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metadata
samples
Instrument_MS
Data_proteins
Data_peptides
Data_PTM
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| # A template for Mass Spec data that was derived from the templates available on the PRIDE website in order to conform to MIAPE and SysMO JERM standards | |||||||||
| Metadata | Values (examples) | Notes | |||||||
| Asset Title | The name of the data file | ||||||||
| Uploader | The person submitting the asset to SEEK | ||||||||
| Uploader SEEK ID | If you add your own SEEK ID, this will help us link this asset with your profile | ||||||||
| Project | Project | The project that the asset belongs to | |||||||
| ASSAY | |||||||||
| Assay SEEK ID | If referring to an exisitng Assay, you can link to it via the Assay SEEK ID. | ||||||||
| Assay Title | The title of an exisitng assay | ||||||||
| Assay_type | proteomics | The assay_type describes the type of experiment you are performing | |||||||
| Technology_type | mass_Spectrometry | Describes the type of instruments and/or equipment used for the experiment | |||||||
| Description | A brief, human readable description. | ||||||||
| Experimentalist | The names of the people who carried out the experiments. These can either be SEEK members or external scientists | ||||||||
| Date | The start date for the experiment if different from the upload date | ||||||||
| SOP (protocol) | Links to SOPs and protocols used to carry out the experiment. If they are already in SEEK, you can refer to them by their SEEK ID | ||||||||
| SOP Type | |||||||||
| Publication (optional) | If this data appears in a publication, you can link it directly, or via the assay or study. If it is already registered in SEEK, you can use the PubMed ID or DOI as a reference. | ||||||||
| Experimental_conditions | |||||||||
| Item | ExperimentalConditions | ExperimentalConditions | The name of the experimental condition you are fixing in your experiment (e.g. temperature, concentration, pH etc). If there is more than 1, please list them in columns across the spreadsheet | ||||||
| Compound (if concentration) | The compound name is only required if the item is concentration. | ||||||||
| Unit | The SI units of the experimental conditions measurements. | ||||||||
| Start_value (optional) | This field is used for recording changes throughout the experiment to measure different conditions (e.g. pH or dilutions) | ||||||||
| End_value (optional) | This field is used for recording changes throughout the experiment to measure different conditions (e.g. pH or dilutions) | ||||||||
| Comments | Additional information that would be useful for people reading this data file | ||||||||
| Culture Growth | CultureGrowth | ||||||||
| FACTORS_STUDIED | |||||||||
| Item | FactorsStudied | FactorsStudied | Factors Studied are the factors that you deliberately change during the course of your experiment to see the effects. For example, if you measure the concentration of compounds at pH 5, 6 & 7, the factor studied is the pH (i.e. it is about the treatment you apply rather than the measurements you make). | ||||||
| Compound (if concentration) | The compound name is only required if the Factors Studied item is concentration. | ||||||||
| Unit | The SI units of the factors studied measurements | ||||||||
| Start_value (optional) | This field is used for recording changes throughout the experiment for one particular factor studied (e.g. pH in crease from 4 - 7 or dilution rate doubling) | ||||||||
| End_value (optional) | This field is used for recording changes throughout the experiment for one particular factor studied (e.g. pH in crease from 4 - 7 or dilution rate doubling) | ||||||||
| SD (optional) | The standard deviation for the difference in factors studied measurements (optional) | ||||||||
| Comments | Additional information that would be useful for people reading this data file | ||||||||
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| Sample Name | Treatments (Factors Studied) | Culture_start_date | Date_at_sampling | Age_at_sampling_hours | ||||||||
| Organism | NCBI_ID | Strain | Genotype | Phenotype | organism/cell part | e.g temperature | e.g Growth medium | date | date | age | Description | |
| A01 | organism | |||||||||||
| B01 | organism | |||||||||||
| C01 | organism | |||||||||||
| D01 | organism | |||||||||||
| E01 | organism | |||||||||||
| A02 | organism | |||||||||||
| B02 | organism | |||||||||||
| C02 | organism | |||||||||||
| D02 | organism | |||||||||||
| E02 | organism | |||||||||||
| Note: this sheet allows you to describe your samples in as much detail as required. Sample names can be used in the data matrix file to relate different conditions to different experimental measurements | ||||||||||||
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| Mass Spec Instrument Details | |||||||||
| Instrument Name | |||||||||
| Source Filename | |||||||||
| Source File Type | |||||||||
| Source descriptions | |||||||||
| Inlet Type | inlet type | ||||||||
| Physical Property | size | Value | |||||||
| Analyser Components | |||||||||
| Component Number | Name | Value | |||||||
| mass analyzer type | |||||||||
| mass analyzer type | |||||||||
| mass analyzer type | |||||||||
| mass analyzer type | |||||||||
| mass analyzer type | |||||||||
| mass analyzer type | |||||||||
| Detector Components | |||||||||
| Name | Value | ||||||||
| detector type | |||||||||
| detector type | |||||||||
| detector type | |||||||||
| detector type | |||||||||
| MS software | |||||||||
| MS Instrument software name | software | ||||||||
| MS Instrument software version | |||||||||
| Comments/Description | |||||||||
| Processing Method | |||||||||
| The processing method is a description of the default peak processing method. The base method used in the generation of an mzData file | |||||||||
| Method Name | |||||||||
| Method Description | data processing software | ||||||||
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| Proteins | ||||||||||||||||
| This sheet is used to enter details of protein identifications. | ||||||||||||||||
| 2D Gel based identifications | ||||||||||||||||
| Protein Unique ID | Type | Protein Accession | Accession Version | Splice Isoform | Search Database | Search DB Version | Spectrum Reference | Score | Threshold | Search Engine | Sequence Coverage | Gel Link | X-Coord | Y-Coord | Molecular Weight | pI |
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| Peptides | |||||||||
| To add details of a peptide, you first need to enter details of the protein that it provides evidence for on the "Proteins" worksheet | |||||||||
| ↓ Peptide Unique ID | ↓ Protein Unique ID | ↓ Protein Accession | Sequence (Please do not include flanking sequences here) | ↓ Start | ↓ End | ↓ Spectrum Reference | |||
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| Post Translational Modifications | |||||||||
| ↓ Peptide Unique ID | ↓ Peptide Sequence | ↓ Location (Relative to Peptide) | ↓ Accession | ↓ PTM Database | ↓ Database Version | ↓ Average Delta Value | ↓ Mono Delta Value | ||
