SPINS: A Laboratory Information Management System for Archiving. Intermediate and Final Results from NMR Protein Structure. Determinations.

Transcription

1 Supplementary Material for: SPINS: A Laboratory Information Management System for Archiving Intermediate and Final Results from NMR Protein Structure Determinations. Michael Baran a, Hunter N. B. Moseley a, James M. Aramini a, Marvin Bayro a, Daniel Monleon a, Jessica Lau a, and Gaetano T. Montelione a,b,* a Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA b Department of Biochemistry and Molecular Biology Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA -1-

2 Experiment Table EXPERIMENT_ID Experiment_ID Unique identifier of experiment SPECTROMETER_ID NMR_spectrometer_ID Spectrometer used to collect data TEMPERATURE Variable_value(In sample_conditions) Temp experiment was conducted at PULSE_SEQUENCE NICKNAME USER_ID EXP_DATE NMR_SAMPLE_ID Pulse_sequence_file_name Contact_person_entry_id Sample_id Pulse Sequence Used Experiment nickname User who ran experiment Date experiment was performed Sample Used T1_NUC Detected_nucleus Nuclei labeled in t1 dimension T2_NUC Detected_nucleus Nuclei labeled in t2 dimension T3_NUC Detected_nucleus Nuclei labeled in t3 dimension T4_NUC Detected_nucleus Nuclei labeled in t4 dimension T5_NUC Detected_nucleus Nuclei labeled in t5 dimension PROCPARS NOTEBOOK_ID LOCATION EXP_PATH All procpar variables name/values Nmr notebook (base) Disk location Disk location of experimental files SOFTWARE_ID Software_id Software used for NMR data collection PROBE_ID NMR_probe_id Probe used in spectrometer REFERENCE_ID NMR_spectral_processing_id Spectrometer reference offset COMMENTS User Comments -2-

3 Pulse Sequence PULSE_SEQUENCE Pulse_sequence_file_name Unique name of pulse sequence T2_NUC Detected_nucleus Possible nuclei detected in t1 T2_NUC Detected_nucleus Possible nuclei detected in t2 T3_NUC Detected_nucleus Possible nuclei detected in t3 T4_NUC Detected_nucleus Possible nuclei detected in t4 T5_NUC Detected_nucleus Possible nuclei detected in t5 SPECTROMETER_TYPE NMR_spectrometer_ID Spectrometer Manufacturer COMMENTS NICKNAME Additional comments Nicknames defining experiment SCHEMATIC_FILE_LOCATION Pulse_sequence_schematic_file_name Physical location of schematic CITATION_LABEL Citation_ID Citation to publication T1_COF Pulse_sequence_parameter_file_name Variable defining center of spectra in t1 dimension T2_COF Pulse_sequence_parameter_file_name Variable defining center of spectra in t2 dimension T3_COF Pulse_sequence_parameter_file_name Variable defining center of spectra in t3 dimension T4_COF Pulse_sequence_parameter_file_name Variable defining center of spectra in t4 dimension T5_COF Pulse_sequence_parameter_file_name Variable defining center of spectra in t5 dimension -3-

4 NMR Sample NMR_SAMPLE_ID Sample_ID Unique identifier of sample BATCH_ID Sample prep batch (wet lab specific) PROTEIN_ID Mol_common_name Foreign key to protein table NOTEBOOK_NUM Sample notebook DATE_PREPARED Date sample was prepared PREPARED_BY Contact_person_entry_ID Link to User_id in user_info PROTEIN_CONCENTRATION Concentration_value Concentration of protein table. SOLVENT Details Solvents sample is in BUFFER1 Details Buffers sample prepared with C13 Isotopic_labeling % enrichment C13 N15 Isotopic_labeling % enrichment N15 H2 Isotopic_labeling % enrichment H2 OTHER_ENRICHMENT Other enrichments yes no REFERENCE Reference compound NMR_TUBE Sample_NMR_tube_type Nmr tube diameter COMMENTS Additional comments PH Variable_value MOLEC_PURITY Mol_purity_value METHOD_OF_COLLECTION_OF_PURITY Mol_purity_measurement_method Method used to determine sample purity STORAGE_PROTOCOL Sample_storage_protocol -4-

