# study_metadata.txt
# Template version: 0.1
# This file encodes human-provided information that is used by the metadata_handler to guide SDRF creation
# SDRF specification: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics
# Format for this file:
#   - Blank lines and lines beginning with # are ignored
#   - All other lines should be in the format of key=value
#     (where key is an SDRF key, and value is an SDRF value)
# If the answer for any of these attributes is "it's not the same for all files", then it probably should be left blank here and filled in later

# Note: The dataset identifier, usually a PXD, PDC, MSV, etc. identifier
# Example: PXD004684
# Example: PDC000068
# Example: MSV000078494
dataset_identifier=

# Note: The PeptideAtlas experiment_tag
experiment_identifier=

# Note: sdrf_template should be one of: Default, Human, Vertebrates, Invertebrates, Plants, Cell lines
sdrf_template=

# Note: This should be left blank and left for RunAssessor or manual entry to fill in
source name=

# Note: Use NCBI taxon name
# Example: Homo sapiens
# Example: Mus Musculus
characteristics[organism]=

# Note: Sometimes relevant for some Invertebrates and Cell lines
characteristics[strain/breed]=

# Note: Relevant for Plants
characteristics[ecotype/cultivar]=

# Note: Relevant for Human
# Example: white
characteristics[ancestry category]=

# Examples: 58Y, 40Y5M, 2M10D, 40Y-85Y
# Documentation: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#age-encoding
characteristics[age]=

# Example: adult
characteristics[developmental stage]=

# Examples: male, female
characteristics[sex]=

# Examples: normal, control, ischemic cardiomyopathy, cardiac hypertrophy, clear cell renal carcinoma
characteristics[disease]=

# Examples: normal, adenoma, colorectal cancer
characteristics[phenotype]=

# Examples: heart left ventricle, lung squamous cell carcinoma tissue, lung tumor-adjacent tissues
characteristics[organism part]=

# Examples: heart cell
characteristics[cell type]=

# Note: This should almost always be filled in later with Excel or lesSDRF, rather than here
characteristics[individual]=

# Note: Unless the same for all files, this should almost always be filled in later with Excel or lesSDRF, rather than here
characteristics[cell line]=

# Documentation: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#122-phosphoproteomics-and-other-post-translational-modifications-enriched-studies
# Example: enrichment of phosphorylated Protein
# Example: enrichment of glycosylated Protein
characteristics[enrichment process]=

# Example: IMAC
characteristics[enrichment method]=

# Note: This should almost always be filled in later with Excel or lesSDRF, rather than here
characteristics[biological replicate]=

# Example: tissue, organism part
material type=

# Note: This should almost always be filled in later with Excel or lesSDRF, rather than here
assay name=

# Note: This always seems to be proteomic profiling by mass spectrometry
# Example: proteomic profiling by mass spectrometry
technology type=proteomic profiling by mass spectrometry

# Note: RunAssessor can usually recognize and fill in DDA vs DIA
# Example: NT=Data-Independent Acquisition;AC=NCIT:C161786
comment[proteomics data acquisition method]=

# Note: This should almost always be filled in by RunAssessor or lesSDRF, rather than here
comment[data file]=

# Note: This should almost always be filled in later with Excel or lesSDRF, rather than here
# Documentation: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#128-encoding-sample-technical-and-biological-replicates
comment[technical replicate]=

# Note: This should almost always be filled in later with Excel or lesSDRF, rather than here
# Documentation: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#128-encoding-sample-technical-and-biological-replicates
comment[fraction identifier]=

# Note: the formatting must be in SDRF "NT;AC" format
# Documentation: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#129-sample-preparation-properties
# Example: NT=High-performance liquid chromatography;AC=PRIDE:0000565
comment[fractionation method]=

# Documentation: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#129-sample-preparation-properties
# CV tree: https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000598?lang=en
# Example: NT=Iodoacetamide (IAA);AC=PRIDE:0000599
# Example: NT=Methyl methanethiosulfonate (MMTS);AC=PRIDE:0000605
comment[alkylation reagent]=

# Note: label may be provided, but isobaric labeling should be extracted with RunAssessor
# Note: the formatting must be in SDRF "NT;AC" format
# Example: NT=label free sample;AC=MS:1002038
comment[label]=

# Note the formatting must be in SDRF "NT;AC" format
# Documentation: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#1042-cleavage-agents
# Example: NT=Trypsin;AC=MS:1001251
# Example: AC=MS:1001309;NT=Lys-C
comment[cleavage agent details]=

# Note: instrument may be provided, but it is discouraged unless the data files do not encode it. It should be extracted with RunAssessor
# Note the formatting must be in SDRF "NT;AC" format
# Example: NT=Q Exactive;AC=MS:1001911
comment[instrument]=

# Note: This is best left filled in by RunAssessor
# Example: NT=collision-induced dissociation;AC=MS:1000133
# Example: NT=HCD;AC=PRIDE:0000590
comment[dissociation method]=

# Note the formatting must be in SDRF "NT;AC;TA;MT" format. Only one modification per line. This "modification parameters=" line can be repeated
# Documentation: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#1041-protein-modifications
# Example: NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed
# Example: NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35
# Example: NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable
# Example: NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21
comment[modification parameters]=

# Note: If left blank, RunAssessor can provide defaults based on the instrument configuration, or you can override it
# Documentation: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#1043-precursor-and-fragment-mass-tolerances
# Example: 20 ppm
comment[precursor mass tolerance]=

# Note: If left blank, RunAssessor can provide defaults based on the instrument configuration, or you can override it
# Documentation: https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#1043-precursor-and-fragment-mass-tolerances
# Example: 20 ppm
# Example: 0.05 Da
comment[fragment mass tolerance]=

# Note: Leave blank for RunAssessor to fill in
comment[tool metadata]=

# Note: The factor value below refers to an SDRF characteristic listed above (or otherwise specified) that was tested as the variable factor in this study
#       i.e. there should be a characteristics[xxxxxxx] above where xxxxxxx is the factor value here
# Note: This should almost always be filled in later with Excel or lesSDRF, rather than here
factor value=




