Update 04.experiment-types.md

content/04.experiment-types.md

@@ -6,7 +6,7 @@ The following sections give an overview of some common proteomics experiments.
 
 ### Protein abundance changes
 A common experiment is unbiased mapping of proteins along with detection of changes in their abundance across sample groups. 
-This is achieved using one of the quantitative methods mentioned elsewhere in this manuscript such as LFQ or TMT. 
+This is achieved using methods such as label free quantification (LFQ) or tandem mass tags (TMT), which are described in more detail in subsequent sections. 
 In these experiments, data should be collected from at least three biological replicates of each condition to estimate the variance of measuring each protein. 
 Depending on the experiment design, different statistical tests are used to ask if there are changes in the measured protein abundances between groups. 
 If there are only two groups, the quantities might be compared with a t-test or with a Wilcoxon signed-rank test. 
@@ -16,7 +16,7 @@ With either testing scheme, the p-values from the first set of tests must be cor
 A common method for p value correction is the Benjamini-Hochberg method [@DOI:10.1111/j.2517-6161.1995.tb02031.x]. 
 These types of experiments have revealed wide ranges of proteomic remodeling from various biological systems. 
 
-### Post-Translational Modifications (PTMs)
+### PTMs
 Proteins are modified after they are translated with various chemical groups, or even by proteolytic cleavage such as n-terminal methionine removal. 
 There are several proteomics methods that are developed specific to each type of modification. 
 See also the section on Protein/Peptide Enrichment and Depletion.
@@ -65,7 +65,7 @@ HDX-MS works by detecting changes in peptide mass due to exchange of amide hydro
 The rate of exchange depends on the protein solvent accessible surface area, dynamics, and the properties of the amino acid sequence [@doi:10.1038/s41592-019-0459-y; @doi:10.1039/C0CS00113A; @PMID:5333290; @doi:10.1017/S0033583500005217].
 Although using D2O as a solvent to make deuterium labeled sample is simple, HDX-MS requires a number of controls to ensure that experimental conditions capture the dynamics of interest [@doi:10.1038/s41592-019-0459-y; @doi:10.1586/epr.10.109; @doi:/10.1007/s13361-012-0377-z; @doi:10.4155/bio.15.46]. 
 If the peptide dissociation process is tuned appropriately, residue-level quantification of changes in solvent accessibility are possible within a measured peptide [@DOI:10.1021/ac0710782].
-If done correctly, HDX can produce precise protein structure measurements with high reproducibility.
+HDX can produce precise protein structure measurements with high reproducibility.
 Masson *et al.* gave recommendations on how to prep samples, conduct data analysis, and present findings in a detailed stepwise manner that will be useful to have if you are new to using this technique [@doi:10.1038/s41592-019-0459-y].
 
 #### Radical Footprinting  
@@ -86,9 +86,9 @@ FPOP is an example of a radical footprinting method.
 In FPOP, a laser-based hydroxyl radical protein footprinting MS method that relies on the irreversible labeling of solvent-exposed amino acid side chains by hydroxyl radicals in order to understand structure of proteins.
 A laser produces 248 nm light that causes hydrogen peroxide to break into a pair of hydroxyl radicals [@doi:10.1016/j.jasms.2005.09.008; @doi:10.1016/j.ijms.2006.08.018]. 
 The flow rate of solution through the capillary and laser frequency are adjusted so that each protein molecule is irradiated only once. 
-After they are irradiated, the sample is collected to a tube that has catalase and free methionine in the buffer so that the H2O2 and hydroxyl radical are quenched to prevent further unwarranted oxidation, which may then modify residues that become exposed due unfolding after the initial labeling. 
+After they are irradiated, the sample is collected to a tube that has catalase and free methionine in the buffer so that the H2O2 and hydroxyl radical are quenched to prevent further unwarranted oxidation, which may then modify residues that become exposed due to unfolding after the initial labeling. 
 Control samples are made by running the sample through the flow system without any irradiation. 
-Another experimental control is done by adding a radical scavenger to tune the extent of protein oxidation [@doi:10.1002/pro.3408; @doi:10.1021/ac901054w].
+Another experimental control involves the addition of a radical scavenger to tune the extent of protein oxidation [@doi:10.1002/pro.3408; @doi:10.1021/ac901054w].
 FPOP has wide application for proteins including measurements of fast protein folding and transient dynamics.
 
 #### Protein Painting [@doi:10.1038/ncomms5413; @doi:10.1074/jbc.RA118.007310]  
@@ -101,10 +101,10 @@ A lack of proteolysis in a region is interpreted as solvent accessibility, which
 #### LiP-MS (limited proteolysis mass spectrometry) [@doi:10.1016/j.tibs.2020.05.006; @DOI:10.1038/nprot.2017.100; @doi:10.1038/s41596-022-00771-x; @doi:10.1038/nprot.2017.100]  
 Limited proteolysis coupled to mass spectrometry (LiP-MS) is a method that tracks structural changes in complex proteomes in response to arbitrary stimuli.
 The idea is to detect changes in protease-accessible protein regions due to the perturbation.
-For example, a drug binding may make a disordered region protected from non-specific proteolysis. 
+For example, a drug binding may render a disordered region protected from non-specific proteolysis. 
 LiP-MS can therefore provide a somewhat unbiased view of structural changes at the proteome scale.
 This may be useful when attempting to discover a mechanism for some treatment that causes a phenotype. 
-For additional information about LiP-MS, please refer to this document: [@url:https://www.eubopen.org/sites/www.eubopen.org/files/attachments/2022/LiP-MS%20protocol.pdf]
+For additional information about LiP-MS, please refer to this article: [@url:https://www.eubopen.org/sites/www.eubopen.org/files/attachments/2022/LiP-MS%20protocol.pdf]
 
 ### Protein stability and small molecule binding  
 #### Cellular Thermal Shift Assay (CETSA) [@PMID:23828940; @doi:10.1016/j.cbpa.2019.11.004]