5 SAMPLE_TYPE Sample_type CONC_MIN_VALUE Concentration_min_value CONC_MAX_VALUE Concentration_max_value CONC_VALUE_UNITS Concentration_value_units SAMPLE_PREPARATION_FILES Sample_preparation_protocol MOLEC_SYS_NAME Link to Molecular_system table MOL_POLYMER_ID Link to Monomeric_Polymers table POLY_RESIDUE_SEQ_ID Link to Polymer_residue_sequence table POLY_RES_ID Link to Polymer_Residues table LIGAND_NAME Link to Ligands table MOLEC_BOND_LINK_DEF_ID Link to Bond_Linkage_defs table BIOL_FUNC_ID Link to Biological_function table EXP_SOURCE_ID Link to Experimental_Source table NATURAL_SOURCE_ID Link to Natural_Source table Protein PROTEIN_ID Mol_common_name Unique protein name DESCRIPTION Mol_common_name Full protein name SEQUENCE Protein sequence -5-

6 Storage LOCATION FULL ACTIVE Base storage disk path Is location full yes no Is location active yes no Nickname Table NICKNAME Pulse Sequence Nickname Spectrometer SPECTROMETER_ID NMR_spectrometer_ID Unique identifier of spectrometer FIELD Field_strength Strength in MHz of spectrometer LOCATION Physical location of spectrometer MODEL_NAME Model Model of spectrometer SPECTROMETER_TYPE Manufacturer Spectometer manufacturer NMR_PROBE_ID NMR_spectrometer_probe_ID Link to nmr_probe table REFERENCE_ID NMR_spectral_processing_ID Link to Spectrometer_reference_offset table -6-

7 Spectrometer Reference Offset REFERENCE_ID NMR_spectral_processing_ID Unique id of reference SPECTROMETER_ID FREQ1H_0 Link to Spectrometer_table 1H Spectrometer freq at 0 ppm TOF_0 1H offset corresponding to 0 ppm FREQ15N_0 15N Spectrometer freq (1H) at 0 ppm DOF_0 15N offset corresponding to 0 ppm (15N) FREQ13C_0 13C Spectrometer freq (1H) at 0 ppm DOF2_0 13C offset corresponding to 0 ppm (13C) DATE_UPDATED T_COEF_1H OFFSET_1H_0_25 T_COEF_15N OFFSET_15N_0_25 T_COEF_13C OFFSET_13C_0_25 Date offsets measured 1H Processing coefficient 1H offset at 25 degrees C 15N Processing coefficient 15N offset at 25 degrees C 13C Processing coefficient 13C offset at 25 degrees C -7-

8 NMR Probe NMR_PROBE_ID NMR_spectrometer_probe_ID Unique identifier of probe MANUFACTURER Manufacturer Manufacturer of probe MODEL Model Model of probe TYPE Type Type of probe DIAMETER Diameter Probe diameter User Info USER_ID Contact_person_entry_ID Unique identifier of user FIRST_NAME Author_given_name First name LAST_NAME Author_family_name Last name LAB Lab affiliation ADDRESS1 Mailing_address Address1 ADDRESS2 Mailing_address Address2 CITY STATE ZIP Mailing_address Mailing_address Mailing_address PHONE Phone_number Lab phone HOME_PHONE _address -8-

9 Software SOFTWARE_ID Software_ID Software name VERSION Version Software version DETAILS Details VENDOR Vendor Software vendor Unassigned Peak List UNASSIGNED_PEAK_LIST_ID EXPERIMENT_ID Experiment which peak list is associated USER_ID DATE LOCATION PATH SOFTWARE_ID User who inserted list Date of insertion Disk location prefix Peak List location path SoftwareId used for peak picking W1 W2 W3 W4 FINAL COMMENTS Nuclei in w1 Nuclei w2 Nuclei w3 Nuclei w4 Final representation General comments -9-

