Datasets:

TopRepo
/

Yeast

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 ({'TOPPIC_proteoform_intensity', 'TOPPIC_number_of_matched_experimental_fragment_ions', 'MZML_ms1_highest_observed_mz', 'TOPPIC_previous_residue', 'TOPPIC_next_residue', 'MZML_ms1_scan', 'MSALIGN_file_name', 'TOPPIC_miscore', 'MZML_ms1_scan_window_upper_limit', 'MSALIGN_ms1_id', 'TOPPIC_unexpected_modifications', 'MZML_ms2_scan', 'MZML_ms2_scan_window_upper_limit', 'MZML_ms2_scan_window_lower_limit', 'TOPPIC_proteoform_mass', 'TOPPIC_last_residue_position', 'MSALIGN_precursor_intensity', 'MZML_ms1_lowest_observed_mz', 'TOPPIC_proteoform-level_q-value', 'MZML_isolation_window_target_mz', 'TOPPIC_fixed_modifications', 'TOPPIC_e-value', 'MSALIGN_precursor_charge', 'DATASET_id', 'SUBDATASET_id', 'MZML_selected_ion_mz', 'TOPPIC_proteoform', 'TOPPIC_number_of_matched_theoretical_fragment_masses', 'TOPPIC_variable_modifications', 'TOPPIC_number_of_unexpected_modifications', 'MZML_ms2_mass_resolving_power', 'TOPPIC_adjusted_precursor_mass', 'TOPPIC_prsm_id', 'MZML_isolation_window_lower_offset', 'MZML_ms1_mass_resolving_power', 'MSALIGN_precursor_monoisotopic_mass', 'MZML_ms2_ion_injection_time', 'MSALIGN_feature_id', 'MZML_ms2_total_ion_current', 'TOPPIC_protein_n-terminal_form', 'TOPPIC_proteoform_id', 'MZML_ms1_retention_time', 'TOPPIC_protein_description', 'TOPPIC_protein_accession', 'TOPPIC_special_amino_acids', 'MZML_selected_ion_charge', 'TOPPIC_spectrum-level_q-value', 'TOPPIC_number_of_protein_hits', 'MSALIGN_number_of_fragment_ions', 'MZML_instrument', 'MZML_ms1_total_ion_current', 'MZML_ms2_highest_observed_mz', 'MZML_ms1_ion_injection_time', 'MZML_activation', 'MZML_ms1_scan_window_lower_limit', 'MZML_ms2_lowest_observed_mz', 'MZML_ms2_retention_time', 'MZML_isolation_window_upper_offset', 'TOPPIC_first_residue_position', 'MSALIGN_feature_intensity', 'PROJECT_id', 'MZML_selected_ion_peak_intensity', 'MZML_collision_energy', 'MSALIGN_ms2_id', 'MSALIGN_feature_score', 'MSALIGN_feature_apex_time', 'TOPPIC_number_of_variable_modifications', 'TOPPIC_database_sequence'}) and 14 missing columns ({'#Msalign_files', 'Dataset_id', '#PrSM_ids', '#MS/MS_spectra', '#Proteoform_ids', 'Sample', 'Instrument', 'Separation', 'Raw_file_name', '#Protein_ids', 'Species', 'Cysteine_protection', 'Dissociation', 'FAIMS'}).

