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The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 68 new columns ({'MZML_ms2_scan_window_upper_limit', 'MZML_ms1_total_ion_current', 'TOPPIC_unexpected_modifications', 'TOPPIC_number_of_protein_hits', 'MZML_isolation_window_target_mz', 'MSALIGN_feature_id', 'TOPPIC_next_residue', 'MZML_selected_ion_peak_intensity', 'TOPPIC_database_sequence', 'MZML_ms2_lowest_observed_mz', 'TOPPIC_previous_residue', 'MSALIGN_feature_score', 'MZML_ms1_scan', 'TOPPIC_number_of_matched_theoretical_fragment_masses', 'MZML_ms2_scan_window_lower_limit', 'TOPPIC_number_of_matched_experimental_fragment_ions', 'MSALIGN_precursor_charge', 'TOPPIC_last_residue_position', 'MZML_ms1_lowest_observed_mz', 'MZML_activation', 'TOPPIC_prsm_id', 'MSALIGN_feature_apex_time', 'MZML_selected_ion_charge', 'MZML_isolation_window_upper_offset', 'MZML_ms2_total_ion_current', 'MSALIGN_file_name', 'MZML_ms1_retention_time', 'MSALIGN_precursor_monoisotopic_mass', 'TOPPIC_proteoform_id', 'MZML_ms2_highest_observed_mz', 'MSALIGN_precursor_intensity', 'MZML_ms2_scan', 'TOPPIC_special_amino_acids', 'DATASET_id', 'TOPPIC_proteoform-level_q-value', 'TOPPIC_spectrum-level_q-value', 'TOPPIC_miscore', 'MZML_ms2_ion_injection_time', 'TOPPIC_protein_n-terminal_form', 'MZML_ms2_retention_time', 'TOPPIC_first_residue_position', 'TOPPIC_protein_description', 'TOPPIC_fixed_modifications', 'TOPPIC_proteoform', 'TOPPIC_number_of_variable_modifications', 'MZML_ms1_scan_window_upper_limit', 'TOPPIC_proteoform_intensity', 'TOPPIC_protein_accession', 'TOPPIC_proteoform_mass', 'MZML_ms1_ion_injection_time', 'MSALIGN_feature_intensity', 'TOPPIC_adjusted_precursor_mass', 'MZML_ms1_mass_resolving_power', 'MSALIGN_ms1_id', 'MZML_ms1_scan_window_lower_limit', 'TOPPIC_e-value', 'MZML_ms1_highest_observed_mz', 'TOPPIC_variable_modifications', 'PROJECT_id', 'MZML_instrument', 'TOPPIC_number_of_unexpected_modifications', 'SUBDATASET_id', 'MSALIGN_ms2_id', 'MZML_selected_ion_mz', 'MZML_isolation_window_lower_offset', 'MZML_collision_energy', 'MSALIGN_number_of_fragment_ions', 'MZML_ms2_mass_resolving_power'}) and 14 missing columns ({'#MS/MS_spectra', 'Separation', 'Dataset_id', 'Dissociation', 'Sample', 'FAIMS', '#Protein_ids', '#Msalign_files', 'Cysteine_protection', '#PrSM_ids', 'Raw_file_name', '#Proteoform_ids', 'Instrument', 'Species'}).
