Table 1 Details of queries used to evaluate the scalability of SemPoD

Q1. Search proteomics experiments in any human sample

Organism = 'Homo Sapiens'

Q2. Search proteomics experiments for 'Embryonic stem' cell line in any human sample

Organism = 'Homo Sapiens' (OR) Cell Line = 'Embryonic stem'

Q3. Search proteomics experiments for Human samples with Cell Line 'Embryonic stem' or Pertubated with 0 Dosage in Cytosol Subcellular Fraction

Organism: 'Homo sapiens' (AND) Cell Line: 'Embryonic stem' (OR) Perturbation: 'Dose = 0' (OR) Subcellular Fraction: 'Cytosol'

Q4. Search Experiments for Bait Gene 'DNMT1' in AP-MS experiments or WNT3A perturbations in Bait Run Group for Cell Line RKO

Bait Gene Symbol = "DNMT1" (AND) Experiment Type = "AP-MS" (OR) Perturbation = "WNT3A" (AND) Run Group = "Bait" (OR) Cell Line = "RKO"

Q5. Search Protein Expression Experiments for T-cells Cell Lines for Drosophila melanogaster organism perturbed with 10 ng in treated cell cultures

Experiment Type: 'Protein Expression' (OR) Cell Line: 'T-cells (Boom)' (AND) Organism: 'Drosophila melanogaster' (AND) Perturbation: '10 ng' (OR) Run Group: 'Treated' (AND) Sample Type: 'Cell culture'

Q6. Search Experiments for 'POU5F1' Bait Genes for 'Embryonic stem' Cell Lines in AP-MS or 'Mus musculus' organisms that are not perturbated or endogenous cell cultures

Bait Gene = 'POU5F1" (OR) Cell Line = 'Embryonic stem" (AND) Experiment Type = "AP-MS" (OR) Organism = "Mus musculus" (AND) Perturbation = "Not Applicable" (OR) Sample Type = "Cell culture" (OR) Bait Type = "Endogenous"

Q7. Search Protein Expression Experiments or 'T-cells Cell Lines for Drosophila melanogaster organism for Tagged cell cultures not perturbated for APC Bait Genes and No vector control run groups

Experiment Type: 'Protein Expression' (OR) Cell Line: 'T-cells (Boom)' (AND) Organism: 'Drosophila melanogaster' (AND) Bait Type: 'Tagged' (AND) Sample Type: 'Cell culture' (OR) Perturbation: 'Not Applicable' (AND) Bait Gene: 'APC' (AND) Run Group: 'No Vector Control'