This happened while the csv dataset builder was generating data using

hf://datasets/TopRepo/Yeast/toprepo_yeast_spectrum_table_ms2_v1.2.0.tsv (at revision 0d996d1393bba5b1431e2fafe8dd8505302542bd), [/tmp/hf-datasets-cache/medium/datasets/34256729965506-config-parquet-and-info-TopRepo-Yeast-9bbd2b35/hub/datasets--TopRepo--Yeast/snapshots/0d996d1393bba5b1431e2fafe8dd8505302542bd/toprepo_yeast_meta_table_v1.2.0.tsv (origin=hf://datasets/TopRepo/Yeast@0d996d1393bba5b1431e2fafe8dd8505302542bd/toprepo_yeast_meta_table_v1.2.0.tsv), /tmp/hf-datasets-cache/medium/datasets/34256729965506-config-parquet-and-info-TopRepo-Yeast-9bbd2b35/hub/datasets--TopRepo--Yeast/snapshots/0d996d1393bba5b1431e2fafe8dd8505302542bd/toprepo_yeast_spectrum_table_ms2_v1.2.0.tsv (origin=hf://datasets/TopRepo/Yeast@0d996d1393bba5b1431e2fafe8dd8505302542bd/toprepo_yeast_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 ({'TOPPIC_proteoform_intensity', 'TOPPIC_number_of_matched_experimental_fragment_ions', 'MZML_ms1_highest_observed_mz', 'TOPPIC_previous_residue', 'TOPPIC_next_residue', 'MZML_ms1_scan', 'MSALIGN_file_name', 'TOPPIC_miscore', 'MZML_ms1_scan_window_upper_limit', 'MSALIGN_ms1_id', 'TOPPIC_unexpected_modifications', 'MZML_ms2_scan', 'MZML_ms2_scan_window_upper_limit', 'MZML_ms2_scan_window_lower_limit', 'TOPPIC_proteoform_mass', 'TOPPIC_last_residue_position', 'MSALIGN_precursor_intensity', 'MZML_ms1_lowest_observed_mz', 'TOPPIC_proteoform-level_q-value', 'MZML_isolation_window_target_mz', 'TOPPIC_fixed_modifications', 'TOPPIC_e-value', 'MSALIGN_precursor_charge', 'DATASET_id', 'SUBDATASET_id', 'MZML_selected_ion_mz', 'TOPPIC_proteoform', 'TOPPIC_number_of_matched_theoretical_fragment_masses', 'TOPPIC_variable_modifications', 'TOPPIC_number_of_unexpected_modifications', 'MZML_ms2_mass_resolving_power', 'TOPPIC_adjusted_precursor_mass', 'TOPPIC_prsm_id', 'MZML_isolation_window_lower_offset', 'MZML_ms1_mass_resolving_power', 'MSALIGN_precursor_monoisotopic_mass', 'MZML_ms2_ion_injection_time', 'MSALIGN_feature_id', 'MZML_ms2_total_ion_current', 'TOPPIC_protein_n-terminal_form', 'TOPPIC_proteoform_id', 'MZML_ms1_retention_time', 'TOPPIC_protein_description', 'TOPPIC_protein_accession', 'TOPPIC_special_amino_acids', 'MZML_selected_ion_charge', 'TOPPIC_spectrum-level_q-value', 'TOPPIC_number_of_protein_hits', 'MSALIGN_number_of_fragment_ions', 'MZML_instrument', 'MZML_ms1_total_ion_current', 'MZML_ms2_highest_observed_mz', 'MZML_ms1_ion_injection_time', 'MZML_activation', 'MZML_ms1_scan_window_lower_limit', 'MZML_ms2_lowest_observed_mz', 'MZML_ms2_retention_time', 'MZML_isolation_window_upper_offset', 'TOPPIC_first_residue_position', 'MSALIGN_feature_intensity', 'PROJECT_id', 'MZML_selected_ion_peak_intensity', 'MZML_collision_energy', 'MSALIGN_ms2_id', 'MSALIGN_feature_score', 'MSALIGN_feature_apex_time', 'TOPPIC_number_of_variable_modifications', 'TOPPIC_database_sequence'}) and 14 missing columns ({'#Msalign_files', 'Dataset_id', '#PrSM_ids', '#MS/MS_spectra', '#Proteoform_ids', 'Sample', 'Instrument', 'Separation', 'Raw_file_name', '#Protein_ids', 'Species', 'Cysteine_protection', 'Dissociation', 'FAIMS'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/TopRepo/Yeast/toprepo_yeast_spectrum_table_ms2_v1.2.0.tsv (at revision 0d996d1393bba5b1431e2fafe8dd8505302542bd), [/tmp/hf-datasets-cache/medium/datasets/34256729965506-config-parquet-and-info-TopRepo-Yeast-9bbd2b35/hub/datasets--TopRepo--Yeast/snapshots/0d996d1393bba5b1431e2fafe8dd8505302542bd/toprepo_yeast_meta_table_v1.2.0.tsv (origin=hf://datasets/TopRepo/Yeast@0d996d1393bba5b1431e2fafe8dd8505302542bd/toprepo_yeast_meta_table_v1.2.0.tsv), /tmp/hf-datasets-cache/medium/datasets/34256729965506-config-parquet-and-info-TopRepo-Yeast-9bbd2b35/hub/datasets--TopRepo--Yeast/snapshots/0d996d1393bba5b1431e2fafe8dd8505302542bd/toprepo_yeast_spectrum_table_ms2_v1.2.0.tsv (origin=hf://datasets/TopRepo/Yeast@0d996d1393bba5b1431e2fafe8dd8505302542bd/toprepo_yeast_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
PXD046651	Diluted_Yeast_1.raw	Diluted_Yeast_1.mzML	1	6,158	2,135	677	178	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Diluted_Yeast_2.raw	Diluted_Yeast_2.mzML	1	6,265	1,976	616	169	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Diluted_Yeast_3.raw	Diluted_Yeast_3.mzML	1	6,371	2,472	726	178	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Diluted_Yeast_4.raw	Diluted_Yeast_4.mzML	1	6,914	2,409	654	179	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Diluted_Yeast_5.raw	Diluted_Yeast_5.mzML	1	7,277	2,552	743	186	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_1.raw	Yeast_1.mzML	1	7,632	4,554	2,058	431	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_10.raw	Yeast_10.mzML	1	9,550	4,522	1,871	375	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_11.raw	Yeast_11.mzML	1	9,635	4,497	1,894	374	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_12.raw	Yeast_12.mzML	1	9,747	4,449	1,750	358	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_13.raw	Yeast_13.mzML	1	9,924	4,642	1,729	348	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_14.raw	Yeast_14.mzML	1	9,054	4,359	1,574	324	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_15.raw	Yeast_15.mzML	1	9,958	4,732	1,640	335	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_16.raw	Yeast_16.mzML	1	6,738	4,068	1,317	274	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_17.raw	Yeast_17.mzML	1	7,900	4,219	1,535	314	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_18.raw	Yeast_18.mzML	1	7,803	4,210	1,497	300	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_19.raw	Yeast_19.mzML	1	7,548	4,305	1,582	319	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_2.raw	