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glycresoft's Introduction

I'm a bioinformatician who works with mass spectrometry data. My PhD was dedicated to developing computational methods for glycomics and glycoproteomics, finding integrated-omics strategies to dig deeper into complex biological samples. My professional work now involves using that knowledge to analyze immunopeptidomics data to help develop better cancer vaccines. :email: Email me if you want to discuss MS data processing techniques, glycoinformatics, or antigenomics

🔬 Active Projects

I'm actively working on these projects. They get updated frequently. Please contact me if you want to know more about them or if you find them useful!

  • glycresoft: A glycan and glycopeptide LC-MS/MS search engine
  • ms_deisotope: A mass spectrometry library and executable for data access, signal processing, deisotoping, and charge state deconvolution suite. Actively working to deconvolute raw ion mobility data supporting Waters Cyclic IMS and Bruker TIMS-TOF data.
  • glypy: A glycoinformatics library for reading, writing, and manipulating glycans, as well as access to glycoinformatics resources around the web.

Supporting Libraries

These libraries receive updates as needed, but their purpose is to serve my other active projects. If they look useful to you, please let me know.

  • psims: Write HUPO PSI-MS mzML and mzIdentML XML formats.
  • brainpy: A library to generate coarse theoretical isotopic patterns.
  • ms_peak_picker: A low level library for signal processing of raw mass spectra
  • glycopeptidepy: A library to model glycopeptides and how they fragment. An extension to glypy.

glycresoft's People

Contributors

heckendorfc avatar mobiusklein avatar

Stargazers

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Watchers

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Forkers

bostonuniversitycbms heckendorfc mstim ksachikonye manuelperisdiaz

glycresoft's Issues

Error during MS Preprocessing

Good morning,

I'm using GlycReSoft to process my glycopeptide MS data, but when I add the sample to the workspace (as MZML file) the preprocess gives me this error after few seconds: ''ERROR-UserIdentity(id=''0'', info= UserMetaDataBundle) @None:error- etc...

How can I fix this issue ?

Have a nice day

Antonio

Error in Begin Evaluating Chromatograms

Hi Joshua,

By observing the processed mzML file. My glycoprofile has adducts with formate, sodium and one Rapifluor tag. For example, the glycan A2FG2 with mass 1786.65 will be 2098.82 with one tag and H in the mass spectrum. So I want to deduct the mass from the adducts. Thus, in the search-glycan, I manually add lots of adducts, but I am confused the parameter to use in -f. First, could you help me check is my parameter right overall ? Second, the code returns the errors like below:

glycresoft mzml preprocess \
--averagine glycan \
--maximum-charge 8 \
--name "20190205_TK-EPO_Expres2ion_04" \
--processes 10 \
--background-reduction 5 \
--start-time 8 \
"/data/bokan/glycretest/20190205_TK-EPO_Expres2ion_04.mzXML" \
"/data/bokan/test_nooff.mzML"

glycresoft build-hypothesis glycan-glyspace \
-m n-linked \
-t 10029 \
glyspace-glycans.db \
-n "CHO N-Linked Glycans"

glycresoft analyze search-glycan \
-a "C-17H-21O-1N-5" 1 \
-a "H-2C-1O-2" 2 \
-a 'H-1' 2 \
-a 'Na-1' 2 \
-f formate-adduct-model \
-o test_nooff_all_0.db \
-m 6e-4 \
glyspace-glycans.db \
test_nooff.mzML 1 --export csv

