-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.massSpectrometry_level1_metadata_r4`
(
  HTAN_Data_File_ID STRING OPTIONS(description="Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)"),
  Id STRING OPTIONS(description="Unique identifier of entity e.g. a96059eb-81af-4b24-ae50-9242c0d8f819"),
  Analyte_Type STRING OPTIONS(description="The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen"),
  Software_and_Version STRING OPTIONS(description="Name of software used to generate expression values. String"),
  LC_Flow_Rate STRING OPTIONS(description="LC flow rate in nL/min."),
  Protocol_Link STRING OPTIONS(description="Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated."),
  Mass_Range_High_Value STRING OPTIONS(description="The high value of the scanned mass range for MS1 in m/z."),
  entityId STRING OPTIONS(description="Synapse ID of entity"),
  LC_Temp_Value STRING OPTIONS(description="LC temperature in C."),
  LC_Mobile_Phase_A STRING OPTIONS(description="Composition of mobile phase A"),
  MS_Scan_Mode STRING OPTIONS(description="Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)"),
  Data_Collection_Mode STRING OPTIONS(description="Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition."),
  MS_Source STRING OPTIONS(description="The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)"),
  Component STRING OPTIONS(description="Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows."),
  MS_Instrument_Metadata_File STRING OPTIONS(description="Additional file containing instrument metadata details. Use either synapse_path or entity_Id"),
  MS_Instrument_Vendor_and_Model STRING OPTIONS(description="An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass."),
  LC_Column_Vendor_and_Model STRING OPTIONS(description="The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'"),
  Polarity STRING OPTIONS(description="The polarity of the mass analysis (positive or negative ion modes)"),
  HTAN_Parent_Biospecimen_ID STRING OPTIONS(description="HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated"),
  LC_ID_Value STRING OPTIONS(description="LC column inner diameter in microns."),
  MS_Labeling STRING OPTIONS(description="Indicates whether samples were labeled prior to MS analysis (e.g., TMT)"),
  LC_Length_Value STRING OPTIONS(description="LC column length in cm."),
  LC_Gradient STRING OPTIONS(description="The program dictates the mobile phase solvent composition over the course of the chromatographic run."),
  LC_Mobile_Phase_B STRING OPTIONS(description="Composition of mobile phase B"),
  MS_based_Assay_Type STRING OPTIONS(description="Analytes are the target molecules being measured with the assay."),
  File_Format STRING OPTIONS(description="Format of a file (e.g. txt, csv, fastq, bam, etc.)"),
  Filename STRING OPTIONS(description="Name of a file"),
  LC_Resin STRING OPTIONS(description="Details of the resin used for lc, including vendor, particle size, pore size"),
  MS_based_Targeted STRING OPTIONS(description="Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids."),