10 Project PROJECT_ID PROJECT_NAME DATE USER_ID DISK_PATH LOCATION Primary Key Name of Project Date of creation User who created Disk location prefix Disk location Experiments Used Project EXPERIMENT_ID PROJECT_ID Experiment Id Project Id Resonance Assignment Runs RESONANCE_ASSIGNMENT_RUN_ID PROJECT_ID USER_ID DATE SOFTWARE_ID DISK_PATH LOCATION PEAK_EDITING_ID Primary Ket Link to Project User who archived Date of archival Software used Disk location prefix Disk location Legacy field Structural Determination AS_RUN_ID PROJECT_ID USER_ID Primary Key Link to Project User who archived -10-

11 DISK_PATH LOCATION DATE_CREATED SOFTWARE_ID Disk Location Prefix Disk Location Date archived Software used Processing Defaults PROCESSING_DEFAULT_ID T1_PHASE_0 T1_PHASE_1 T2_PHASE_0 T2_PHASE_1 T3_PHASE_0 T3_PHASE_1 T4_PHASE_0 T4_PHASE_1 WINDOW_FUNCTION_T1 WINDOW_FUNCTION_T2 WINDOW_FUNCTION_T3 WINDOW_FUNCTION_T4 WF_PAR1_T1 WF_PAR2_T1 WF_PAR3_T1 WF_PAR1_T2 WF_PAR2_T2 WF_PAR3_T2 WF_PAR1_T3 WF_PAR2_T3 WF_PAR3_T3 WF_PAR1_T4 WF_PAR2_T4 WF_PAR3_T4 Primary Key Zero Order Phase t1 1 st Order Phase t1 Zero Order Phase t2 1 st Order Phase t2 Zero Order Phase t3 1 st Order Phase t3 Zero Order Phase t4 1 st Order Phase t4 Default Window Function t1 Default Window Function t2 Default Window Function t3 Default Window Function t4 Default WF parameter1 t1 Default WF parameter2 t1 Default WF parameter3 t1 Default WF parameter1 t2 Default WF parameter2 t2 Default WF parameter3 t2 Default WF parameter1 t3 Default WF parameter2 t13 Default WF parameter3 t3 Default WF parameter1 t4 Default WF parameter2 t4 Default WF parameter3 t4-11-

12 FIRST_POINT_MULTI_T1 FIRST_POINT_MULTI_T2 FIRST_POINT_MULTI_T3 FIRST_POINT_MULTI_T4 FT_NEG_T1 FT_NEG_T2 FT_NEG_T3 FT_NEG_T4 T1_MODE T2_MODE T3_MODE T4_MODE First point correction t1 First point correction t2 First point correction t3 First point correction t4 Uses FT neg flagyes/no Uses FT neg flagyes/no Uses FT neg flagyes/no Uses FT neg flagyes/no Acquisition Mode t1 Acquisition Mode t2 Acquisition Mode t3 Acquisition Mode t4 Processing Table Parameter Field NMR-STAR Parameter Description EXPERIMENT_ID FIELD DATE PULSE_SEQUENCE NICKNAME T1_NUC_OBS T2_NUC_OBS T3_NUC_OBS T4_NUC_OBS T1_COF T2_COF T3_COF T4_COF OFFSET_1H_0 OFFSET_15N_0 OFFSET _13C_0 Experiment ID Magnetic field strength of spectrometer used Date of the experiment Name of pulse sequence Nickname (abbreviation) of pulse sequence Nucleus detected in t1 Nucleus detected in t2 Nucleus detected in t3 Nucleus detected in t4 T1 offset frequency variable name T2 offset frequency variable name T3 offset frequency variable name T4 offset frequency variable name Offset frequency of H 1 (Hz) Offset frequency of N 15 (Hz) Offset frequency of C 13 (Hz) -12-