Then it shows the following error

01:17:09 - glycresoft:task         :22   - INFO - glycresoft: version 0.3.12
01:17:09 - glycresoft:task         :264  - INFO - Begin MzML Glycan Chromatogram Analyzer
{'analysis': None,
 'analysis_name': u'20190205_TK-EPO_Expres2ion_04 @ CHO N-Linked Glycans',
 'database_connection': u'glyspace-glycans.db',
 'delta_rt': 0.5,
 'grouping_error_tolerance': 1.5e-05,
 'hypothesis_id': 1,
 'mass_error_tolerance': 0.0006,
 'mass_shifts': [MassShift(C-17H-21O-1N-5, Composition({'H': -21, 'C': -17, 'O': -1, 'N': -5})),
                 MassShift(Na-1, Composition({'Na': -1})),
                 MassShift(C-17H-21O-1N-5 + Na-1, Composition({'C': -17, 'Na': -1, 'O': -1, 'N': -5, 'H': -21})),
                 MassShift(Na-1 * 2, Composition({'Na': -2})),
                 MassShift(C-17H-21O-1N-5 + Na-1 * 2, Composition({'C': -17, 'Na': -2, 'O': -1, 'N': -5, 'H': -21})),
                 MassShift(H-1, Composition({'H': -1})),
                 MassShift(C-17H-21O-1N-5 + H-1, Composition({'H': -22, 'C': -17, 'O': -1, 'N': -5})),
                 MassShift(H-1 + Na-1, Composition({'Na': -1, 'H': -1})),
                 MassShift(C-17H-21O-1N-5 + H-1 + Na-1, Composition({'C': -17, 'Na': -1, 'O': -1, 'N': -5, 'H': -22})),
                 MassShift(H-1 + Na-1 * 2, Composition({'Na': -2, 'H': -1})),
                 MassShift(C-17H-21O-1N-5 + H-1 + Na-1 * 2, Composition({'C': -17, 'Na': -2, 'O': -1, 'N': -5, 'H': -22})),
                 MassShift(H-1 * 2, Composition({'H': -2})),
                 MassShift(C-17H-21O-1N-5 + H-1 * 2, Composition({'H': -23, 'C': -17, 'O': -1, 'N': -5})),
                 MassShift(H-1 * 2 + Na-1, Composition({'Na': -1, 'H': -2})),
                 MassShift(C-17H-21O-1N-5 + H-1 * 2 + Na-1, Composition({'C': -17, 'Na': -1, 'O': -1, 'N': -5, 'H': -23})),
                 MassShift(H-1 * 2 + Na-1 * 2, Composition({'Na': -2, 'H': -2})),
                 MassShift(C-17H-21O-1N-5 + H-1 * 2 + Na-1 * 2, Composition({'C': -17, 'Na': -2, 'O': -1, 'N': -5, 'H': -23})),
                 MassShift(H-2C-1O-2, Composition({'H': -2, 'C': -1, 'O': -2})),
                 MassShift(C-17H-21O-1N-5 + H-2C-1O-2, Composition({'H': -23, 'C': -18, 'O': -3, 'N': -5})),
                 MassShift(H-2C-1O-2 + Na-1, Composition({'Na': -1, 'C': -1, 'O': -2, 'H': -2})),
                 MassShift(C-17H-21O-1N-5 + H-2C-1O-2 + Na-1, Composition({'C': -18, 'Na': -1, 'O': -3, 'N': -5, 'H': -23})),
                 MassShift(H-2C-1O-2 + Na-1 * 2, Composition({'Na': -2, 'C': -1, 'O': -2, 'H': -2})),
                 MassShift(C-17H-21O-1N-5 + H-2C-1O-2 + Na-1 * 2, Composition({'C': -18, 'Na': -2, 'O': -3, 'N': -5, 'H': -23})),
                 MassShift(H-1 + H-2C-1O-2, Composition({'H': -3, 'C': -1, 'O': -2})),
                 MassShift(C-17H-21O-1N-5 + H-1 + H-2C-1O-2, Composition({'H': -24, 'C': -18, 'O': -3, 'N': -5})),