This happened while the csv dataset builder was generating data using
hf://datasets/TopRepo/M-mazei/toprepo_m_mazei_spectrum_table_ms2_v1.2.0.tsv (at revision b296efe2b8b3a83c464f2a0fcfd8dbd6e01a784b), [/tmp/hf-datasets-cache/medium/datasets/45047220143055-config-parquet-and-info-TopRepo-M-mazei-646b1b6a/hub/datasets--TopRepo--M-mazei/snapshots/b296efe2b8b3a83c464f2a0fcfd8dbd6e01a784b/toprepo_m_mazei_meta_table_v1.2.0.tsv (origin=hf://datasets/TopRepo/M-mazei@b296efe2b8b3a83c464f2a0fcfd8dbd6e01a784b/toprepo_m_mazei_meta_table_v1.2.0.tsv), /tmp/hf-datasets-cache/medium/datasets/45047220143055-config-parquet-and-info-TopRepo-M-mazei-646b1b6a/hub/datasets--TopRepo--M-mazei/snapshots/b296efe2b8b3a83c464f2a0fcfd8dbd6e01a784b/toprepo_m_mazei_spectrum_table_ms2_v1.2.0.tsv (origin=hf://datasets/TopRepo/M-mazei@b296efe2b8b3a83c464f2a0fcfd8dbd6e01a784b/toprepo_m_mazei_spectrum_table_ms2_v1.2.0.tsv)]
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1800, in _prepare_split_single
writer.write_table(table)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 765, in write_table
self._write_table(pa_table, writer_batch_size=writer_batch_size)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 773, in _write_table
pa_table = table_cast(pa_table, self._schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2321, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2249, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
PROJECT_id: int64
SUBDATASET_id: int64
DATASET_id: string
MZML_file_name: string
MZML_instrument: string
MZML_ms1_scan: int64
MZML_ms1_scan_window_lower_limit: double
MZML_ms1_scan_window_upper_limit: double
MZML_ms1_retention_time: double
MZML_ms1_total_ion_current: double
MZML_ms1_mass_resolving_power: double
MZML_ms1_ion_injection_time: double
MZML_ms1_lowest_observed_mz: double
MZML_ms1_highest_observed_mz: double
MZML_ms2_scan: int64
MZML_ms2_scan_window_lower_limit: double
MZML_ms2_scan_window_upper_limit: double
MZML_ms2_retention_time: double
MZML_ms2_total_ion_current: double
MZML_ms2_mass_resolving_power: double
MZML_ms2_ion_injection_time: double
MZML_ms2_lowest_observed_mz: double
MZML_ms2_highest_observed_mz: double
MZML_isolation_window_target_mz: double
MZML_isolation_window_lower_offset: double
MZML_isolation_window_upper_offset: double
MZML_selected_ion_mz: double
MZML_selected_ion_peak_intensity: double
MZML_selected_ion_charge: double
MZML_activation: string
MZML_collision_energy: double
MSALIGN_file_name: string
MSALIGN_ms1_id: int64
MSALIGN_ms2_id: int64
MSALIGN_precursor_charge: string
MSALIGN_precursor_monoisotopic_mass: string
MSALIGN_precursor_intensity: string
MSALIGN_feature_id: string
MSALIGN_feature_intensity: string
MSALIGN_feature_score: string
MSALIGN_feature_apex_time: string
MSALIGN_number_of_fragment_ions: int64
TOPPIC_prsm_id: double
TOPPIC_adjusted_precursor_mass: double
TOPPIC_proteoform_id: double
TOPPIC_proteoform_intensity: double
TOPPIC_number_of_protein_hits: double
TOPPIC_protein_accession: string
TOPPIC_protein_description: string
TOPPIC_first_residue_position: double
TOPPIC_last_residue_position: double
TOPPIC_special_amino_acids: double
TOPPIC_database_sequence: string
TOPPIC_proteoform_mass: double
TOPPIC_protein_n-terminal_form: string
TOPPIC_fixed_modifications: double
TOPPIC_number_of_unexpected_modifications: double
TOPPIC_unexpected_modifications: string
TOPPIC_number_of_variable_modifications: double
TOPPIC_variable_modifications: double
TOPPIC_miscore: string
TOPPIC_number_of_matched_experimental_fragment_ions: double
