# Introduction to TPP2D for 2D-TPP analysis

# Abstract

Thermal proteome profiling (TPP) (Mateus et al., 2020; Savitski et al., 2014) is an unbiased mass spectrometry-based method to assess protein-ligand interactions. It works by employing the cellular thermal shift assay (CETSA) (Molina et al., 2013) on a proteome-wide scale which monitors the profiles of proteins in cells over a temperature gradient and aims to detect shifts induced by ligand-protein interactions. 2D-TPP represents a refined version of the assay (Becher et al., 2016) which uses a concentration gradient of the ligand of interest over a temperature gradient. This package aims to analyze data retrieved from 2D-TPP experiments by a functional analysis approach.

# General information

This package implements a method to detect ligand-protein interactions from datasets obtained with the 2D-TPP assay. Please note that methods for analyzing convential TPP datasets (e.g. single dose, melting curve approach) can be found at: `TPP` and `NPARC` .

This vignette is not aiming to give an in-depth introduction to thermal proteome profiling, please refer to other sources for this purpose:

- Original TPP publication
- 2D-TPP publication
- review article

Note: if you use `TPP2D` in published research, please cite:

> Kurzawa, N.*, Becher, I.* et al. (2020) A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles. Nat. Commun., 10.1038/s41467-020-19529-8

# Installation

1. Download the package from Bioconductor.

    if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
    BiocManager::install("TPP2D")

Or install the development version of the package from Github.

    BiocManager::install("nkurzaw/TPP2D")

2. Load the package into R session.

    library(TPP2D)

# Introduction

The 2D-TPP assay is usually set up in a way that for each temperature different ligand concentrations (including a vehicle condition) are used and two adjacent temperatures each are multiplexed in a single mass spectrometry (MS) run. Typically up to 10 or 12 temperatures are used in total that add up to 5 or 6 MS runs respectively (Figure 1).
This package aims to provide a tool for finding ligand-protein interactions, i.e. proteins affected in their thermal stability by the treatment used in the experiment) at a given false disscovery rate (FDR). Please note that a change in thermal stability of a protein is not a guarantee for it interacting with the molecule used as treatment. However, we try to give the user additional information by specifying whether an observed effect is likely due to stabilization or a change in expression or solubility of a given protein to make the interpretation of detected hits as easy as possible.

# Step-by-step workflow

    library(dplyr)
    library(TPP2D)

After having loaded `dplyr` and the `TPP2D` package itself we start by loading an example dataset which is supplied with the package. Therefore, we use the `import2dDataset` function.
For this puporse we need to supply a config table that essentially describes which experimental conditions the different TMT labels used correspond to and supplies paths to the raw data files (note: since this example dataset is included in the package it does not contain a “Path” column, this is however mandatory if the data should be read in from external raw files).

    data("config_tab")
    data("raw_dat_list")

    config_tab

    ##     Compound Experiment Temperature 126 127L 127H 128L 128H 129L 129H 130L 130H
    ## 1  Compound1       exp1        37.0   0  0.5    2   10   40    -    -    -    -
    ## 2  Compound1       exp1        37.8   -    -    -    -    -    0  0.5    2   10
    ## 3  Compound1       exp2        40.4   0  0.5    2   10   40    -    -    -    -
    ## 4  Compound1       exp2        44.0   -    -    -    -    -    0  0.5    2   10
    ## 5  Compound1       exp3        46.9   0  0.5    2   10   40    -    -    -    -
    ## 6  Compound1       exp3        49.8   -    -    -    -    -    0  0.5    2   10
    ## 7  Compound1       exp4        52.9   0  0.5    2   10   40    -    -    -    -
    ## 8  Compound1       exp4        55.5   -    -    -    -    -    0  0.5    2   10
    ## 9  Compound1       exp5        58.6   0  0.5    2   10   40    -    -    -    -
    ## 10 Compound1       exp5        62.0   -    -    -    -    -    0  0.5    2   10
    ## 11 Compound1       exp6        65.4   0  0.5    2   10   40    -    -    -    -
    ## 12 Compound1       exp6        66.3   -    -    -    -    -    0  0.5    2   10
    ##    131L RefCol
    ## 1     -    126
    ## 2    40   129L
    ## 3     -    126
    ## 4    40   129L
    ## 5     -    126
    ## 6    40   129L
    ## 7     -    126
    ## 8    40   129L
    ## 9     -    126
    ## 10   40   129L
    ## 11    -    126
    ## 12   40   129L

