assay proteomics template
Template for Proteomics [Source]
| Attribute | Description | Required | columnType | DependsOn | Source | Parent | Valid Values |
|---|---|---|---|---|---|---|---|
| dataFile | Name of additional file(s) accompanying the data. The file(s) provide, for example, the name of any raw files generated by the instrument, generated reports from a vendor, an Rscript, or an instructions document. The files can be instrument raw files, converted peak lists such as mzML, MGF, or result files like mzIdentML. The files can be additional documentation submitted alongside the data needed for reuse and sharing purposes. Provide the file names of any additional files submitted alongside the data (ex., an ADAT file). Multiple file names can be separated by (;)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| databaseName | The name of the search database (nr, SwissProt or est_human, and/or mass spectral library). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| databaseSource | The name of the organization, project, or laboratory from where the database is obtained (UniProt, NCBI, EBI, other). | True | STRING | ManifestColumn | |||
| databaseWeblink | An internet address that may provide details of a database or software search, as well as for labs that generate their own search method (web link). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| digestionMethod | The type of digestion (ex. in-solution, in-gel)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| digestionReagent | Enzymes or reagents used for digestion. | True | STRING | ManifestColumn | 2-iodobenzoate,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Glutamyl endopeptidase,Leukocyte elastase,Lys-C,Lys-C/P,No cleavage,NoEnzyme,Not available,Not collected,Not specified,PepsinA,Proline endopeptidase,TrypChymo,Trypsin,Trypsin/P,Unknown,Unspecific cleavage,V8-DE,V8-E | ||
| enrichment | Protocol or reagent used for enrichment (ex. Fe3+NTA-Agarose (Qiagen)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| enrichmentStrategy | Type of peptide or protein enrichment | True | STRING | ManifestColumn | Acetylome Proteome,Glycoproteome,Lipidome,Metabolome,Not applicable,Not available,Not collected,Not specified,Phosphoproteome,Ubiquitylome,Unknown | ||
| experimentType | The type of experiment used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| fractionIdentifier | Number of fractions in the experimental runProvide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| instrumentModel | The model of the instrument used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| isobaricLabelingReagent | Reagent set used for isobaric labeling. Examples- iTRAQ113 TMT126Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| labelFreeQuantitation | Type of label-free data analysis strategyProvide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | Label-free gene level quantitation,Label-free peptide level quantitation,Label-free protein group level quantitation,Label-free protein level quantitation,Label-free raw feature quantitation,Not applicable,Not available,Not collected,Not specified,Unknown | ||
| labelQuantitation | Type of labeling usedProvide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | AminoxyTMT,DiART,DiLeu,Glyco-TMT,Hydrazide TMT,IodoTMT,IPTL,iTRAQ,iTRAQH,Label Free,Not available,Not collected,Not specified,TMT,Unknown | ||
| measurementTechnique | The name of the measurement technique describing the assay method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| modificationParameters | Modification parameters for a search engine run. (ex. PSI- PI http-//www.w3.org/2002/07/owl#Axiom) or used in the peptide identification database search. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| msAnalyteType | The type of biospecimen subjected to analysis (ex., peptide, protein, metabolite, lipid)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| msAssayTechnique | Specified the mass spectrometer technique used or the name of the proteomics assay used (ex. DDA)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| msTarget | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay | True | STRING | ManifestColumn | Not applicable,Not available,Not collected,Not specified,Targeted,Unknown,Untargeted | ||
| quantationStrategy | The general strategy used for differential analysis Example - Absolute quantitation analysis, Isobaric label quantitation analysis, LC-MS label-free quantitation analysis,Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| samplePrepProtocol | An internet address that may provide more details of the protocol information (web link). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| sampleType | The type of sample collected or the term used to describe the source of a biospecimen used for a laboratory test. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| technologyPlatformVersion | The specific version (application, manufacturer, model, lab, etc.) of a technology that is used to carry out a laboratory or computational experiment. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| Component | False | ||||||
| Filename | False | ||||||
| specimenID | Identifying string linked to a particular sample or specimen, provide by the data contributor | True | STRING | sage.annotations-experimentalData.specimenID-0.0.2 | ManifestColumn | ||
| platformLocation | The name of the laboratory, facility, vendor, company, or location where the data generation platform was located, provided by the data contributor. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | sage.annotations-experimentalData.platformLocation-0.0.2 | ManifestColumn |