TOPPIC_number_of_matched_theoretical_fragment_masses: double
TOPPIC_e-value: double
TOPPIC_spectrum-level_q-value: double
TOPPIC_proteoform-level_q-value: double
TOPPIC_proteoform: string
TOPPIC_previous_residue: string
TOPPIC_next_residue: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 10669
to
{'Dataset_id': Value('string'), 'Raw_file_name': Value('string'), 'MZML_file_name': Value('string'), '#Msalign_files': Value('int64'), '#MS/MS_spectra': Value('int64'), '#PrSM_ids': Value('int64'), '#Proteoform_ids': Value('int64'), '#Protein_ids': Value('int64'), 'Species': Value('string'), 'Instrument': Value('string'), 'Dissociation': Value('string'), 'Sample': Value('string'), 'Separation': Value('string'), 'Cysteine_protection': Value('float64'), 'FAIMS': Value('string')}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1348, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 980, in convert_to_parquet
builder.download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 882, in download_and_prepare
self._download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 943, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1646, in _prepare_split
for job_id, done, content in self._prepare_split_single(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1802, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 68 new columns ({'MZML_ms2_scan_window_upper_limit', 'MZML_ms1_total_ion_current', 'TOPPIC_unexpected_modifications', 'TOPPIC_number_of_protein_hits', 'MZML_isolation_window_target_mz', 'MSALIGN_feature_id', 'TOPPIC_next_residue', 'MZML_selected_ion_peak_intensity', 'TOPPIC_database_sequence', 'MZML_ms2_lowest_observed_mz', 'TOPPIC_previous_residue', 'MSALIGN_feature_score', 'MZML_ms1_scan', 'TOPPIC_number_of_matched_theoretical_fragment_masses', 'MZML_ms2_scan_window_lower_limit', 'TOPPIC_number_of_matched_experimental_fragment_ions', 'MSALIGN_precursor_charge', 'TOPPIC_last_residue_position', 'MZML_ms1_lowest_observed_mz', 'MZML_activation', 'TOPPIC_prsm_id', 'MSALIGN_feature_apex_time', 'MZML_selected_ion_charge', 'MZML_isolation_window_upper_offset', 'MZML_ms2_total_ion_current', 'MSALIGN_file_name', 'MZML_ms1_retention_time', 'MSALIGN_precursor_monoisotopic_mass', 'TOPPIC_proteoform_id', 'MZML_ms2_highest_observed_mz', 'MSALIGN_precursor_intensity', 'MZML_ms2_scan', 'TOPPIC_special_amino_acids', 'DATASET_id', 'TOPPIC_proteoform-level_q-value', 'TOPPIC_spectrum-level_q-value', 'TOPPIC_miscore', 'MZML_ms2_ion_injection_time', 'TOPPIC_protein_n-terminal_form', 'MZML_ms2_retention_time', 'TOPPIC_first_residue_position', 'TOPPIC_protein_description', 'TOPPIC_fixed_modifications', 'TOPPIC_proteoform', 'TOPPIC_number_of_variable_modifications', 'MZML_ms1_scan_window_upper_limit', 'TOPPIC_proteoform_intensity', 'TOPPIC_protein_accession', 'TOPPIC_proteoform_mass', 'MZML_ms1_ion_injection_time', 'MSALIGN_feature_intensity', 'TOPPIC_adjusted_precursor_mass', 'MZML_ms1_mass_resolving_power', 'MSALIGN_ms1_id', 'MZML_ms1_scan_window_lower_limit', 'TOPPIC_e-value', 'MZML_ms1_highest_observed_mz', 'TOPPIC_variable_modifications', 'PROJECT_id', 'MZML_instrument', 'TOPPIC_number_of_unexpected_modifications', 'SUBDATASET_id', 'MSALIGN_ms2_id', 'MZML_selected_ion_mz', 'MZML_isolation_window_lower_offset', 'MZML_collision_energy', 'MSALIGN_number_of_fragment_ions', 'MZML_ms2_mass_resolving_power'}) and 14 missing columns ({'#MS/MS_spectra', 'Separation', 'Dataset_id', 'Dissociation', 'Sample', 'FAIMS', '#Protein_ids', '#Msalign_files', 'Cysteine_protection', '#PrSM_ids', 'Raw_file_name', '#Proteoform_ids', 'Instrument', 'Species'}).
