mass_spec_proteomics

Name	experimentSamples.Mass_Spectrometry_Proteomics.txt
Type	combined-multiple
Schema Version	3.36
Description	The Mass Spectrometry experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and resultstogether. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described.

Template Column	Required	Description
Study ID	False	An experiment and biological sample may be linked to a single study.
Expsample ID	True	The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.
Reagent ID(s)	False	One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.
Treatment ID(s)	False	One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.
Expsample Name	False	The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.
Expsample Description	False	Describe important characteristics of the sample being assayed.
Additional Result File Names	False	Separate file names by a semi-colon (;). The file size name limit is 240 characters.
ImmPort Template?	False	If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the "Result File Name" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the "Result File Name" column.
Result File Name	False	Completing this column is conditional upon whether the "ImmPort Template?" column value is set to "Yes" or "No". If the "ImmPort Template?" column value is set to "Yes", do not enter a file name in the "Result File Name" column. If the "ImmPort Template?" column value is set to "No", enter a file name in the "Result File Name" column. ImmPort supports results templates for many of the commonly used immunological assay methods. These templates facilitate the sharing and re-use of results data in a standard format. The standard parsable template file for this template is Mass_Spectrometry_Proteomic_Results.txt. The file size name limit is 240 characters.
Protein Sequence Database File Name	False	Protein sequence file in fasta sequence format.
Repository Name	False	ImmPort expects Protein Mass spectrometry results are expected to be deposited in PRIDE or MassIVE. Please choose one these repositorys name from the list.
Repository Accession	False	The public repository accession should be the most granular or highest resolution provided (e.g. sample level accession, not sample group accession).
Biosample ID	True	The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.
Subject ID	False	Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.
Planned Visit ID	False	The link to a study's planned visit provides temporal context for a sample's derivation from a subject.
Type	False	The sample types are adopted from Uberon, Cell and CHEBI ontologies.
Subtype	False	Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.
Biosample Name	False	The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.
Biosample Description	False	The biological sample description is used to describe details of the sample not captured in other columns.
Study Time Collected	False	Study time collected describes the time value for when a sample was derived from a subject.
Study Time Collected Unit	False	The time units are standard terms recommended by the HIPC Standards group.
Study Time T0 Event	False	The time zero event refers to the study milestone upon which time is based.
Study Time T0 Event Specify	False	Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.
Experiment ID	True	The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.
Protocol ID(s)	False	Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).
Experiment Name	False	The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.
Experiment Description	False	The experiment description is used to describe details of the experiment not captured in other columns.
Measurement Technique	False	The measurement technique describes the assay method.