Yeast_2.mzML	1	8,302	4,379	1,984	414	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_20.raw	Yeast_20.mzML	1	7,630	4,227	1,449	301	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_21.raw	Yeast_21.mzML	1	7,274	4,480	1,537	312	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_22.raw	Yeast_22.mzML	1	7,592	4,222	1,309	270	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_23.raw	Yeast_23.mzML	1	7,742	4,176	1,328	271	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_24.raw	Yeast_24.mzML	1	10,076	4,859	1,117	238	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_25.raw	Yeast_25.mzML	1	7,847	4,098	1,993	422	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_26.raw	Yeast_26.mzML	1	8,884	3,000	1,541	314	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_27.raw	Yeast_27.mzML	1	8,956	2,776	1,367	291	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_28.raw	Yeast_28.mzML	1	7,305	3,079	1,487	322	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_29.raw	Yeast_29.mzML	1	8,393	3,504	1,633	345	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_3.raw	Yeast_3.mzML	1	9,480	4,492	2,133	438	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_30.raw	Yeast_30.mzML	1	9,581	3,689	1,669	330	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_31.raw	Yeast_31.mzML	1	9,914	2,904	1,318	275	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_32.raw	Yeast_32.mzML	1	9,855	3,076	1,354	274	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_33.raw	Yeast_33.mzML	1	9,258	3,856	1,661	356	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_34.raw	Yeast_34.mzML	1	8,157	3,689	1,568	320	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_35.raw	Yeast_35.mzML	1	7,778	3,514	1,570	336	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_36.raw	Yeast_36.mzML	1	8,128	3,532	1,465	305	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_37.raw	Yeast_37.mzML	1	7,506	3,519	1,495	312	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_38.raw	Yeast_38.mzML	1	8,834	3,760	1,423	293	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_39.raw	Yeast_39.mzML	1	8,397	3,559	1,337	280	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_4.raw	Yeast_4.mzML	1	8,753	3,780	1,804	373	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_40.raw	Yeast_40.mzML	1	7,406	3,853	1,167	233	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_41.raw	Yeast_41.mzML	1	7,213	4,082	1,242	256	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_42.raw	Yeast_42.mzML	1	9,244	4,438	1,308	261	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_43.raw	Yeast_43.mzML	1	9,351	4,381	1,349	254	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_44.raw	Yeast_44.mzML	1	9,482	4,260	1,254	243	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_45.raw	Yeast_45.mzML	1	9,382	4,209	1,220	238	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_46.raw	Yeast_46.mzML	1	9,442	4,165	1,213	235	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_47.raw	Yeast_47.mzML	1	9,689	4,327	1,204	237	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_48.raw	Yeast_48.mzML	1	9,742	4,156	1,221	239	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_49.raw	Yeast_49.mzML	1	9,855	4,067	1,167	230	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_5.raw	Yeast_5.mzML	1	9,921	4,440	2,045	409	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_50.raw	Yeast_50.mzML	1	7,154	4,090	1,052	245	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_51.raw	Yeast_51.mzML	1	8,423	3,977	1,161	259	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_52.raw	Yeast_52.mzML	1	8,232	3,930	1,139	249	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_53.raw	Yeast_53.mzML	1	9,055	3,981	1,194	254	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_54.raw	Yeast_54.mzML	1	8,554	3,933	1,164	253	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_55.raw	Yeast_55.mzML	1	9,836	3,839	1,156	247	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_56.raw	Yeast_56.mzML	1	9,995	3,789	1,138	234	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_57.raw	Yeast_57.mzML	1	9,979	3,750	1,130	239	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_58.raw	Yeast_58.mzML	1	6,909	3,850	1,107	239	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_59.raw	Yeast_59.mzML	1	7,575	3,954	1,131	247	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_6.raw	Yeast_6.mzML	1	9,896	4,443	2,019	415	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_60.raw	Yeast_60.mzML	1	7,801	3,952	1,111	243	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_61.raw	Yeast_61.mzML	1	8,138	3,838	1,144	254	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_62.raw	Yeast_62.mzML	1	8,942	3,877	1,174	257	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_7.raw	Yeast_7.mzML	1	9,892	4,487	2,016	405	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_8.raw	Yeast_8.mzML	1	9,885	4,422	1,951	393	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
PXD046651	Yeast_9.raw	Yeast_9.mzML	1	9,792	4,428	1,954	395	Yeast	Q Exactive HF	HCD	Yeast S288c	CZE	null	No
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null
null	null	Diluted_Yeast_1.mzML	null	null	null	null	null	null	null	null	null	null	null	null

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 Yeast.

Metadata Table toprepo_yeast_meta_table_v1.2.0.tsv Contains experiment-level metadata including:

dataset identifiers
species information
instrument metadata
dissociation methods
counts of spectra, proteins, and proteoforms

Spectrum Table toprepo_yeast_spectrum_table_ms2_v1.2.0.tsv Contains 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

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