13 T1_PHASE_0_CONV T1_PHASE_1_CONV T2_PHASE_0_CONV T2_PHASE_1_CONV T3_PHASE_0_CONV T3_PHASE_1_CONV T4_PHASE_0_CONV T4_PHASE_1_CONV T1_PHASE_0 T1_PHASE_1 T2_PHASE_0 T2_PHASE_1 T3_PHASE_0 T3_PHASE_1 T4_PHASE_0 T4_PHASE_1 WINDOW_FUNCTION_T1 WINDOW_FUNCTION_T2 WINDOW_FUNCTION_T3 WINDOW_FUNCTION_T4 WF_PAR1_T1 WF_PAR2_T1 WF_PAR3_T1 WF_PAR1_T2 WF_PAR2_T2 WF_PAR3_T2 WF_PAR1_T3 WF_PAR2_T3 WF_PAR4_T3 WF_PAR1_T4 WF_PAR2_T4 WF_PAR3_T4 FIRST_POINT_MULT_T1 FIRST_POINT_MULT_T2 FIRST_POINT_MULT_T3 Zero order phase of pre-conversion data First order phase of pre-conversion data zero order phase of pre-conversion data First order phase of pre-conversion data Zero order phase of pre-conversion data First order phase of pre-conversion data Zero order phase of pre-conversion data First order phase of pre-conversion data Zero order phase correction First order phase correction Zero order phase correction First order phase correction Zero order phase correction First order phase correction Zero order phase correction First order phase correction Window function applied to t1 dimension Window function applied to t2 dimension Window function applied to t3 dimension Window function applied to t4 dimension First parameter of window function in t1 Second parameter of window function in t1 Third parameter of window function in t1 First parameter of window function in t1 Second parameter of window function in t1 third parameter of window function in t1 First parameter of window function in t1 Second parameter of window function in t1 Third parameter of window function in t1 First parameter of window function in t1 Second parameter of window function in t1 Third parameter of window function in t1 First-point correction coefficient applied to t1 First-point correction coefficient applied to t2 First-point correction coefficient applied to t3-13-

14 FIRST_POINT_MULT_T4 T1_N T2_N T3_N T4_N T1_T T2_T T3_T T4_T T1_MODE T2_MODE T3_MODE T4_MODE T1_SW T2_SW T3_SW T4_SW T1_OBS T2_OBS T3_OBS T4_OBS T1_CAR T2_CAR T3_CAR T4_CAR T1_LAB T2_LAB T3_LAB T4_LAB NDIM AQ2D WF_SIZE_T1 WF_SIZE_T2 WF_SIZE_T3 WF_SIZE_T4 First-point correction coefficient applied to t4 Number of total data points in t1 Number of total data points in t2 Number of total data points in t3 Number of total data points in t4 Number of real data points in t1 Number of real data points in t2 Number of real data points in t3 Number of real data points in t4 Data acquisition mode used in t1 dimension Data acquisition mode used in t2 dimension Data acquisition mode used in t3 dimension Data acquisition mode used in t4 dimension Spectral sweep width in t1 dimension (Hz) Spectral sweep width in t2 dimension (Hz) Spectral sweep width in t3 dimension (Hz) Spectral sweep width in t4 dimension (Hz) Observed frequency in t1 dimension (MHz) Observed frequency in t2 dimension (MHz) Observed frequency in t3 dimension (MHz) Observed frequency in t4 dimension (MHz) Carrier position in t1 dimension (ppm) Carrier position in t2 dimension (ppm) Carrier position in t3 dimension (ppm) Carrier position in t4 dimension (ppm) T1 axis label (atom type) T2 axis label (atom type) T3 axis label (atom type) T4 axis label (atom type) Number of dimenstions in the input data Kind of 2D planes created by data conversion Number of points in window function on t1 Number of points in window function on t2 Number of points in window function on t3 Number of points in window function on t4-14-