                 MassShift(H-1 + H-2C-1O-2 + Na-1, Composition({'Na': -1, 'C': -1, 'O': -2, 'H': -3})),
                 MassShift(C-17H-21O-1N-5 + H-1 + H-2C-1O-2 + Na-1, Composition({'C': -18, 'Na': -1, 'O': -3, 'N': -5, 'H': -24})),
                 MassShift(H-1 + H-2C-1O-2 + Na-1 * 2, Composition({'Na': -2, 'C': -1, 'O': -2, 'H': -3})),
                 MassShift(C-17H-21O-1N-5 + H-1 + H-2C-1O-2 + Na-1 * 2, Composition({'C': -18, 'Na': -2, 'O': -3, 'N': -5, 'H': -24})),
                 MassShift(H-1 * 2 + H-2C-1O-2, Composition({'H': -4, 'C': -1, 'O': -2})),
                 MassShift(C-17H-21O-1N-5 + H-1 * 2 + H-2C-1O-2, Composition({'H': -25, 'C': -18, 'O': -3, 'N': -5})),
                 MassShift(H-1 * 2 + H-2C-1O-2 + Na-1, Composition({'Na': -1, 'C': -1, 'O': -2, 'H': -4})),
                 MassShift(C-17H-21O-1N-5 + H-1 * 2 + H-2C-1O-2 + Na-1, Composition({'C': -18, 'Na': -1, 'O': -3, 'N': -5, 'H': -25})),
                 MassShift(H-1 * 2 + H-2C-1O-2 + Na-1 * 2, Composition({'Na': -2, 'C': -1, 'O': -2, 'H': -4})),
                 MassShift(C-17H-21O-1N-5 + H-1 * 2 + H-2C-1O-2 + Na-1 * 2, Composition({'C': -18, 'Na': -2, 'O': -3, 'N': -5, 'H': -25})),
                 MassShift(H-2C-1O-2 * 2, Composition({'H': -4, 'C': -2, 'O': -4})),
                 MassShift(C-17H-21O-1N-5 + H-2C-1O-2 * 2, Composition({'H': -25, 'C': -19, 'O': -5, 'N': -5})),
                 MassShift(H-2C-1O-2 * 2 + Na-1, Composition({'Na': -1, 'C': -2, 'O': -4, 'H': -4})),
                 MassShift(C-17H-21O-1N-5 + H-2C-1O-2 * 2 + Na-1, Composition({'C': -19, 'Na': -1, 'O': -5, 'N': -5, 'H': -25})),
                 MassShift(H-2C-1O-2 * 2 + Na-1 * 2, Composition({'Na': -2, 'C': -2, 'O': -4, 'H': -4})),
                 MassShift(C-17H-21O-1N-5 + H-2C-1O-2 * 2 + Na-1 * 2, Composition({'C': -19, 'Na': -2, 'O': -5, 'N': -5, 'H': -25})),
                 MassShift(H-1 + H-2C-1O-2 * 2, Composition({'H': -5, 'C': -2, 'O': -4})),
                 MassShift(C-17H-21O-1N-5 + H-1 + H-2C-1O-2 * 2, Composition({'H': -26, 'C': -19, 'O': -5, 'N': -5})),
                 MassShift(H-1 + H-2C-1O-2 * 2 + Na-1, Composition({'Na': -1, 'C': -2, 'O': -4, 'H': -5})),
                 MassShift(C-17H-21O-1N-5 + H-1 + H-2C-1O-2 * 2 + Na-1, Composition({'C': -19, 'Na': -1, 'O': -5, 'N': -5, 'H': -26})),
                 MassShift(H-1 + H-2C-1O-2 * 2 + Na-1 * 2, Composition({'Na': -2, 'C': -2, 'O': -4, 'H': -5})),
                 MassShift(C-17H-21O-1N-5 + H-1 + H-2C-1O-2 * 2 + Na-1 * 2, Composition({'C': -19, 'Na': -2, 'O': -5, 'N': -5, 'H': -26})),
                 MassShift(H-1 * 2 + H-2C-1O-2 * 2, Composition({'H': -6, 'C': -2, 'O': -4})),
                 MassShift(C-17H-21O-1N-5 + H-1 * 2 + H-2C-1O-2 * 2, Composition({'H': -27, 'C': -19, 'O': -5, 'N': -5})),
                 MassShift(H-1 * 2 + H-2C-1O-2 * 2 + Na-1, Composition({'Na': -1, 'C': -2, 'O': -4, 'H': -6})),