  MS_Batch_ID STRING OPTIONS(description="Batch ID indicating a set of samples that were run together."),
  LC_Instrument_Vendor_and_Model STRING OPTIONS(description="The manufacturer of the instrument used for LC."),
  Mass_Range_Low_Value STRING OPTIONS(description="The low value of the scanned mass range for MS1 in m/z."),
  HTAN_Center STRING OPTIONS(description="Name of HTAN Center e.g. HTAN HTAPP"),
  Manifest_Id STRING OPTIONS(description="Synapse ID of manifest containing file annotation"),
  Manifest_Version INT64 OPTIONS(description="Latest version of metadata manifest"),
  File_Size INT64 OPTIONS(description="Size of file (bucket object) in bytes"),
  md5 STRING OPTIONS(description="md5 hash of file"),
  Data_Release STRING OPTIONS(description="Inclusion in HTAN Data Release e.g. Release 1.0"),
  CDS_Release STRING OPTIONS(description="CDS transfer package in which file was included e.g. v22.6.1.seq")
)
OPTIONS(
  friendly_name="HTAN MASS SPECTROMETRY LEVEL 1 METADATA R4 VERSIONED",
  description="This table contains the file metadata for the first level of Mass Spectrometry. Data was extracted from HTAN Synapse projects in October 2023. More details: see https://humantumoratlas.org/standards",
  labels=[("access", "open"), ("data_type", "file_metadata"), ("program", "htan"), ("source", "htan"), ("category", "metadata"), ("status", "current")]
);

INSERT INTO `isb-cgc-bq.HTAN_versioned.massSpectrometry_level1_metadata_r4` (HTAN_Data_File_ID, Id, Analyte_Type, Software_and_Version, LC_Flow_Rate, Protocol_Link, Mass_Range_High_Value, entityId, LC_Temp_Value, LC_Mobile_Phase_A, MS_Scan_Mode, Data_Collection_Mode, MS_Source, Component, MS_Instrument_Metadata_File, MS_Instrument_Vendor_and_Model, LC_Column_Vendor_and_Model, Polarity, HTAN_Parent_Biospecimen_ID, LC_ID_Value, MS_Labeling, LC_Length_Value, LC_Gradient, LC_Mobile_Phase_B, MS_based_Assay_Type, File_Format, Filename, LC_Resin, MS_based_Targeted, MS_Batch_ID, LC_Instrument_Vendor_and_Model, Mass_Range_Low_Value, HTAN_Center, Manifest_Id, Manifest_Version, File_Size, md5, Data_Release, CDS_Release) VALUES ('HTA10_0000_06001', '06458999-77f9-4500-acd5-e62bf41ace45', 'Tissue Block Analyte', 'Proteome Discoverer2.5', '600nl/min', '10.17504/protocols.io.bf6bjran', '1500', 'syn23875727', '45C', 'Water with 0.1% Formic acid', 'MS3', 'DDA', 'nESI', 'MassSpectrometryLevel1', '/proteomics_level_1/sample-tmt-tags.zip', NULL, 'self packed', 'Positive', 'HTA10_01_004,HTA10_01_005,HTA10_01_021,HTA10_01_102,HTA10_01_107,HTA10_01_122,HTA10_01_124,HTA10_01_210,HTA10_01_214,HTA10_01_219,HTA10_01_222,HTA10_02_010,HTA10_02_016,HTA10_02_019,HTA10_02_021,HTA10_02_023,HTA10_02_024,HTA10_02_025,HTA10_02_103,HTA10_02_107,HTA10_02_116,HTA10_02_121,HTA10_02_122,HTA10_02_123,HTA10_02_201,HTA10_02_202,HTA10_02_203,HTA10_02_204,HTA10_02_207,HTA10_02_209,HTA10_02_211,HTA10_02_212,HTA10_02_213,HTA10_03_001,HTA10_03_052,HTA10_03_055,HTA10_03_114,HTA10_03_201,HTA10_04_002,HTA10_04_008,HTA10_04_010