|theoretical mass=1659.7522486039798 [2]MS:1001045|cleavage agent name=MS:1001251|Trypsin [2]MS:1001112|n-terminal flanking residue=K [2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" +[2]MS:1000885|protein accession=tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1 MS:1003079|total unassigned intensity fraction=0.339 MS:1003080|top 20 peak unassigned intensity fraction=0.0816