SDRF template for single-cell proteomics (SCP) experiments. Works with any organism - combine with appropriate sample template (human, vertebrates, invertebrates, or plants). Aligned with Nature Methods SCP guidelines (Gatto et al., 2023).
The single-cell template follows the Nature Methods SCP guidelines (Gatto et al., 2023)
for standardized annotation of single-cell proteomics experiments.
Key guidance:
characteristics[single cell isolation protocol]: Required. The method used to isolatesingle cells (FACS, cellenONE, LCM, nanoPOTS, microfluidics, manual picking).
characteristics[cell identifier]: Required. Unique per-cell label within the experiment.Use special values carrier, reference, or empty for non-single-cell wells in
multiplexed designs (e.g., SCoPE-MS, plexDIA).
characteristics[cells per well]: Recommended. Use 1 for true single cells. Higher numbers(5, 10, 100) for small cell pools.
comment[carrier channel] / comment[reference channel]: Recommended for TMT-based SCP.Specify the TMT channel used for carrier proteome and reference normalization.
comment[sample preparation batch]: Critical for batch effect correction in SCP.Plate-level batch effects are a major confounder in single-cell studies.
characteristics[individual]: Recommended. Links cells to the same donor/patient.for cell size and identity documentation.
characteristics[spatial coordinates] / comment[tissue section]: For spatially resolved SCP(e.g., LCM-based isolation from tissue sections).
comment[facs nozzle size],comment[facs sorting mode], comment[microfluidics chip type],
comment[lcm microscope model], comment[nanopots chip version].
| Column | Requirement | Source | Description | |
|---|---|---|---|---|
| characteristics[single cell isolation protocol] | required | single-cell | Method used to isolate single cells (FACS, cellenONE, LCM, etc.) | |
|
Method used to isolate single cells (FACS, cellenONE, LCM, etc.)
values
— values:
FACS, cellenONE, microfluidics, laser capture microdissection, manual picking, nanoPOTS, …
Single cell isolation method
|
||||
| characteristics[cell identifier] | required | single-cell | Unique identifier for each single cell within the experiment. Required per SCP guidelines for tra... | |
|
Unique identifier for each single cell within the experiment. Required per SCP guidelines for tracking cells through analysis.
identifier
Cell identifier
cell_001, SC_A1, well_B3, barcode_ATCGATCG, carrier, reference
|
||||
| characteristics[sample type] | recommended | single-cell | Classification of the sample role in the experiment. Distinguishes experimental samples from cont... | |
|
Classification of the sample role in the experiment. Distinguishes experimental samples from controls, references, and other roles in multiplexed or plate-based experiments.
ontology
— ontologies: pride
Sample type should be a child of PRIDE:0000895 (sample type)
single cell, reference, bridge, carrier, pooled, empty, quality control sample, negative control
|
||||
| comment[sample preparation batch] | recommended | single-cell | Batch identifier for sample preparation (plate, chip, processing batch). Critical for batch effec... | |
|
Batch identifier for sample preparation (plate, chip, processing batch). Critical for batch effect correction.
pattern
— pattern:
^.+$
Sample preparation batch identifier
plate1, batch_20220601, prep_A
|
||||
| characteristics[cells per well] | recommended | single-cell | Number of cells per well/reaction. Use 1 for true single cells, higher numbers for small pools. | |
|
Number of cells per well/reaction. Use 1 for true single cells, higher numbers for small pools.
