SDRF-Proteomics

dia-acquisition

v1.1.0 experiment

SDRF template for Data-independent acquisition (DIA) experiments. Extends ms-proteomics with DIA-specific columns.

Key Guidance

The dia-acquisition template restricts the acquisition method to DIA (or a DIA

descendant under PRIDE:0000659) and adds DIA-specific window parameters.

Key guidance:

  • comment[proteomics data acquisition method]: Must be DIA or a DIA

descendant of PRIDE:0000659. Recommended form:

NT=Data-independent acquisition;AC=PRIDE:0000450. Plain free-text

Data-independent acquisition is also allowed. Specific DIA variants

(e.g. diaPASEF, SWATH MS) are recorded in this same column as DIA

descendants, e.g. NT=diaPASEF;AC=PRIDE:0000650.

  • comment[scan window lower limit] / comment[scan window upper limit]: The overall

m/z range of the DIA method (e.g., 400-1200 for a typical SWATH experiment).

  • comment[isolation window width]: Width of individual isolation windows in m/z.

Common values: 25 (wide SWATH), 8 (narrow windows), 4 (high-resolution DIA).

This template inherits all ms-proteomics columns (instrument, label, cleavage agent, etc.).

The ms-proteomics range columns (ms min/max mz, rt, im) are also relevant for DIA methods.

Inheritance

base sample-metadata ms-proteomics dia-acquisition

Columns

4 own + 58 inherited = 62 total · click a row for details
Column Requirement Source Description
comment[proteomics data acquisition method] required dia-acquisition Mass spectrometry acquisition method restricted to DIA or a DIA descendant under PRIDE:0000659. P...
Mass spectrometry acquisition method restricted to DIA or a DIA descendant under PRIDE:0000659. Prefer NT=Data-independent acquisition;AC=PRIDE:0000450; plain free-text labels are allowed.
single_cardinality_validator
ontology — ontologies: pride
Must be a PRIDE ontology term under proteomics data acquisition method (PRIDE:0000659). Prefer a DIA term.
values — values: Data-independent acquisition, NT=Data-independent acquisition;AC=PRIDE:0000450, diaPASEF, NT=diaPASEF;AC=PRIDE:0000650, SWATH MS, NT=SWATH MS;AC=PRIDE:0000447
This template requires DIA or a named DIA descendant under PRIDE:0000659 (plain label or recommended NT+AC form)
NT=Data-independent acquisition;AC=PRIDE:0000450, Data-independent acquisition, NT=diaPASEF;AC=PRIDE:0000650, NT=SWATH MS;AC=PRIDE:0000447
comment[scan window lower limit] recommended dia-acquisition Lower m/z limit of the DIA scan window
Lower m/z limit of the DIA scan window
allows N/A allows not available
pattern — pattern: ^\d+(\.\d+)?$
m/z value as a number
400, 350.5
comment[scan window upper limit] recommended dia-acquisition Upper m/z limit of the DIA scan window
Upper m/z limit of the DIA scan window
allows N/A allows not available
pattern — pattern: ^\d+(\.\d+)?$
m/z value as a number
1200, 1000
comment[isolation window width] recommended dia-acquisition Width of the isolation window in m/z units
Width of the isolation window in m/z units
allows N/A allows not available
pattern — pattern: ^\d+(\.\d+)?$
Width in m/z
25, 8, 4

Contributors