                 MassShift(C-17H-21O-1N-5 + H-1 * 2 + H-2C-1O-2 * 2 + Na-1, Composition({'C': -19, 'Na': -1, 'O': -5, 'N': -5, 'H': -27})),
                 MassShift(H-1 * 2 + H-2C-1O-2 * 2 + Na-1 * 2, Composition({'Na': -2, 'C': -2, 'O': -4, 'H': -6})),
                 MassShift(C-17H-21O-1N-5 + H-1 * 2 + H-2C-1O-2 * 2 + Na-1 * 2, Composition({'C': -19, 'Na': -2, 'O': -5, 'N': -5, 'H': -27}))],
 'minimum_mass': 500.0,
 'msn_mass_error_tolerance': 2e-05,
 'n_processes': 4,
 'network': None,
 'output_path': u'test_nooff_all_0.db',
 'regularization_model': None,
 'regularize': None,
 'require_msms_signature': 0.0,
 'sample_path': 'test_nooff.mzML',
 'sample_run_id': -1,
 'scoring_model': ChromatogramScorer('line_score': <glycan_profiling.scoring.shape_fitter.ChromatogramShapeModel object at 0x7fad904585d0>, 'isotopic_fit': <glycan_profiling.scoring.isotopic_fit.IsotopicPatternConsistencyModel object at 0x7fad90458610>, 'spacing_fit': <glycan_profiling.scoring.spacing_fitter.ChromatogramSpacingModel object at 0x7fad90458650>, 'charge_count': <glycan_profiling.scoring.base.CompositionDispatchingModel object at 0x7fad90798190>, 'mass_shift_score': <glycan_profiling.models.mass_shift_models.GeneralizedFormateMassShiftModel object at 0x7fad9046b550>),
 'start_time': datetime.datetime(2019, 4, 13, 1, 17, 9, 591775),
 'status': 'started'}
00:52:18 - glycresoft:process      :53   - INFO - Begin Matching Chromatograms
00:52:18 - glycresoft:extract      :75   - INFO - ... Begin Extracting Chromatograms
00:52:40 - glycresoft:extract      :77   - INFO - ...... Aggregating Chromatograms
00:52:41 - glycresoft:extract      :56   - INFO - ... 661 Chromatograms Extracted.
00:52:42 - glycresoft:match        :286  - INFO - Matching Chromatograms
00:52:42 - glycresoft:match        :305  - INFO - Handling mass_shifts
00:52:42 - glycresoft:match        :180  - INFO - Begin Forward Search
01:00:35 - glycresoft:match        :123  - INFO - Begin Reverse Search
01:01:11 - glycresoft:match        :233  - INFO - Building Connected Components
01:01:26 - glycresoft:match        :239  - INFO - Validating 8 Components
01:01:27 - glycresoft:process      :55   - INFO - End Matching Chromatograms
01:01:27 - glycresoft:process      :56   - INFO - 303 Chromatogram Candidates Found
01:01:27 - glycresoft:process      :60   - INFO - Begin Evaluating Chromatograms
Could not resolve element_symbol any
Could not find element any
Could not resolve element_symbol any
Could not find element any
Could not resolve element_symbol any
Could not find element any
Could not resolve element_symbol any
Could not find element any
Could not resolve element_symbol any
Could not find element any
Could not resolve element_symbol any
Could not find element any
Could not resolve element_symbol any
Could not find element any
Could not resolve element_symbol any
Could not find element any
Could not resolve element_symbol any
Could not find element any

