Dose differences in L1000 and Cell Painting

[gwaybio]

The column identifying dose in the LINCS Cell Painting dataset is Metadata_mmoles_per_liter. However, the compound dose used in the L1000 set (column name pert_idose) is in "uM" units. Typically, mmoles means millimolar and uM means micromolar. 1 uM = 0.001 mM.

Are the compound doses not aligned between the datasets? Or, does mmoles_per_liter mean micromolar?

[gwaybio]

One strategy to answer this question is to use the mg_per_ml column since "mg" and "ml" are more standard in some ways.

Using compound molarity, I can convert one column to the other and determine if the conversion factor is uM or mM. I tried this with the first two compounds in this document

Example 1: BRD-K25114078-003-08-1

pert_iname: aminoguanidine Expected molarity: 74.059 mg_per_ml: 1.10546000000000006 mmoles_per_liter: 9.99999999999999999

Conversion

Step 1: 1.105 mg/ml = 1105 mg/L = 1.105 g/L Step 2: 1.105 g/L / 74.059 g/mole =0.0149 moles / L

0.0149 moles / L = 14.9 mmoles / L = 14,900 umoles / L

This does not align with the given mmoles_per_liter above, but it is on the same scale as mmoles.

Example 2: BRD-K25140590-001-03-0

pert_iname: CX-516 Expected molarity: 233.105 mg_per_ml: 2.33263100000000008 mmoles_per_liter: 9.99999999999999999

Conversion

Step 1: 2.333 mg/ml = 2.333 mg/L = 2.333 g/L Step 2: 2.333 g/L / 233.105 g/mole = 0.010008 moles / L

0.010008 moles / L = 10.008 mmoles / L = 10,008 umoles / L

This is within rounding error of the provided mmoles (millimoles)

[gwaybio]

My conclusion is that mmoles_per_liter means millimoles in the Cell Painting dataset, as is standard. The next thing to confirm is if the L1000 dataset is actually measuring in micromoles.

Although it is kinda weird that the first example above didn't work out. I retrieved molarity from this link, and also confirmed it on pubchem. Maybe someone performed a different calculation when compiling the dose.

[AnneCarpenter]

Sometimes concentrations as a column heading reflect the compound source concentration and sometimes they reflect the actual treatment concentration. It may be the source of confusion/discrepancy here. Hopefully Shantanu can add some concrete detail because I hope he recalls this.

[gwaybio]

For completeness, we cleared this issue up in slack:

compound source concentration and sometimes they reflect the actual treatment concentration

This is the missing step:

0.37mM * 0.05uL / 50uL = 0.37uM

0.05 uL is the volume of compound added to the total well volume of 50uL.