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E-coli

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

This happened while the csv dataset builder was generating data using

hf://datasets/TopRepo/E-coli/toprepo_e_coli_spectrum_table_ms2_v1.2.0.tsv (at revision 63dc6f526e696f448dd8536525b5fb5b7f511a14), ['hf://datasets/TopRepo/E-coli@63dc6f526e696f448dd8536525b5fb5b7f511a14/toprepo_e_coli_meta_table_v1.2.0.tsv', 'hf://datasets/TopRepo/E-coli@63dc6f526e696f448dd8536525b5fb5b7f511a14/toprepo_e_coli_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: string
              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, "' + 10668
              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('string'), '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 1343, in compute_config_parquet_and_info_response
                  parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
                                                                        ^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 907, in stream_convert_to_parquet
                  builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
                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_number_of_matched_theoretical_fragment_masses', 'MSALIGN_ms2_id', 'MZML_ms1_scan_window_lower_limit', 'TOPPIC_first_residue_position', 'TOPPIC_proteoform_mass', 'TOPPIC_number_of_matched_experimental_fragment_ions', 'TOPPIC_database_sequence', 'TOPPIC_spectrum-level_q-value', 'MZML_collision_energy', 'MZML_ms1_total_ion_current', 'MSALIGN_precursor_intensity', 'MZML_ms1_ion_injection_time', 'MZML_ms2_scan_window_lower_limit', 'MZML_instrument', 'TOPPIC_miscore', 'MSALIGN_number_of_fragment_ions', 'MZML_ms1_lowest_observed_mz', 'TOPPIC_proteoform', 'TOPPIC_number_of_unexpected_modifications', 'MZML_ms1_retention_time', 'MSALIGN_precursor_monoisotopic_mass', 'MZML_selected_ion_charge', 'TOPPIC_protein_accession', 'MSALIGN_file_name', 'MZML_ms2_ion_injection_time', 'TOPPIC_prsm_id', 'MZML_ms1_highest_observed_mz', 'MZML_ms2_retention_time', 'TOPPIC_fixed_modifications', 'SUBDATASET_id', 'TOPPIC_proteoform-level_q-value', 'TOPPIC_protein_description', 'MSALIGN_feature_intensity', 'MZML_ms2_scan', 'MSALIGN_feature_id', 'MSALIGN_feature_score', 'TOPPIC_proteoform_id', 'MZML_ms1_scan_window_upper_limit', 'TOPPIC_number_of_variable_modifications', 'TOPPIC_proteoform_intensity', 'MZML_isolation_window_lower_offset', 'TOPPIC_number_of_protein_hits', 'TOPPIC_e-value', 'TOPPIC_last_residue_position', 'MZML_activation', 'TOPPIC_previous_residue', 'MSALIGN_feature_apex_time', 'MZML_ms2_mass_resolving_power', 'MZML_isolation_window_upper_offset', 'MZML_selected_ion_mz', 'TOPPIC_next_residue', 'MZML_ms1_mass_resolving_power', 'DATASET_id', 'MSALIGN_precursor_charge', 'TOPPIC_protein_n-terminal_form', 'TOPPIC_variable_modifications', 'TOPPIC_special_amino_acids', 'MZML_ms2_lowest_observed_mz', 'TOPPIC_unexpected_modifications', 'MZML_ms1_scan', 'PROJECT_id', 'MZML_ms2_highest_observed_mz', 'MSALIGN_ms1_id', 'MZML_ms2_scan_window_upper_limit', 'MZML_ms2_total_ion_current', 'MZML_selected_ion_peak_intensity', 'TOPPIC_adjusted_precursor_mass', 'MZML_isolation_window_target_mz'}) and 14 missing columns ({'#PrSM_ids', 'Instrument', 'Raw_file_name', 'Dissociation', '#MS/MS_spectra', 'Sample', 'Cysteine_protection', '#Protein_ids', 'Species', '#Msalign_files', 'Dataset_id', '#Proteoform_ids', 'Separation', 'FAIMS'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/TopRepo/E-coli/toprepo_e_coli_spectrum_table_ms2_v1.2.0.tsv (at revision 63dc6f526e696f448dd8536525b5fb5b7f511a14), ['hf://datasets/TopRepo/E-coli@63dc6f526e696f448dd8536525b5fb5b7f511a14/toprepo_e_coli_meta_table_v1.2.0.tsv', 'hf://datasets/TopRepo/E-coli@63dc6f526e696f448dd8536525b5fb5b7f511a14/toprepo_e_coli_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