,HTA10_04_102,HTA10_04_109,HTA10_04_206,HTA10_05_002,HTA10_05_004,HTA10_05_007,HTA10_05_008,HTA10_05_025,HTA10_05_027,HTA10_05_037,HTA10_05_038,HTA10_05_039,HTA10_05_040,HTA10_05_046,HTA10_05_053,HTA10_05_061,HTA10_05_063,HTA10_05_065,HTA10_05_072,HTA10_05_073,HTA10_05_074,HTA10_05_076,HTA10_05_105,HTA10_05_088,HTA10_05_092,HTA10_05_095,HTA10_05_098,HTA10_05_103,HTA10_05_104,HTA10_06_105,HTA10_06_002,HTA10_06_004,HTA10_06_005,HTA10_06_024,HTA10_06_025,HTA10_06_032,HTA10_06_043,HTA10_06_044,HTA10_06_045,HTA10_06_049,HTA10_06_051,HTA10_06_055,HTA10_06_061,HTA10_06_062,HTA10_06_065,HTA10_06_107,HTA10_06_110,HTA10_07_001,HTA10_07_006,HTA10_07_101,HTA10_07_201,HTA10_04_001', '100um', 'TMT', '25cm', '0-5 min: 5% B; 5-180min: 5-25% B; 180-188min: 25-40% B; 188-195min: 40-95% B; 195-200min: 5% B', 'Acetonitrile with 0.1% Formic acid', 'bottom up', 'raw', 'proteomics/raw-data/replicate01/Lumos1_FAP2_C1S1_091120_Fr01.raw', 'Sepex GP-C18 1.8um, 120A', 'Untargeted', '1', 'Thermo Fisher Scientific', '400', 'HTAN Stanford', 'syn51703772', 4, 747842628, 'b215bc47bb82a557d7c3ae536f2ead88', 'Release 1.0', NULL), ('HTA10_0000_06002', '428b53be-d635-402f-8f3b-0010d4e1dab4', 'Tissue Block Analyte', 'Proteome Discoverer2.5', '600nl/min', '10.17504/protocols.io.bf6bjran', '1500', 'syn23875785', '45C', 'Water with 0.1% Formic acid', 'MS3', 'DDA', 'nESI', 'MassSpectrometryLevel1', '/proteomics_level_1/sample-tmt-tags.zip', NULL, 'self packed', 'Positive', 'HTA10_01_004,HTA10_01_005,HTA10_01_021,HTA10_01_102,HTA10_01_107,HTA10_01_122,HTA10_01_124,HTA10_01_210,HTA10_01_214,HTA10_01_219,HTA10_01_222,HTA10_02_010,HTA10_02_016,HTA10_02_019,HTA10_02_021,HTA10_02_023,HTA10_02_024,HTA10_02_025,HTA10_02_103,HTA10_02_107,HTA10_02_116,HTA10_02_121,HTA10_02_122,HTA10_02_123,HTA10_02_201,HTA10_02_202,HTA10_02_203,HTA10_02_204,HTA10_02_207,HTA10_02_209,HTA10_02_211,HTA10_02_212,HTA10_02_213,HTA10_03_001,HTA10_03_052,HTA10_03_055,HTA10_03_114,HTA10_03_201,HTA10_04_002,HTA10_04_008,HTA10_04_010,HTA10_04_102,HTA10_04_109,HTA10_04_206,HTA10_05_002,HTA10_05_004,HTA10_05_007,HTA10_05_008,HTA10_05_025,HTA10_05_027,HTA10_05_037,HTA10_05_038,HTA10_05_039,HTA10_05_040,HTA10_05_046,HTA10_05_053,HTA10_05_061,HTA10_05_063,HTA10_05_065,HTA10_05_072,HTA10_05_073,HTA10_05_074,HTA10_05_076,HTA10_05_105,HTA10_05_088,HTA10_05_092,HTA10_05_095,HTA10_05_098,HTA10_05_103,HTA10_05_104,HTA10_06_105,HTA10_06_002,HTA10_06_004,HTA10_06_005,HTA10_06_024,HTA10_06_025,HTA10_06_032,HTA10_06_043,HTA10_06_044,HTA10_06_045,HTA10_06_049,HTA10_06_051,HTA10_06_055,HTA10_06_061,HTA10_06_062,HTA10_06_065,HTA10_06_107,HTA10_06_110,HTA10_07_001,HTA10_07_006,HTA10_07_101,HTA10_07_201,HTA10_04_001', '100um', 'TMT', '25cm', '0-5 min: 5% B; 5-180min: 5-25% B; 180-188min: 25-40% B; 188-195min: 40-95% B; 195-200min: 5% B', 'Acetonitrile with 0.1% Formic acid', 'bottom up', 'raw', 'proteomics/raw-data/replicate01/Lumos1_FAP2_C1S1_091120_Fr02.raw', 'Sepex GP-C18 1.8um, 120A', 'Untargeted', '1', 'Thermo Fisher Scientific', '400', 'HTAN Stanford', 'syn51703772', 