We then call the import function (note: we here supply a list of data frames for the “data” argument, replacing the raw data files that would be normally specified in the above mentioned column of the config table. If this is supplied the argument “data” can simply be ignored):

    import_df <- import2dDataset(
        configTable = config_tab,
        data = raw_dat_list,
        idVar = "protein_id",
        intensityStr = "signal_sum_",
        fcStr = "rel_fc_",
        nonZeroCols = "qusm",
        geneNameVar = "gene_name",
        addCol = NULL,
        qualColName = "qupm",
        naStrs = c("NA", "n/d", "NaN"),
        concFactor = 1e6,
        medianNormalizeFC = TRUE,
        filterContaminants = TRUE)

    ## The following valid label columns were detected:
    ## 126, 127L, 127H, 128L, 128H, 129L, 129H, 130L, 130H, 131L.

    ## Importing 2D-TPP dataset: exp1

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 20 out of 20 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp1

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 20 out of 20 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp2

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 20 out of 20 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp2

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 20 out of 20 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp3

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 15 out of 15 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp3

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 15 out of 15 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp4

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 14 out of 14 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp4

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 14 out of 14 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp5

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 9 out of 9 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp5

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 9 out of 9 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp6

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 4 out of 4 rows kept for further analysis.

    ## Importing 2D-TPP dataset: exp6

    ## Removing duplicate identifiers using quality column 'qupm'...

    ## 4 out of 4 rows kept for further analysis.

    ## Ratios were correctly computed!

    ## Median normalizing fold changes...

    recomp_sig_df <- recomputeSignalFromRatios(import_df)

    # resolve ambiguous protein names
    preproc_df <- resolveAmbiguousProteinNames(recomp_sig_df)
    # alternatively one could choose to run
    # preproc_df <- resolveAmbiguousProteinNames(
    #     recomp_sig_df, includeIsoforms = TRUE)

Please refer to the help page of the function to retrieve in-depth description of the different arguments. Essentially the function needs to know the names or prefixes of the columns in the raw data files, that contain different informations like protein id or the raw or relative signal intensities measured for the different TMT labels.
The imported synthetic dataset consists of 17 simulated protein 2D thermal profiles (protein1-17) and 3 spiked-in true positives (tp1-3). It represents a data frame with the columns:

column | description | required
--- | --- | ---
representative | protein identifier | Yes
qupm | number of unique quantified peptides | No
qusm | number of unique spectra | No
clustername | gene name | Yes
temperature | temperature incubated at | Yes
experiment | experiment identifier | No
label | TMT label | No
RefCol | RefCol | No
conc | treatment concentration | No
raw_value | raw reporter ion intensity sum | No
raw_rel_value | raw relative fold change compared to vehicle condition at the same temperature | No
log_conc | log10 treatment concentration | Yes
rel_value | median normalized fold change | No
value | recomputed reporter ion intensity | No
log2_value | recomputed log2 reporter ion intensity | Yes

Here the column “required” indicates which of these columns is neccessary for usage of the downstream functions.