string
FAIMS
string
PXD017265
1M_05AA_ecoli_400nL_01.raw
1M_05AA_ecoli_400nL_01.mzML
1
5,356
2,471
808
208
E. coli
Q Exactive HF
HCD
E. coli K-12 MG1655
CZE
Carbamidomethylation
No
PXD017265
1M_05AA_ecoli_400nL_02.raw
1M_05AA_ecoli_400nL_02.mzML
1
6,173
3,233
830
215
E. coli
Q Exactive HF
HCD
E. coli K-12 MG1655
CZE
Carbamidomethylation
No
PXD017265
1M_05AA_ecoli_400nL_03.raw
1M_05AA_ecoli_400nL_03.mzML
1
6,446
3,443
843
210
E. coli
Q Exactive HF
HCD
E. coli K-12 MG1655
CZE
Carbamidomethylation
No
PXD017265
1M_20AA_ecoli_400nL_01.raw
1M_20AA_ecoli_400nL_01.mzML
1
5,903
3,062
1,355
290
E. coli
Q Exactive HF
HCD
E. coli K-12 MG1655
CZE
Carbamidomethylation
No
PXD017265
1M_20AA_ecoli_400nL_02.raw
1M_20AA_ecoli_400nL_02.mzML
1
5,162
3,190
1,410
316
E. coli
Q Exactive HF
HCD
E. coli K-12 MG1655
CZE
Carbamidomethylation
No
PXD017265
1M_20AA_ecoli_400nL_03.raw
1M_20AA_ecoli_400nL_03.mzML
1
5,491
3,403
1,401
319
E. coli
Q Exactive HF
HCD
E. coli K-12 MG1655
CZE
Carbamidomethylation
No
PXD017265
1M_20AA15DMA10IPA_ecoli_400nL_01.raw
1M_20AA15DMA10IPA_ecoli_400nL_01.mzML
1
6,740
3,797
1,059
254
E. coli
Q Exactive HF
HCD
E. coli K-12 MG1655
CZE
Carbamidomethylation
No
PXD017265
1M_20AA15DMA10IPA_ecoli_400nL_02.raw
1M_20AA15DMA10IPA_ecoli_400nL_02.mzML
1
7,128
3,778
1,030
256
E. coli
Q Exactive HF
HCD
E. coli K-12 MG1655
CZE
Carbamidomethylation
No
PXD017265
1M_20AA15DMA10IPA_ecoli_400nL_04.raw
1M_20AA15DMA10IPA_ecoli_400nL_04.mzML
1
5,034
2,759
990
214
E. coli
Q Exactive HF
HCD
E. coli K-12 MG1655
CZE
Carbamidomethylation
No
MSV000085258
DSB_201900906_M9-J-20190404_PEPPI_F01_01.raw
DSB_201900906_M9-J-20190404_PEPPI_F01_01.mzML
1
1,490
511
258
100
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900906_M9-J-20190404_PEPPI_F01_02.raw
DSB_201900906_M9-J-20190404_PEPPI_F01_02.mzML
1
1,494
536
253
98
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900906_M9-J-20190404_PEPPI_F02_01.raw
DSB_201900906_M9-J-20190404_PEPPI_F02_01.mzML
1
1,576
674
293
106
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900906_M9-J-20190404_PEPPI_F02_02.raw
DSB_201900906_M9-J-20190404_PEPPI_F02_02.mzML
1
1,563
714
315
117
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900906_M9-J-20190404_PEPPI_F03_01.raw
DSB_201900906_M9-J-20190404_PEPPI_F03_01.mzML
1
1,578
719
296
117
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900906_M9-J-20190404_PEPPI_F03_02.raw
DSB_201900906_M9-J-20190404_PEPPI_F03_02.mzML
1
1,600
694
301
114
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900907_M9-J-20190404_PEPPI_F04_01.raw
DSB_201900907_M9-J-20190404_PEPPI_F04_01.mzML
1
1,625
367
136
69
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900907_M9-J-20190404_PEPPI_F04_02.raw
DSB_201900907_M9-J-20190404_PEPPI_F04_02.mzML
1
1,604
369
145
66
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900907_M9-J-20190404_PEPPI_F05_01.raw
DSB_201900907_M9-J-20190404_PEPPI_F05_01.mzML
1
1,650
405
219
93
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900907_M9-J-20190404_PEPPI_F05_02.raw
DSB_201900907_M9-J-20190404_PEPPI_F05_02.mzML
1
1,624
375
165
74
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900907_M9-J-20190404_PEPPI_F06_01.raw
DSB_201900907_M9-J-20190404_PEPPI_F06_01.mzML
1
1,523
60
34
22
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900907_M9-J-20190404_PEPPI_F06_02.raw
DSB_201900907_M9-J-20190404_PEPPI_F06_02.mzML
1
1,541
78
48
30
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900908_M9-J-20190404_PEPPI_F07_01.raw
DSB_201900908_M9-J-20190404_PEPPI_F07_01.mzML
1
1,692
102
67
36
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900908_M9-J-20190404_PEPPI_F08_01.raw
DSB_201900908_M9-J-20190404_PEPPI_F08_01.mzML
1
1,647
33
22
16
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900915_M9-J-20190404_PEPPI_F09_01.raw