This happened while the csv dataset builder was generating data using
hf://datasets/TopRepo/M-mazei/toprepo_m_mazei_spectrum_table_ms2_v1.2.0.tsv (at revision b296efe2b8b3a83c464f2a0fcfd8dbd6e01a784b), [/tmp/hf-datasets-cache/medium/datasets/45047220143055-config-parquet-and-info-TopRepo-M-mazei-646b1b6a/hub/datasets--TopRepo--M-mazei/snapshots/b296efe2b8b3a83c464f2a0fcfd8dbd6e01a784b/toprepo_m_mazei_meta_table_v1.2.0.tsv (origin=hf://datasets/TopRepo/M-mazei@b296efe2b8b3a83c464f2a0fcfd8dbd6e01a784b/toprepo_m_mazei_meta_table_v1.2.0.tsv), /tmp/hf-datasets-cache/medium/datasets/45047220143055-config-parquet-and-info-TopRepo-M-mazei-646b1b6a/hub/datasets--TopRepo--M-mazei/snapshots/b296efe2b8b3a83c464f2a0fcfd8dbd6e01a784b/toprepo_m_mazei_spectrum_table_ms2_v1.2.0.tsv (origin=hf://datasets/TopRepo/M-mazei@b296efe2b8b3a83c464f2a0fcfd8dbd6e01a784b/toprepo_m_mazei_spectrum_table_ms2_v1.2.0.tsv)]
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Dataset_id string | Raw_file_name string | MZML_file_name string | #Msalign_files int64 | #MS/MS_spectra int64 | #PrSM_ids int64 | #Proteoform_ids int64 | #Protein_ids int64 | Species string | Instrument string | Dissociation string | Sample string | Separation string | Cysteine_protection null | FAIMS string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PXD019792 | 191018_Mmazei_BR1-3_1_ETHCD_5sec.raw | 191018_Mmazei_BR1-3_1_ETHCD_5sec.mzML | 1 | 2,211 | 59 | 38 | 17 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR1-3_1_HCD_5sec.raw | 191018_Mmazei_BR1-3_1_HCD_5sec.mzML | 1 | 2,472 | 134 | 60 | 24 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR1-3_2_ETHCD_5sec.raw | 191018_Mmazei_BR1-3_2_ETHCD_5sec.mzML | 1 | 2,374 | 203 | 125 | 39 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR1-3_2_HCD_5sec.raw | 191018_Mmazei_BR1-3_2_HCD_5sec.mzML | 1 | 2,544 | 213 | 64 | 23 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR1-3_3_ETHCD_5sec.raw | 191018_Mmazei_BR1-3_3_ETHCD_5sec.mzML | 1 | 3,802 | 1,378 | 471 | 79 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR1-3_3_HCD_5sec.raw | 191018_Mmazei_BR1-3_3_HCD_5sec.mzML | 1 | 4,337 | 933 | 259 | 65 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR2-2_1_ETHCD_5sec.raw | 191018_Mmazei_BR2-2_1_ETHCD_5sec.mzML | 1 | 2,342 | 48 | 24 | 14 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR2-2_1_HCD_5sec.raw | 191018_Mmazei_BR2-2_1_HCD_5sec.mzML | 1 | 2,498 | 57 | 28 | 17 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR2-2_2_ETHCD_5sec.raw | 191018_Mmazei_BR2-2_2_ETHCD_5sec.mzML | 1 | 1,938 | 52 | 15 | 9 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR2-2_2_HCD_5sec.raw | 191018_Mmazei_BR2-2_2_HCD_5sec.mzML | 1 | 2,127 | 63 | 24 | 16 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR2-2_3_ETHCD_5sec.raw | 191018_Mmazei_BR2-2_3_ETHCD_5sec.mzML | 1 | 3,161 | 1,046 | 267 | 49 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR2-2_3_HCD_5sec.raw | 191018_Mmazei_BR2-2_3_HCD_5sec.mzML | 1 | 3,503 | 660 | 188 | 48 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR3-4_1_ETHCD_5sec.raw | 191018_Mmazei_BR3-4_1_ETHCD_5sec.mzML | 1 | 2,579 | 166 | 142 | 50 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR3-4_1_HCD_5sec.raw | 191018_Mmazei_BR3-4_1_HCD_5sec.mzML | 1 | 2,785 | 342 | 205 | 55 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR3-4_2_ETHCD_5sec.raw | 191018_Mmazei_BR3-4_2_ETHCD_5sec.mzML | 1 | 2,477 | 285 | 207 | 48 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR3-4_2_HCD_5sec.raw | 191018_Mmazei_BR3-4_2_HCD_5sec.mzML | 1 | 2,639 | 268 | 139 | 47 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR3-4_3_ETHCD_5sec.raw | 191018_Mmazei_BR3-4_3_ETHCD_5sec.mzML | 1 | 3,880 | 1,425 | 465 | 79 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR3-4_3_HCD_5sec.raw | 191018_Mmazei_BR3-4_3_HCD_5sec.mzML | 1 | 4,275 | 1,045 | 319 | 76 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR4-1_1_ETHCD_5sec.raw | 191018_Mmazei_BR4-1_1_ETHCD_5sec.mzML | 1 | 2,781 | 361 | 155 | 52 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR4-1_1_HCD_5sec.raw | 191018_Mmazei_BR4-1_1_HCD_5sec.mzML | 1 | 2,959 | 366 | 199 | 51 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR4-1_2_ETHCD_5sec.raw | 191018_Mmazei_BR4-1_2_ETHCD_5sec.mzML | 1 | 2,312 | 324 | 115 | 36 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR4-1_2_HCD_5sec.raw | 191018_Mmazei_BR4-1_2_HCD_5sec.mzML | 1 | 2,419 | 200 | 63 | 24 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR4-1_3_ETHCD_5sec.raw | 191018_Mmazei_BR4-1_3_ETHCD_5sec.mzML | 1 | 3,918 | 1,524 | 486 | 73 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_BR4-1_3_HCD_5sec.raw | 191018_Mmazei_BR4-1_3_HCD_5sec.mzML | 1 | 4,232 | 920 | 285 | 66 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_R2_12_ETHCD_5sec.raw | 191018_Mmazei_R2_12_ETHCD_5sec.mzML | 1 | 2,541 | 133 | 98 | 33 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_R2_12_HCD_5sec.raw | 191018_Mmazei_R2_12_HCD_5sec.mzML | 1 | 2,719 | 289 | 154 | 33 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_R2_3_ETHCD_5sec.raw | 191018_Mmazei_R2_3_ETHCD_5sec.mzML | 1 | 2,190 | 85 | 48 | 21 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_R2_3_HCD_5sec.raw | 191018_Mmazei_R2_3_HCD_5sec.mzML | 1 | 2,561 | 164 | 69 | 23 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191018_Mmazei_R2_4_HCD_5sec.raw | 191018_Mmazei_R2_4_HCD_5sec.mzML | 1 | 3,977 | 763 | 201 | 51 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191025_Mmazei_BR1-3_3_Red_ETHCD_5sec.raw | 191025_Mmazei_BR1-3_3_Red_ETHCD_5sec.mzML | 1 | 2,314 | 734 | 253 | 67 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191025_Mmazei_BR1-3_3_Red_HCD_5sec.raw | 191025_Mmazei_BR1-3_3_Red_HCD_5sec.mzML | 1 | 3,533 | 1,011 | 293 | 74 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191025_Mmazei_BR2-2_3_Red_HCD_5sec.raw | 191025_Mmazei_BR2-2_3_Red_HCD_5sec.mzML | 1 | 3,069 | 692 | 163 | 49 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191025_Mmazei_BR3-4_3_Red_HCD_5sec.raw | 191025_Mmazei_BR3-4_3_Red_HCD_5sec.mzML | 1 | 3,510 | 974 | 270 | 77 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191025_Mmazei_BR4-1_3_Red_HCD_5sec.raw | 191025_Mmazei_BR4-1_3_Red_HCD_5sec.mzML | 1 | 3,309 | 1,075 | 291 | 74 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191025_Mmazei_R2_4_Red_ETHCD_5sec.raw | 191025_Mmazei_R2_4_Red_ETHCD_5sec.mzML | 1 | 2,486 | 780 | 147 | 51 