.....hundreds of this.......

Segmentation fault (core dumped)```

Cannot install all dependencies in python 2.7 virtual env

I seem to be running into a problem with installing the software. I tried using both make and pip to install all plus those in external-requirements.txt and I still cannot install it. Is it possible for me to get a standalone executable for use in python 3.9 ?

Error when run the search-glycan

Hi Joshua,

Thanks for the help through email. But I have error when I run the glycresoft analyze search-glycan here. I cloned the latest glycresoft and make it on Ubuntu 16.04.5 LTS (GNU/Linux 4.4.0-130-generic x86_64). Could you help check it thanks!

Bokan

glycresoft mzml preprocess \
--mass-offset -311.17 \
--averagine glycan \
--maximum-charge 4 \
--name "20190205_TK-EPO_Expres2ion_04" \
--processes 10 \
--background-reduction 5 \
--start-time 12 \
"./glycretest/20190205_TK-EPO_Expres2ion_04.mzXML" \
"test_off.mzML"

glycresoft build-hypothesis glycan-glyspace \
-m n-linked \
-t 10029 \
glyspace-glycans.db \
-n "CHO N-Linked Glycans"


glycresoft analyze search-glycan \
-a Formate 1 \
-f formate-adduct-model \
-o test_nooff_search.db \
-m 6e-4 \
glyspace-glycans.db \
test_off.mzML "CHO N-Linked Glycans" \
--export csv



{'analysis': None,
 'analysis_name': u'20190205_TK-EPO_Expres2ion_04 @ CHO N-Linked Glycans',
 'database_connection': u'glyspace-glycans.db',
 'delta_rt': 0.5,
 'grouping_error_tolerance': 1.5e-05,
 'hypothesis_id': 1,
 'mass_error_tolerance': 0.0006,
 'mass_shifts': [MassShift(Formate, Composition({'H': 2, 'C': 1, 'O': 2}))],
 'minimum_mass': 500.0,
 'msn_mass_error_tolerance': 2e-05,
 'n_processes': 4,
 'network': None,
 'output_path': u'test_nooff_search.db',
 'regularization_model': None,
 'regularize': None,
 'require_msms_signature': 0.0,
 'sample_path': 'test_off.mzML',
 'sample_run_id': -1,
 'scoring_model': ChromatogramScorer('line_score': <glycan_profiling.scoring.shape_fitter.ChromatogramShapeModel object at 0x7f0da0cb3690>, 'isotopic_fit': <glycan_profiling.scoring.isotopic_fit.IsotopicPatternConsistencyModel object at 0x7f0da0cb36d0>, 'spacing_fit': <glycan_profiling.scoring.spacing_fitter.ChromatogramSpacingModel object at 0x7f0da0cb3710>, 'charge_count': <glycan_profiling.scoring.base.CompositionDispatchingModel object at 0x7f0da1178250>, 'mass_shift_score': <glycan_profiling.models.mass_shift_models.GeneralizedFormateMassShiftModel object at 0x7f0da0cc6610>),
 'start_time': datetime.datetime(2019, 4, 11, 0, 8, 26, 868321),
 'status': 'started'}
00:08:29 - glycresoft:profiler     :458  - INFO - The smallest possible database mass is 910.327780, raising the minimum mass to extract.
00:08:29 - glycresoft:process      :53   - INFO - Begin Matching Chromatograms
00:08:29 - glycresoft:extract      :75   - INFO - ... Begin Extracting Chromatograms
00:09:04 - glycresoft:extract      :77   - INFO - ...... Aggregating Chromatograms
00:09:04 - glycresoft:extract      :56   - INFO - ... 382 Chromatograms Extracted.
00:09:04 - glycresoft:match        :286  - INFO - Matching Chromatograms
00:09:04 - glycresoft:match        :305  - INFO - Handling mass_shifts
00:09:04 - glycresoft:match        :180  - INFO - Begin Forward Search
00:09:04 - glycresoft:match        :123  - INFO - Begin Reverse Search
00:09:04 - glycresoft:match        :233  - INFO - Building Connected Components
00:09:04 - glycresoft:match        :239  - INFO - Validating 59 Components
00:09:04 - glycresoft:process      :55   - INFO - End Matching Chromatograms
00:09:04 - glycresoft:process      :56   - INFO - 83 Chromatogram Candidates Found
00:09:04 - glycresoft:process      :60   - INFO - Begin Evaluating Chromatograms
00:09:39 - glycresoft:evaluate     :138  - INFO - Collapsing Duplicates
00:09:40 - glycresoft:evaluate     :91   - INFO - Pruning mass shift branches
00:09:40 - glycresoft:evaluate     :93   - INFO - Re-evaluating after mass shift pruning
00:09:41 - glycresoft:evaluate     :138  - INFO - Collapsing Duplicates
00:09:41 - glycresoft:process      :73   - INFO - End Evaluating Chromatograms
00:09:41 - glycresoft:profiler     :506  - INFO - Saving solutions
00:09:41 - glycresoft:analysis_migr:231  - INFO - Migrating Hypothesis
<SQLITE3-LOG> (2067) abort at 21 in [INSERT INTO "GlycanHypothesis" (name, uuid, parameters, status) VALUES (?, ?, ?, ?)]: UNIQUE constraint failed: GlycanHypothesis.name
Traceback (most recent call last):
  File "/home/bokan/miniconda2/bin/glycresoft", line 11, in <module>
    load_entry_point('glycan-profiling==0.3.12', 'console_scripts', 'glycresoft')()
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/glycan_profiling-0.3.12-py2.7-linux-x86_64.egg/glycan_profiling/cli/__main__.py", line 39, in main