DSB_201900915_M9-J-20190404_PEPPI_F09_01.mzML
1
1,121
69
57
22
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900915_M9-J-20190404_PEPPI_F09_02.raw
DSB_201900915_M9-J-20190404_PEPPI_F09_02.mzML
1
1,107
68
59
25
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_201900917_M9-J-20190404_PEPPI_F08_02.raw
DSB_201900917_M9-J-20190404_PEPPI_F08_02.mzML
1
2,397
58
49
23
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190914_MG1655_M9-OL-20190515_GF_01_01.raw
DSB_20190914_MG1655_M9-OL-20190515_GF_01_01.mzML
1
2,475
599
287
134
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190914_MG1655_M9-OL-20190515_GF_01_02.raw
DSB_20190914_MG1655_M9-OL-20190515_GF_01_02.mzML
1
2,485
579
277
131
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190914_MG1655_M9-OL-20190515_GF_02_01.raw
DSB_20190914_MG1655_M9-OL-20190515_GF_02_01.mzML
1
2,481
4
3
3
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190914_MG1655_M9-OL-20190515_GF_02_02.raw
DSB_20190914_MG1655_M9-OL-20190515_GF_02_02.mzML
1
2,472
4
2
1
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190914_MG1655_M9-OL-20190515_GF_03_01.raw
DSB_20190914_MG1655_M9-OL-20190515_GF_03_01.mzML
1
2,482
168
84
51
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190914_MG1655_M9-OL-20190515_GF_03_02_190915191709.raw
DSB_20190914_MG1655_M9-OL-20190515_GF_03_02_190915191709.mzML
1
1,240
124
58
38
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190917_MG1655_M9-OL-20190515_GF_04_01.raw
DSB_20190917_MG1655_M9-OL-20190515_GF_04_01.mzML
1
2,485
589
252
133
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190917_MG1655_M9-OL-20190515_GF_04_02.raw
DSB_20190917_MG1655_M9-OL-20190515_GF_04_02.mzML
1
2,494
621
267
133
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190917_MG1655_M9-OL-20190515_GF_05_01.raw
DSB_20190917_MG1655_M9-OL-20190515_GF_05_01.mzML
1
2,494
902
458
201
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190917_MG1655_M9-OL-20190515_GF_05_02.raw
DSB_20190917_MG1655_M9-OL-20190515_GF_05_02.mzML
1
2,477
819
425
192
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190917_MG1655_M9-OL-20190515_GF_06_01.raw
DSB_20190917_MG1655_M9-OL-20190515_GF_06_01.mzML
1
2,416
266
161
80
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190917_MG1655_M9-OL-20190515_GF_06_02.raw
DSB_20190917_MG1655_M9-OL-20190515_GF_06_02.mzML
1
2,379
180
115
56
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190918_MG1655_M9-OL-20190515_GF_07_01.raw
DSB_20190918_MG1655_M9-OL-20190515_GF_07_01.mzML
1
2,328
53
39
23
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190918_MG1655_M9-OL-20190515_GF_07_02.raw
DSB_20190918_MG1655_M9-OL-20190515_GF_07_02.mzML
1
2,325
48
35
19
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190918_MG1655_M9-OL-20190515_GF_08_01.raw
DSB_20190918_MG1655_M9-OL-20190515_GF_08_01.mzML
1
2,567
116
88
35
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190918_MG1655_M9-OL-20190515_GF_08_02.raw
DSB_20190918_MG1655_M9-OL-20190515_GF_08_02.mzML
1
2,557
65
44
26
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190921_MG1655_M9-OL-20190515_GF_09_01.raw
DSB_20190921_MG1655_M9-OL-20190515_GF_09_01.mzML
1
2,519
111
69
33
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20190921_MG1655_M9-OL-20190515_GF_09_02.raw
DSB_20190921_MG1655_M9-OL-20190515_GF_09_02.mzML
1
2,509
53
44
21
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200124_M9-J-20190404_PEPPI01_01.raw
DSB_20200124_M9-J-20190404_PEPPI01_01.mzML
1
1,431
356
192
90
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200124_M9-J-20190404_PEPPI01_02.raw
DSB_20200124_M9-J-20190404_PEPPI01_02.mzML
1
1,411
337
184
86
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200124_M9-J-20190404_PEPPI02_01.raw
DSB_20200124_M9-J-20190404_PEPPI02_01.mzML
1
1,533
