Update README.md

Author: thomas-enzlein

README.md

@@ -6,7 +6,7 @@ M²ara is based on the R package [MALDIcellassay](https://github.com/CeMOS-Mannh
 
 ## How to use
 
-This application simplifies the analysis of Molecular High Content Screening (MHCS) MALDI-TOF MS assay data and the evaluation of complex drug actions. After your data has been loaded, you can adjust settings as needed and start the processing. From here, you can analyze your data by selecting entries in the data table, visually inspect and rank mass features using the Curve Response Score (CRS) fingerprints, and save the curve fit and peak profile of your chosen **m/z** value. 
+This application simplifies the analysis of Molecular High Content Screening (MHCS) MALDI-TOF MS assay data and the evaluation of complex drug actions. After your data has been loaded, you can adjust settings as needed and start the processing. From here, you can analyze your data by selecting entries in the data table, visually inspect and rank mass features using the Curve Response Score (CRS) fingerprints, and save the curve fit and peak profile of your chosen *m/z* value. 
 
 This app is specifically designed for use with Bruker flex series raw data but also features support for mzML.
 
@@ -49,32 +49,35 @@ The installer can be downloaded [here](https://github.com/CeMOS-Mannheim/M2ara/r
 ## Example data
 To test the app please use the example data on [FigShare](https://dx.doi.org/10.6084/m9.figshare.25736541). 
 
-File Unger2020_OATP2B1_inhibition_mzML.zip contains mzML data (converted from Bruker Flex using MSConvert) originally published in Unger, et. al., 2020.
+### Unger2020_OATP2B1_inhibition_mzML.zip
 
+The file contains mzML data (converted from Bruker Flex using MSConvert) originally published in Unger, et. al., 2020.
 
 To replicate the results shown use the following parameters:
 
 - under Settings set File Format to mzML
 - set Concentration unit to nM
-- set Normalization/re-calibration **m/z** to 354.1418 (D4-E3S, [M-H]-)
+- set Normalization/re-calibration *m/z* to 354.1418 (D4-E3S, [M-H]-)
 - set recalibration tolerance to 0.1 Da
-- set normalization to **m/z**
+- set normalization to *m/z*
 - activate smoothing and baseline removal
 - set Aggregation method to mean
 - set SNR to 3
 - set alignment to 0 mDa (no alignment)
 - set binning tolerance to 100 ppm
 - select the folder `mzML` (parent folder of the mzML files) from the .zip file, please make sure that no other files are in this folder.
 
-The target **m/z** is 349.11 (E3S, [M-H]-) the pIC50 value should be 6.1.
+The target *m/z* is 349.11 (E3S, [M-H]-) the pIC50 value should be 6.1.
 
-The file Weigt2018_BCR-ABL_inhibition_Dasatinib_BrukerFlex.zip contains data in the Bruker Flex format originally published in Weigt, et. al., 2018.
+### Weigt2018_BCR-ABL_inhibition_Dasatinib_BrukerFlex.zip
+
+The file contains data in the Bruker Flex format originally published in Weigt, et. al., 2018.
 
 To replicate the results shown use the following parameters:
 
 - under Settings set File Format to Bruker Flex
 - set Concentration unit to µM
-- set Normalization/re-calibration **m/z** to 760.5851 (PC(34:1) [M+H]+)
+- set Normalization/re-calibration *m/z* to 760.5851 (PC(34:1) [M+H]+)
 - set recalibration tolerance to 0.1 Da
 - set normalization to TIC
 - activate smoothing and baseline removal
@@ -84,5 +87,5 @@ To replicate the results shown use the following parameters:
 - set binning tolerance to 100 ppm
 - select the the folder `curve` from the .zip file, make sure no other files/folders are present.
 
-The target is **m/z** 826.5722 (PC(36:1) [M+K]+) and **m/z** 616.1767 (Heme B [M+H]+) the pIC50 values should be 9.5 and 9.7.
+The target is *m/z* 826.5722 (PC(36:1) [M+K]+) and *m/z* 616.1767 (Heme B [M+H]+) the pIC50 values should be 9.5 and 9.7.