Table 3 Selection of requirements of the OECD Transcriptomics Reporting Framework which are relevant for PROTEOMAS

Normalization

- Normalization method

- Background data subtraction

- Method of background calculation

- Weighting procedure

- Log transformation

- Data trimmed?

- Control samples removed before

normalization?

- Formulas

- Link/repository/accession number for

deposited normalized data + format + 

description of raw data tables

Data filtering

- Low signal intensities

- High variability between technical replicates

- Which methods?

- Which cut-offs?

Outlier removal

- Method for identification and thresholds

- Exclusion at which processing step

- List of samples excluded and per sample

Justification

- Removal before or after normalization and

Justification

Discovery of differentially abundant molecules (DAMs)

- Name and version of software

- Operating system

- Name and version of additional libraries

- Availability of software, hyperlinks or source

codes

- Table of all contrasts / conditions compared for

DAM identification

- Table of number of samples in each group for

DAM identification

- Identification of samples with expected

covariances (due to shared conditions during

processing)

- Identification of technical replicates

- Name and description of statistical approach

- Data transformation performed

- For effects models: Specification of effects

models used and effects that were modelled

- For pairwise comparison approaches:

specification of test and values (any

transformation or adjustment) being used

- Specification of decision criteria (nominal alpha

value, p-value threshold, multiple testing

correction method, adjusted threshold value,

log fold-change cut-off level) including exact

order of operations

- Output and supporting files according to the file

manifest, list all files including a description,

describe rows and columns of tables, analysis

scripts, software configurations or tables of

metadata