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191025_Mmazei_R2_4_Red_HCD_5sec.raw | 191025_Mmazei_R2_4_Red_HCD_5sec.mzML | 1 | 3,221 | 949 | 308 | 68 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191216_Mmazei_BR1-4_noSCX_EThcD_5sec.raw | 191216_Mmazei_BR1-4_noSCX_EThcD_5sec.mzML | 1 | 3,710 | 521 | 186 | 64 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191216_Mmazei_BR1-4_noSCX_HCD_All.raw | 191216_Mmazei_BR1-4_noSCX_HCD_All.mzML | 1 | 5,048 | 435 | 170 | 58 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191216_Mmazei_BR2-1_noSCX_EThcD_5sec_20191216180254.raw | 191216_Mmazei_BR2-1_noSCX_EThcD_5sec_20191216180254.mzML | 1 | 3,593 | 395 | 168 | 66 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191216_Mmazei_BR2-1_noSCX_HCD_All.raw | 191216_Mmazei_BR2-1_noSCX_HCD_All.mzML | 1 | 4,842 | 281 | 122 | 51 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191216_Mmazei_BR4-4_noSCX_EThcD_5sec.raw | 191216_Mmazei_BR4-4_noSCX_EThcD_5sec.mzML | 1 | 3,704 | 485 | 179 | 59 | M. mazei | Orbitrap Fusion Lumos | EThcD | Archaea Methanosarcina mazei | RPLC | null | No |
PXD019792 | 191216_Mmazei_BR4-4_noSCX_HCD_All.raw | 191216_Mmazei_BR4-4_noSCX_HCD_All.mzML | 1 | 4,843 | 384 | 198 | 59 | M. mazei | Orbitrap Fusion Lumos | HCD | Archaea Methanosarcina mazei | RPLC | null | No |
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End of preview.
TopRepo is a top-down spectral repository containing more than 12 million MS/MS spectra from 12 species. For each MS raw file in TopRepo, msconvert is used to convert the raw file to a centroided mzML file, and then TopFD is employed to deconvolute spectra in the centroided mzML file to one or several msalign files and proteoform feature files. The msalign files are searched against its corresponding proteome sequence database for spectral identification using TopPIC. The identification results are stored in TSV files.
Using mzML files, msalign files, feature files, and spectral identification (TSV) files generated from the data analysis pipeline, Python scripts in this repository are used to generate TSV files with comprehensive spectral information, annotated msalign files, and annotated mgf files.
Dataset Structure
The dataset consists of two TSV files for the species Methanosarcina mazei.
- Metadata Table
toprepo_m_mazei_meta_table_v1.2.0.tsvContains experiment-level metadata including:
- dataset identifiers
- species information
- instrument metadata
- dissociation methods
- counts of spectra, proteins, and proteoforms
- Spectrum Table
toprepo_m_mazei_spectrum_table_ms2_v1.2.0.tsvContains spectrum-level MS/MS analytical data including:
- scan identifiers
- precursor ion information
- fragmentation measurements
- proteoform annotations
- protein identifications
- statistical confidence metrics
- Annotated .msalign file
Sources
- Repository https://toprepo.org/
- Paper https://www.biorxiv.org/content/10.64898/2026.02.20.707032v1
- Github https://github.com/toppic-suite/toprepo
Contact
For questions regarding this dataset, please contact the TopRepo team through: xwliu@tulane.edu kli7@tulane.edu
Copyright (c) 2025 - 2026, Tulane University.
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