4, 584764714, 'cd02e76c9c37ac6f8e961694c18d093c', 'Release 1.0', NULL), ('HTA10_0000_06003', '67255c09-ca3a-40fb-a6a8-4728b2c614d6', 'Tissue Block Analyte', 'Proteome Discoverer2.5', '600nl/min', '10.17504/protocols.io.bf6bjran', '1500', 'syn23875860', '45C', 'Water with 0.1% Formic acid', 'MS3', 'DDA', 'nESI', 'MassSpectrometryLevel1', '/proteomics_level_1/sample-tmt-tags.zip', NULL, 'self packed', 'Positive', 'HTA10_01_004,HTA10_01_005,HTA10_01_021,HTA10_01_102,HTA10_01_107,HTA10_01_122,HTA10_01_124,HTA10_01_210,HTA10_01_214,HTA10_01_219,HTA10_01_222,HTA10_02_010,HTA10_02_016,HTA10_02_019,HTA10_02_021,HTA10_02_023,HTA10_02_024,HTA10_02_025,HTA10_02_103,HTA10_02_107,HTA10_02_116,HTA10_02_121,HTA10_02_122,HTA10_02_123,HTA10_02_201,HTA10_02_202,HTA10_02_203,HTA10_02_204,HTA10_02_207,HTA10_02_209,HTA10_02_211,HTA10_02_212,HTA10_02_213,HTA10_03_001,HTA10_03_052,HTA10_03_055,HTA10_03_114,HTA10_03_201,HTA10_04_002,HTA10_04_008,HTA10_04_010,HTA10_04_102,HTA10_04_109,HTA10_04_206,HTA10_05_002,HTA10_05_004,HTA10_05_007,HTA10_05_008,HTA10_05_025,HTA10_05_027,HTA10_05_037,HTA10_05_038,HTA10_05_039,HTA10_05_040,HTA10_05_046,HTA10_05_053,HTA10_05_061,HTA10_05_063,HTA10_05_065,HTA10_05_072,HTA10_05_073,HTA10_05_074,HTA10_05_076,HTA10_05_105,HTA10_05_088,HTA10_05_092,HTA10_05_095,HTA10_05_098,HTA10_05_103,HTA10_05_104,HTA10_06_105,HTA10_06_002,HTA10_06_004,HTA10_06_005,HTA10_06_024,HTA10_06_025,HTA10_06_032,HTA10_06_043,HTA10_06_044,HTA10_06_045,HTA10_06_049,HTA10_06_051,HTA10_06_055,HTA10_06_061,HTA10_06_062,HTA10_06_065,HTA10_06_107,HTA10_06_110,HTA10_07_001,HTA10_07_006,HTA10_07_101,HTA10_07_201,HTA10_04_001', '100um', 'TMT', '25cm', '0-5 min: 5% B; 5-180min: 5-25% B; 180-188min: 25-40% B; 188-195min: 40-95% B; 195-200min: 5% B', 'Acetonitrile with 0.1% Formic acid', 'bottom up', 'raw', 'proteomics/raw-data/replicate01/Lumos1_FAP2_C1S1_091120_Fr03.raw', 'Sepex GP-C18 1.8um, 120A', 'Untargeted', '1', 'Thermo Fisher Scientific', '400', 'HTAN Stanford', 'syn51703772', 4, 1147991886, 'c0d4b476433ccde41d072a30aa0128ac', 'Release 1.0', NULL), ('HTA10_0000_06004', '7025cf9a-806b-40a2-8270-4db682174eb6', 'Tissue Block Analyte', 'Proteome Discoverer2.5', '600nl/min', '10.17504/protocols.io.bf6bjran', '1500', 'syn23874264', '45C', 'Water with 0.1% Formic acid', 'MS3', 'DDA', 'nESI', 'MassSpectrometryLevel1', '/proteomics_level_1/sample-tmt-tags.zip', NULL, 'self packed', 'Positive', 'HTA10_01_004,HTA10_01_005,HTA10_01_021,HTA10_01_102,HTA10_01_107,HTA10_01_122,HTA10_01_124,HTA10_01_210,HTA10_01_214,HTA10_01_219,HTA10_01_222,HTA10_02_010,HTA10_02_016,HTA10_02_019,HTA10_02_021,HTA10_02_023,HTA10_02_024,HTA10_02_025,HTA10_02_103,HTA10_02_107,HTA10_02_116,HTA10_02_121,HTA10_02_122,HTA10_02_123,HTA10_02_201,HTA10_02_202,HTA10_02_203,HTA10_02_204,HTA10_02_207,HTA10_02_209,HTA10_02_211,HTA10_02_212,HTA10_02_213,HTA10_03_001,HTA10_03_052,HTA10_03_055,HTA10_03_114,HTA10_03_201,HTA10_04_002,HTA10_04_008,HTA10_04_010,HTA10_04_102,HTA10_04_109,HTA10_04_206,HTA10_05_002,HTA10_05_004,HTA10_05_007,