700
338
120
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200124_M9-J-20190404_PEPPI02_02.raw
DSB_20200124_M9-J-20190404_PEPPI02_02.mzML
1
1,496
670
313
110
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200124_M9-J-20190404_PEPPI03_01.raw
DSB_20200124_M9-J-20190404_PEPPI03_01.mzML
1
1,533
741
329
124
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200124_M9-J-20190404_PEPPI03_02.raw
DSB_20200124_M9-J-20190404_PEPPI03_02.mzML
1
1,497
722
339
128
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200124_M9-J-20190404_PEPPI04_01.raw
DSB_20200124_M9-J-20190404_PEPPI04_01.mzML
1
1,488
530
238
87
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200124_M9-J-20190404_PEPPI04_02.raw
DSB_20200124_M9-J-20190404_PEPPI04_02.mzML
1
1,494
511
220
87
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200125_M9-J-20190404_PEPPI05_01.raw
DSB_20200125_M9-J-20190404_PEPPI05_01.mzML
1
1,654
341
156
48
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200125_M9-J-20190404_PEPPI05_02.raw
DSB_20200125_M9-J-20190404_PEPPI05_02.mzML
1
1,642
345
155
46
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200125_M9-J-20190404_PEPPI06_01.raw
DSB_20200125_M9-J-20190404_PEPPI06_01.mzML
1
1,532
122
67
29
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200125_M9-J-20190404_PEPPI06_02.raw
DSB_20200125_M9-J-20190404_PEPPI06_02.mzML
1
1,532
116
61
29
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200125_M9-J-20190404_PEPPI07_01.raw
DSB_20200125_M9-J-20190404_PEPPI07_01.mzML
1
1,547
105
68
35
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200125_M9-J-20190404_PEPPI07_02.raw
DSB_20200125_M9-J-20190404_PEPPI07_02.mzML
1
1,502
86
59
28
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200125_M9-J-20190404_PEPPI08_01.raw
DSB_20200125_M9-J-20190404_PEPPI08_01.mzML
1
1,477
81
61
30
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200125_M9-J-20190404_PEPPI08_02.raw
DSB_20200125_M9-J-20190404_PEPPI08_02.mzML
1
1,465
74
55
23
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200125_M9-J-20190404_PEPPI09_01.raw
DSB_20200125_M9-J-20190404_PEPPI09_01.mzML
1
1,271
20
11
9
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200125_M9-J-20190404_PEPPI09_02.raw
DSB_20200125_M9-J-20190404_PEPPI09_02.mzML
1
1,241
15
6
5
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000085258
DSB_20200315_M9-J-20190404_PEPPI_F07_02.raw
DSB_20200315_M9-J-20190404_PEPPI_F07_02.mzML
1
2,732
34
30
12
E. coli
FT-ICR (LTQ FT Ultra)
CID
E. coli K-12 MG1655
RPLC
Carbamidomethylation
No
MSV000091610
Ecoli_FAIMS_AC_bio1_tech1.raw
Ecoli_FAIMS_AC_bio1_tech1.mzML
3
11,265
6,897
1,567
398
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio1_tech2.raw
Ecoli_FAIMS_AC_bio1_tech2.mzML
3
11,241
6,639
1,541
383
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio1_tech3.raw
Ecoli_FAIMS_AC_bio1_tech3.mzML
3
11,071
6,558
1,555
381
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio2_tech1.raw
Ecoli_FAIMS_AC_bio2_tech1.mzML
3
11,705
6,511
1,560
372
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio2_tech2.raw
Ecoli_FAIMS_AC_bio2_tech2.mzML
3
11,166
6,130
1,453
354
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio2_tech3.raw
Ecoli_FAIMS_AC_bio2_tech3.mzML
3
10,948
6,192
1,368
344
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio3_tech1.raw
Ecoli_FAIMS_AC_bio3_tech1.mzML
3
11,719
6,926
1,620
377
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio3_tech2.raw
Ecoli_FAIMS_AC_bio3_tech2.mzML
3
10,885
6,544
1,490
373
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio3_tech3.raw
Ecoli_FAIMS_AC_bio3_tech3.mzML
3
10,748
6,467
1,516
357
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio4_tech1.raw
Ecoli_FAIMS_AC_bio4_tech1.mzML
3
11,589
6,527
1,565
363
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio4_tech2.raw