pattern
— pattern:
^\d+$
Number of cells
1, 5, 10, 100
|
||||
| comment[carrier channel] | recommended | single-cell | TMT/TMTpro channel used for the carrier proteome | |
|
TMT/TMTpro channel used for the carrier proteome
pattern
— pattern:
^.+$
TMT channel label for carrier
TMT131C, TMTpro134N, TMT126
|
||||
| comment[reference channel] | recommended | single-cell | TMT/TMTpro channel used for the reference sample (for normalization across sets) | |
|
TMT/TMTpro channel used for the reference sample (for normalization across sets)
pattern
— pattern:
^.+$
TMT channel label for reference
TMT131N, TMTpro133C, TMT127N
|
||||
| characteristics[forward scatter] | optional | single-cell | Forward scatter (FSC) value from flow cytometry - proxy for cell size | |
|
Forward scatter (FSC) value from flow cytometry - proxy for cell size
pattern
— pattern:
^[\d.]+$
FSC value (numeric)
316.0, 250
|
||||
| characteristics[side scatter] | optional | single-cell | Side scatter (SSC) value from flow cytometry - proxy for cell granularity/complexity | |
|
Side scatter (SSC) value from flow cytometry - proxy for cell granularity/complexity
pattern
— pattern:
^[\d.]+$
SSC value (numeric)
301.0, 184
|
||||
| characteristics[enrichment marker] | optional | single-cell | Markers used for cell sorting/enrichment with optional intensity values | |
|
Markers used for cell sorting/enrichment with optional intensity values
pattern
— pattern:
^.+$
Enrichment marker(s) and optional intensity
CD45+, GFP+, CD3+CD4+, CD34:APC-Cy7-A=276.0, PI-
|
||||
| characteristics[cell viability] | optional | single-cell | Viability status of the cell at isolation | |
|
Viability status of the cell at isolation
values
— values:
live, viable, dead, unknown
Cell viability status
|
||||
| characteristics[cell cycle phase] | optional | single-cell | Cell cycle phase if determined (e.g., by FACS or computational inference) | |
|
Cell cycle phase if determined (e.g., by FACS or computational inference)
values
— values:
G1, S, G2, G2/M, M, G0, …
Cell cycle phase
|
||||
| characteristics[cell diameter] | optional | single-cell | Physical diameter of the isolated cell if measured (in micrometers) | |
|
Physical diameter of the isolated cell if measured (in micrometers)
number_with_unit
Cell diameter with unit
15 um, 20.5 um, 12 μm
|
||||
| characteristics[spatial coordinates] | optional | single-cell | X,Y coordinates if cells were isolated from a spatial context (e.g., LCM from tissue) | |
|
X,Y coordinates if cells were isolated from a spatial context (e.g., LCM from tissue)
pattern
— pattern:
^X=[\d.]+;Y=[\d.]+$
Spatial coordinates
X=100;Y=250, X=50.5;Y=120.3
|
||||
| comment[tissue section] | optional | single-cell | Tissue section identifier for spatially resolved single-cell proteomics | |
|
Tissue section identifier for spatially resolved single-cell proteomics
pattern
— pattern:
^.+$
Tissue section identifier
section_001, slide_A_section_3
|
||||
| comment[facs nozzle size] | optional | single-cell | Nozzle diameter used for FACS-based single cell isolation (in micrometers) | |
|
Nozzle diameter used for FACS-based single cell isolation (in micrometers)
number_with_unit
Nozzle size with unit
70 um, 100 um, 130 μm
|
||||
| comment[facs sorting mode] | optional | single-cell | Sorting mode used during FACS isolation | |
|
Sorting mode used during FACS isolation
values
— values:
single cell, purity, yield, 4-way purity
FACS sorting mode
|
||||
| comment[microfluidics chip type] | optional | single-cell | Type and manufacturer of the microfluidics chip used for single cell isolation | |
|
Type and manufacturer of the microfluidics chip used for single cell isolation
pattern
— pattern:
^.+$
Chip type/manufacturer identifier
Fluidigm C1, Cellenion cellenCHIP, nanowell chip
|
||||
| comment[lcm microscope model] | optional | single-cell | Model of the laser capture microdissection microscope used for cell isolation | |
|
Model of the laser capture microdissection microscope used for cell isolation
pattern
— pattern:
^.+$
LCM microscope model name
Leica LMD7, Zeiss PALM MicroBeam, Thermo LCM
|
||||
| comment[nanopots chip version] | optional | single-cell | Version of the nanoPOTS chip used for single cell sample preparation | |
|
Version of the nanoPOTS chip used for single cell sample preparation
pattern
— pattern:
^.+$
nanoPOTS chip version identifier
nanoPOTS v1, nanoPOTS v2, 9-well chip
|
||||