HTA10_05_008,HTA10_05_025,HTA10_05_027,HTA10_05_037,HTA10_05_038,HTA10_05_039,HTA10_05_040,HTA10_05_046,HTA10_05_053,HTA10_05_061,HTA10_05_063,HTA10_05_065,HTA10_05_072,HTA10_05_073,HTA10_05_074,HTA10_05_076,HTA10_05_105,HTA10_05_088,HTA10_05_092,HTA10_05_095,HTA10_05_098,HTA10_05_103,HTA10_05_104,HTA10_06_105,HTA10_06_002,HTA10_06_004,HTA10_06_005,HTA10_06_024,HTA10_06_025,HTA10_06_032,HTA10_06_043,HTA10_06_044,HTA10_06_045,HTA10_06_049,HTA10_06_051,HTA10_06_055,HTA10_06_061,HTA10_06_062,HTA10_06_065,HTA10_06_107,HTA10_06_110,HTA10_07_001,HTA10_07_006,HTA10_07_101,HTA10_07_201,HTA10_04_001', '100um', 'TMT', '25cm', '0-5 min: 5% B; 5-180min: 5-25% B; 180-188min: 25-40% B; 188-195min: 40-95% B; 195-200min: 5% B', 'Acetonitrile with 0.1% Formic acid', 'bottom up', 'raw', 'proteomics/raw-data/replicate01/Lumos1_FAP2_C1S1_091120_Fr04.raw', 'Sepex GP-C18 1.8um, 120A', 'Untargeted', '1', 'Thermo Fisher Scientific', '400', 'HTAN Stanford', 'syn51703772', 4, 1182904518, '2cae192444357ac9ca12fb350e94b9bb', 'Release 1.0', NULL), ('HTA10_0000_06005', 'dac4316a-70d5-4a39-a611-7107d12394d5', 'Tissue Block Analyte', 'Proteome Discoverer2.5', '600nl/min', '10.17504/protocols.io.bf6bjran', '1500', 'syn23875534', '45C', 'Water with 0.1% Formic acid', 'MS3', 'DDA', 'nESI', 'MassSpectrometryLevel1', '/proteomics_level_1/sample-tmt-tags.zip', NULL, 'self packed', 'Positive', 'HTA10_01_004,HTA10_01_005,HTA10_01_021,HTA10_01_102,HTA10_01_107,HTA10_01_122,HTA10_01_124,HTA10_01_210,HTA10_01_214,HTA10_01_219,HTA10_01_222,HTA10_02_010,HTA10_02_016,HTA10_02_019,HTA10_02_021,HTA10_02_023,HTA10_02_024,HTA10_02_025,HTA10_02_103,HTA10_02_107,HTA10_02_116,HTA10_02_121,HTA10_02_122,HTA10_02_123,HTA10_02_201,HTA10_02_202,HTA10_02_203,HTA10_02_204,HTA10_02_207,HTA10_02_209,HTA10_02_211,HTA10_02_212,HTA10_02_213,HTA10_03_001,HTA10_03_052,HTA10_03_055,HTA10_03_114,HTA10_03_201,HTA10_04_002,HTA10_04_008,HTA10_04_010,HTA10_04_102,HTA10_04_109,HTA10_04_206,HTA10_05_002,HTA10_05_004,HTA10_05_007,HTA10_05_008,HTA10_05_025,HTA10_05_027,HTA10_05_037,HTA10_05_038,HTA10_05_039,HTA10_05_040,HTA10_05_046,HTA10_05_053,HTA10_05_061,HTA10_05_063,HTA10_05_065,HTA10_05_072,HTA10_05_073,HTA10_05_074,HTA10_05_076,HTA10_05_105,HTA10_05_088,HTA10_05_092,HTA10_05_095,HTA10_05_098,HTA10_05_103,HTA10_05_104,HTA10_06_105,HTA10_06_002,HTA10_06_004,HTA10_06_005,HTA10_06_024,HTA10_06_025,HTA10_06_032,HTA10_06_043,HTA10_06_044,HTA10_06_045,HTA10_06_049,HTA10_06_051,HTA10_06_055,HTA10_06_061,HTA10_06_062,HTA10_06_065,HTA10_06_107,HTA10_06_110,HTA10_07_001,HTA10_07_006,HTA10_07_101,HTA10_07_201,HTA10_04_001', '100um', 'TMT', '25cm', '0-5 min: 5% B; 5-180min: 5-25% B; 180-188min: 25-40% B; 188-195min: 40-95% B; 195-200min: 5% B', 'Acetonitrile with 0.1% Formic acid', 'bottom up', 'raw', 'proteomics/raw-data/replicate01/Lumos1_FAP2_C1S1_091120_Fr05.raw', 'Sepex GP-C18 1.8um, 120A', 'Untargeted', '1', 'Thermo Fisher Scientific', '400', 'HTAN Stanford', 'syn51703772', 4, 1095557538, '578c1e3a146ef5f995bacbbde691950b', 'Release 1.0', NULL);