We then begin our actual data analysis by fitting two nested models to each protein profile: A null model that is expected when a protein profile remains unaffected by a given treatment and an alternative model which is a constrained sigmoidal dose-response model across all temperatures.

    model_params_df <- getModelParamsDf(
        df = preproc_df)

The goodness of fit of both models for each protein is then compared and a \(F\)-statistic is computed.

    fstat_df <- computeFStatFromParams(model_params_df)

Then we create a null model using our dataset to be able to estimate the FDR for a given \(F\)-statistic in the next step.

    set.seed(12, kind = "L'Ecuyer-CMRG")
    null_model <- bootstrapNullAlternativeModel(
        df = preproc_df,
        params_df = model_params_df,
        B = 2)

    ## [1] "Warning: You have specificed B < 20, it is recommended to use at least B = 20 in order to obtain reliable results."
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Please note that setting \(B = 2\) (corresponsing to \(2\) permutations) is not enough to guarantee faithful FDR estimation, this has simply been set for fast demonstration purposes. We recommend to use at least \(B = 20\) for applications in praxis.

To estimate the FDR for all given \(F\)-statistics and retrieve all significant hits at a set FDR \(\alpha\) we use the following functions:

    fdr_tab <- getFDR(
        df_out = fstat_df,
        df_null = null_model)

    hits <- findHits(
        fdr_df = fdr_tab,
        alpha = 0.1)

    hits %>%
        dplyr::select(clustername, nObs, F_statistic, FDR)

    ## # A tibble: 6 × 4
    ##   clustername  nObs F_statistic   FDR
    ##   <chr>       <int>       <dbl> <dbl>
    ## 1 tp2            30       53.9      0
    ## 2 tp1            20       46.2      0
    ## 3 tp3            50       31.4      0
    ## 4 protein10      50        2.35     0
    ## 5 protein15      50        1.91     0
    ## 6 protein16      40        1.34     0

We can now plot our obtained result as a (one-sided) volcano plot:

    plot2dTppVolcano(fdr_df = fdr_tab, hits_df = hits)

Finally, we can fit and plot proteins that have come up as significant in our analysis by using:

    plot2dTppFit(recomp_sig_df, "tp1",
                 model_type = "H0",
                 dot_size = 1,
                 fit_color = "darkorange")

or respectively for the H1 model:

    plot2dTppFit(recomp_sig_df, "tp1",
                 model_type = "H1",
                 dot_size = 1,
                 fit_color = "darkgreen")

An alternative option to visualize thermal profiles of proteins of interest is to use `plot2dTppFcHeatmap`:

    plot2dTppFcHeatmap(recomp_sig_df, "tp1",
                       drug_name = "drug X")

    plot2dTppFcHeatmap(recomp_sig_df, "tp3",
                       drug_name = "drug X")

# Acknowledgements

We thank the following people for valuable feedback and help with the `TPP2D` package:

- André Mateus
- Constantin Ahlmann-Eltze
- Alexander Helmboldt
- Stefan Gade
- Dorothee Childs
- Nikos Ignatiadis
- Britta Velten

    sessionInfo()

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    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
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    ## [1] TPP2D_1.28.0     dplyr_1.2.1      BiocStyle_2.40.0
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# References

Becher, I., Werner, T., Doce, C., Zaal, E.A., Tögel, I., Khan, C.A., Rueger, A., Muelbaier, M., Salzer, E., Berkers, C.R., et al. (2016). Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat. Nature Chemical Biology 12, 908–910.
Mateus, A., Kurzawa, N., Becher, I., Sridharan, S., Helm, D., Stein, F., Typas, A., and Savitski, M.M. (2020). Thermal proteome profiling for interrogating protein interactions. Molecular Systems Biology 16, e9232.
Molina, D.M., Jafari, R., Ignatushchenko, M., Seki, T., Larsson, E.A., Dan, C., Sreekumar, L., Cao, Y., and Nordlund, P. (2013). Monitoring Drug Target Engagement in Cells and Tissues Using the Cellular Thermal Shift Assay. Science 341, 84–88.
Savitski, M.M., Reinhard, F.B.M., Franken, H., Werner, T., Savitski, M.F., Eberhard, D., Martinez Molina, D., Jafari, R., Dovega, R.B., Klaeger, S., et al. (2014). Tracking cancer drugs in living cells by thermal profiling of the proteome. Science 346, 1255784.