Merge pull request #89 from jessegmeyerlab/jessegmeyerlab-patch-7

add Rex data analysis figure

content/07.peptide-quantification.md

@@ -39,7 +39,7 @@ Commercial isobaric tags include tandem mass tags (TMT) [@DOI:10.1021/ac0262560]
 10- and 11-plex TMT kits were recently supplanted by proline-based TMT tags (TMTpro), originally introduced as 16-plex kits in 2019 [@DOI:10.1021/acs.analchem.9b04474] and upgraded to an 18-plex platform in 2021 [@DOI:10.1021/acs.jproteome.1c00168]. 
 
 The isobaric tag labeling-based peptide quantitation strategy uses derivatization of every peptide sample with a different isotopic incorporation from a set of isobaric mass tags. 
-All isobaric tags have a common structural theme consisting of 1) an amine-reactive groups (usually triazine ester or N-hydroxysuccinimide [NHS] esters) which react with peptide N-termini and ε-amino group of the lysine side chain of peptides, 2) a balancer group, and 3) a reporter ion group.  
+All isobaric tags have a common structural theme consisting of 1) an amine-reactive groups (usually triazine ester or N-hydroxysuccinimide [NHS] esters) which react with peptide N-termini and ε-amino group of the lysine side chain of peptides, 2) a balancer group, and 3) a reporter ion group (**Figure 4**).  
 Peptide labeling is followed by pooling the labelled samples, which undergo MS and MS/MS analysis simultaneously. 
 As the isobaric tags are used, peptides labeled with these tags give a single MS peak with the same precursor m/z value in an MS1 scan and identical retention time of liquid chromatography analysis. 
 The modified parent ions undergo fragmentation during MS/MS analysis generating two kinds of fragment ions: (a) reporter ions and (b) peptide fragment ions. 
@@ -51,7 +51,8 @@ Because the size of the reporter ions is small and sometimes the mass difference
 There are examples, however, of using isobaric tags with pulsed q dissociation on linear ion traps (LTQs) [@PMID:22397766]. 
 Suitable instruments are the Thermo Q-Exactive, Exploris, Tribrid, and Astral lines, or TOFs such as the TripleTOF or timsTOFs [@DOI:10.1038/s41467-022-34919-w; @PMID:30967486]. 
 
-<!-- todo: put the isobaric tagging figure Rex made here and refer to it -->
+![**Example chemical structure of isobaric tage "Tandem Mass Tags (TMT)".**
+](images/TMT.png){#fig:DIA-types tag="4" width="100%"}
 
 The following are some of the isobaric labeling techniques:
 

content/09.peptide-purification.md

@@ -17,7 +17,7 @@ For the separation of glycosylated proteins and peptides, the preferred material
 SPE materials which are less commonly used are silica- or polystyrene-based ones [@PMID:17625912; @PMID:15317408]. 
 The other types of SPE methods are IEX, metal chelation, and affinity-based [@PMID:25692071].
 
-The basic idea behind the choice of binding and wash versus elution solutions for SPE is that that the binding and wash solutions should favor the interaction between the analytes of interest and the solid phase, whereas the elution solution should favor the interaction of the analyte with the liquid phase (**Figure 4**). 
+The basic idea behind the choice of binding and wash versus elution solutions for SPE is that that the binding and wash solutions should favor the interaction between the analytes of interest and the solid phase, whereas the elution solution should favor the interaction of the analyte with the liquid phase (**Figure 5**). 
 For example, with reversed phase SPE, the solid phase is C18 or some other hydrophobic chemistry. 
 Binding of peptides to this solid phase is based on the hydrophobicity of peptides, mostly due to their peptide backbone, but also due to the presence of amino acid side chains like leucine and phenylalanine. 
 To encourage peptides to ‘like’ the stationary phase more than the liquid phase, the peptides are loaded in aqueous solution. 
@@ -33,7 +33,7 @@ This can be performed with the aid of positive or negative pressure to ensure a
 In this step molecules bind the adsorbent and interferences pass through. 
 Next, the column is washed with the mobile phase to eliminate the contaminants while ensuring the analyte remains bound. 
 Finally, peptides are eluted in an appropriate buffer solution with polarity or charge that competes with interaction with the solid phase. 
-](images/SPE_v03.png){#fig:SPE tag="4" width="100%"}
+](images/SPE_v03.png){#fig:SPE tag="5" width="100%"}
 