    base.cli.main(standalone_mode=True)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/click/decorators.py", line 17, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/glycan_profiling-0.3.12-py2.7-linux-x86_64.egg/glycan_profiling/cli/analyze.py", line 573, in search_glycan
    analyzer.start()
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/glycan_profiling-0.3.12-py2.7-linux-x86_64.egg/glycan_profiling/task.py", line 299, in start
    out = self.run()
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/glycan_profiling-0.3.12-py2.7-linux-x86_64.egg/glycan_profiling/profiler.py", line 465, in run
    self.save_solutions(proc.solutions, extractor, database, proc.evaluator)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/glycan_profiling-0.3.12-py2.7-linux-x86_64.egg/glycan_profiling/profiler.py", line 528, in save_solutions
    exporter.run()
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/glycan_profiling-0.3.12-py2.7-linux-x86_64.egg/glycan_profiling/database/analysis/analysis_migration.py", line 232, in run
    self.migrate_hypothesis()
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/glycan_profiling-0.3.12-py2.7-linux-x86_64.egg/glycan_profiling/database/analysis/analysis_migration.py", line 269, in migrate_hypothesis
    self.glycan_db.hypothesis)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/glycan_profiling-0.3.12-py2.7-linux-x86_64.egg/glycan_profiling/database/builder/glycan/migrate.py", line 39, in migrate_hypothesis
    self.session.flush()
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 162, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2446, in flush
    self._flush(objects)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2584, in _flush
    transaction.rollback(_capture_exception=True)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 67, in __exit__
    compat.reraise(exc_type, exc_value, exc_tb)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2544, in _flush
    flush_context.execute()
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 416, in execute
    rec.execute(self)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 583, in execute
    uow,
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 245, in save_obj
    insert,
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 1116, in _emit_insert_statements
    statement, params
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 980, in execute
    return meth(self, multiparams, params)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 273, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1099, in _execute_clauseelement
    distilled_params,
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1240, in _execute_context
    e, statement, parameters, cursor, context
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1458, in _handle_dbapi_exception
    util.raise_from_cause(sqlalchemy_exception, exc_info)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 296, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=cause)
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1236, in _execute_context
    cursor, statement, parameters, context
  File "/home/bokan/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 536, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.IntegrityError: (pysqlite2.dbapi2.IntegrityError) UNIQUE constraint failed: GlycanHypothesis.name [SQL: u'INSERT INTO "GlycanHypothesis" (name, uuid, parameters, status) VALUES (?, ?, ?, ?)'] [parameters: (u'CHO N-Linked Glycans', '23369c6ae7bd4b6fa3a70db47466c856', <read-only buffer for 0x7f0d8a08ea80, size -1, offset 0 at 0x7f0d8944faf0>, u'complete')] (Background on this error at: http://sqlalche.me/e/gkpj)
bokan@jabba:/data/bokan$

About PREGENERATED DATABASE

Hi Joshua,
I am using your Glycresoft software to analyze the mass spectrum of the glycosaminoglycan standard. When establishing the database, I encountered some problems about the Pregenerated database.
Can the Pregenerated Database in your program be directly used to analyze the glycosaminoglycan extracted from Marine shellfish?
image

If not, please help me to look at my own database is this correct?
image

Thank you very much for your help!
Thank you very much!

Hello, excuse me, I am using your software, I want to ask about the matching problem

According to your instructions before, I created the database and uploaded the samples in the corresponding format.When matching samples from the database, I found that the following Settings had a significant impact on the results,So I increased the fault tolerance accordingly,Is that justified?It would be better if you could help me explain the principle.
Thank you so much for your help! Thank you very much!
image

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