Ecoli_FAIMS_AC_bio4_tech2.mzML
3
11,105
6,316
1,465
348
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_AC_bio4_tech3.raw
Ecoli_FAIMS_AC_bio4_tech3.mzML
3
10,959
6,295
1,491
343
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio1_tech1b.raw
Ecoli_FAIMS_LB_bio1_tech1b.mzML
3
11,818
6,661
1,403
387
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio1_tech2.raw
Ecoli_FAIMS_LB_bio1_tech2.mzML
3
11,866
6,552
1,276
373
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio1_tech3.raw
Ecoli_FAIMS_LB_bio1_tech3.mzML
3
11,554
6,515
1,215
361
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio2_tech1.raw
Ecoli_FAIMS_LB_bio2_tech1.mzML
3
12,352
6,913
1,398
395
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio2_tech2.raw
Ecoli_FAIMS_LB_bio2_tech2.mzML
3
11,763
6,672
1,309
391
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio2_tech3.raw
Ecoli_FAIMS_LB_bio2_tech3.mzML
3
11,547
6,742
1,236
372
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio3_tech1.raw
Ecoli_FAIMS_LB_bio3_tech1.mzML
3
12,150
7,585
1,546
426
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio3_tech2.raw
Ecoli_FAIMS_LB_bio3_tech2.mzML
3
11,769
7,008
1,326
393
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio3_tech3.raw
Ecoli_FAIMS_LB_bio3_tech3.mzML
3
11,514
7,006
1,253
361
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio4_tech1.raw
Ecoli_FAIMS_LB_bio4_tech1.mzML
3
12,285
7,505
1,517
414
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio4_tech2.raw
Ecoli_FAIMS_LB_bio4_tech2.mzML
3
11,733
7,092
1,381
391
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_FAIMS_LB_bio4_tech3.raw
Ecoli_FAIMS_LB_bio4_tech3.mzML
3
11,216
6,770
1,287
356
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
Yes
MSV000091610
Ecoli_noFAIMS_AC_bio1_tech1.raw
Ecoli_noFAIMS_AC_bio1_tech1.mzML
1
21,559
12,177
566
211
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio1_tech2.raw
Ecoli_noFAIMS_AC_bio1_tech2.mzML
1
21,725
12,024
553
202
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio1_tech3.raw
Ecoli_noFAIMS_AC_bio1_tech3.mzML
1
22,212
12,270
557
198
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio2_tech1.raw
Ecoli_noFAIMS_AC_bio2_tech1.mzML
1
22,017
12,745
636
230
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio2_tech2.raw
Ecoli_noFAIMS_AC_bio2_tech2.mzML
1
22,165
12,857
613
218
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio2_tech3.raw
Ecoli_noFAIMS_AC_bio2_tech3.mzML
1
22,256
12,904
609
216
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio3_tech1.raw
Ecoli_noFAIMS_AC_bio3_tech1.mzML
1
21,262
11,896
569
203
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio3_tech2.raw
Ecoli_noFAIMS_AC_bio3_tech2.mzML
1
21,685
12,174
580
202
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio3_tech3.raw
Ecoli_noFAIMS_AC_bio3_tech3.mzML
1
21,701
12,036
582
199
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio4_tech1.raw
Ecoli_noFAIMS_AC_bio4_tech1.mzML
1
20,890
10,992
575
198
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio4_tech2.raw
Ecoli_noFAIMS_AC_bio4_tech2.mzML
1
21,516
11,343
557
199
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_AC_bio4_tech3.raw
Ecoli_noFAIMS_AC_bio4_tech3.mzML
1
21,823
11,143
549
185
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
MSV000091610
Ecoli_noFAIMS_LB_bio1_tech1.raw
Ecoli_noFAIMS_LB_bio1_tech1.mzML
1
21,988
12,161
368
185
E. coli
Orbitrap Eclipse
HCD
E. coli K-12 25922
RPLC
null
No
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 Escherichia coli.

  1. Metadata Table : toprepo_e_coli_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
  1. Spectrum Table toprepo_e_coli_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
  1. Annotated .msalign file

Sources

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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