 #### Specific Types of peptide purification
 There are many additional peptide purification methods that are commonly used in proteomics currently. 

content/11.peptide-ionization.md

@@ -10,7 +10,7 @@ It was Koichi Tanaka who first applied this idea to whole proteins in 1987 and t
 A few months later, Karas and Hillenkamp also demonstrated MALDI applied to protein ionization [@DOI:10.1021/ac00171a028].
 This resulted in controversy about who should have won the Nobel prize [@URL:https://web.archive.org/web/20070517202246/http://cmbi.bjmu.edu.cn/news/0212/55.htm].
 
-MALDI first requires the peptide sample to be co-crystallized with a matrix molecule, which is usually a volatile, low molecular-weight, organic aromatic compound (**Figure 5**).
+MALDI first requires the peptide sample to be co-crystallized with a matrix molecule, which is usually a volatile, low molecular-weight, organic aromatic compound (**Figure 6**).
 Some examples of such compounds are cyno-hydroxycinnamic acid, dihyrobenzic acid, sinapinic acid, alpha-hydroxycinnamic acid, ferulic acid etc [@PMID:23681820].
 Subsequently, the analyte is placed in a vacuum chamber in which it is irradiated with a LASER, usually at 337nm [@DOI:10.1021/cr010375i].
 This laser energy is absorbed by the matrix, which then transfers that energy along with its free protons to the co-crystalized peptides without significantly breaking them.
@@ -23,13 +23,13 @@ Peptides ionized by MALDI almost always take up a single charge and thus observe
 #### MALDI Mechanism
 ![**MALDI**
 The analyte-matrix mixture is irradiated by a laser source, leading to ablation. 
-Desorption and proton transfer ionize the analyte molecules that can then be accelerated into a mass spectrometer.](images/MALDI.png){#fig:MALDI-mechanism tag="5" width="100%"}
+Desorption and proton transfer ionize the analyte molecules that can then be accelerated into a mass spectrometer.](images/MALDI.png){#fig:MALDI-mechanism tag="6" width="100%"}
 
 ### Electrospray Ionization
 ESI was first applied to peptides by John Fenn and coworkers in 1989 [@DOI:10.1126/science.2675315].
 Concepts related to electrospray Ionization (ESI) were published at least as early as 1882, when Lord Rayleigh described the number of charges that could assemble on the surface of a droplet [@DOI:10.1080/14786448208628425]. 
 ESI is usually coupled with reverse-phase liquid-chromatography of peptides directly interfaced to a mass spectrometer.
-A high voltage (~ 2 kV) is applied between the spray needle and the mass spectrometer (**Figure 6**).
+A high voltage (~ 2 kV) is applied between the spray needle and the mass spectrometer (**Figure 7**).
 As solvent exits the needle, it forms droplets that take on charge at the surface, and through a debated mechanism, those charges are imparted to peptide ions.
 The liquid phase is generally kept acidic to help impart protons easily to the analytes.
 
@@ -40,7 +40,7 @@ Evidence suggests that the distribution of peptide charge states can be manipula
 
 #### Electrospray Mechanism
 ![**Electrospray Ionization** 
-Charged droplets are formed, their size is reduced due to evaporation until charge repulsion leads to Coulomb fission and results in charged analyte molecules.](images/ESI.png){#fig:ESI-mechanism tag="6" width="100%"}
+Charged droplets are formed, their size is reduced due to evaporation until charge repulsion leads to Coulomb fission and results in charged analyte molecules.](images/ESI.png){#fig:ESI-mechanism tag="7" width="100%"}
 
 The main goal of ESI is the production of gas-phase ions from electrolyte ions in solution. 
 During the process of ionization, the solution emerging from the electrospray needle or capillary is distorted into a Taylor cone and charged droplets are formed.