15 WF_START_T1 WF_START_T2 WF_START_T3 WF_START_T4 WF_ONE_T1 WF_ONE_T2 WF_ONE_T3 WF_ONE_T4 WF_HDR_T1 WF_HDR_T2 WF_HDR_T3 WF_HDR_T4 WF_INV_T1 WF_INV_T2 WF_INV_T3 WF_INV_T4 ZF_T1 ZF_T2 ZF_T3 ZF_T4 ZF_PAD_T1 ZF_PAD_T2 ZF_PAD_T3 ZF_PAD_T4 ZF_SIZE_T1 ZF_SIZE_T2 ZF_SIZE_T3 ZF_SIZE_T4 ZF_MID_T1 ZF_MID_T2 ZF_MID_T3 ZF_MID_T4 ZF_AUTO_T1 ZF_AUTO_T2 ZF_AUTO_T3 Starting point of window function on t1 Starting point of window function on t2 Starting point of window function on t3 Starting point of window function on t4 Keeps points outside window function in t1 Keeps points outside window function in t2 Keeps points outside window function in t3 Keeps points outside window function in t4 Extracts t1 window parameters from data header Extracts t2 window parameters from data header Extracts t3 window parameters from data header Extracts t4 window parameters from data header Applies inverse of selected window to t1 Applies inverse of selected window to t2 Applies inverse of selected window to t3 Applies inverse of selected window to t4 Number of times to double data size by zero filling Number of times to double data size by zero filling Number of times to double data size by zero filling Number of times to double data size by zero filling Number of zeros to add to the data in t1 Number of zeros to add to the data in t2 Number of zeros to add to the data in t3 Number of zeros to add to the data in t4 Final size of t1 data after zero filling Final size of t2 data after zero filling Final size of t3 data after zero filling Final size of t4 data after zero filling Inserts the zeros in the middle of the data in t1 Inserts the zeros in the middle of the data in t2 Inserts the zeros in the middle of the data in t3 Inserts the zeros in the middle of the data in t4 Rounds the final size up to the nearest power of two Rounds the final size up to the nearest power of two Rounds the final size up to the nearest power of two -15-

16 ZF_AUTO_T4 ZF_INV_T1 ZF_INV_T2 ZF_INV_T3 ZF_INV_T4 FT_REAL_T1 FT_REAL_T2 FT_REAL_T3 FT_REAL_T4 FT_ALT_T1 FT_ALT_T2 FT_ALT_T3 FT_ALT_T4 FT_NEG_T1 FT_NEG_T2 FT_NEG_T3 FT_NEG_T4 FT_BRUK_T1 FT_BRUK_T2 FT_BRUK_T3 FT_BRUK_T4 FT_AUTO_T1 FT_AUTO_T2 FT_AUTO_T3 FT_AUTO_T4 FT_INV_T1 FT_INV_T2 FT_INV_T3 FT_INV_T4 Rounds the final size up to the nearest power of two Removes zeros previously appended in t1 Removes zeros previously appended in t2 Removes zeros previously appended in t3 Removes zeros previously appended in t4 Fourier transform for real-only data in t1 Fourier transform for real-only data in t2 Fourier transform for real-only data in t3 Fourier transform for real-only data in t4 Sign alternation before the Fourier transform in t1 Sign alternation before the Fourier transform in t2 Sign alternation before the Fourier transform in t3 Sign alternation before the Fourier transform in t4 Negates imaginary part of the data before FT in t1 Negates imaginary part of the data before FT in t2 Negates imaginary part of the data before FT in t3 Negates imaginary part of the data before FT in t4 Applies a sign-altered real Fourier transform in t1 Applies a sign-altered real Fourier transform in t2 Applies a sign-altered real Fourier transform in t3 Applies a sign-altered real Fourier transform in t4 Enables automatic selection of FT modes in t1 Enables automatic selection of FT modes in t2 Enables automatic selection of FT modes in t3 Enables automatic selection of FT modes in t4 Inverse Fourier transform in t1 Inverse Fourier transform in t2 Iverse Fourier transform in t3 Inverse Fourier transform in t4-16-

17 Figure Legends Figure 1S. SPINS Project Creation Tool. The Project Creation tool is designed for fast archival of a complete NMR dataset. A. Archival requires the user to input preliminary information describing the project. B. Next the user is presented with a table of experiments to insert into SPINS where sample and spectrometer specific information is associated with each experiment. After completing this form, the experiments are inserted into SPINS and associated with the newly created project. -17-