TPC_edits.enrichment.md

content/08.enrichment.md

@@ -18,7 +18,7 @@ One must take into account which class or classes of glycopeptides they are inte
 Glycopeptides can be enriched via glycan affinity, for example to glycan-binding proteins, chemical properties like charge or hydrophilicity, chemical coupling of glycans to stationary phases, and by bioorthogonal, chemical biology approaches.
 Glycan affinity-based enrichment strategies include the use of lectins, antibodies, inactivated enzymes, immobilized metal affinity chromatography (IMAC), and metal oxide affinity chromatography (MOAC).
 The enrichment of glycopeptides by their chemical properties, for example by biopolymer charge and hydrophobicity, include hydrophilic interaction chromatography (HILIC), electrostatic repulsion-hydrophilic interaction chromatography (ERLIC), and porous graphitic carbon (PGC).
-One variation of ERLIC combines strong anion exchange, electrostatic repulsion, and hydrophilic interaction chromatography (SAX-ERLIC) has risen in popularity thanks to robustness and commercially available enrichment kits [@DOI:10.1007/978-1-0716-1241-5_8].
+One variation of ERLIC combines strong anion exchange, electrostatic repulsion, and hydrophilic interaction chromatography (SAX-ERLIC) has risen in popularity thanks to robustness and commercially available enrichment kits [@DOI:10.1007/978-1-0716-1241-5_8; @DOI:10.1016/j.celrep.2023.112368].
 
 Chemical coupling methods most often used to enrich the glycoproteome employ hydrazide chemistry for sialylated glycopeptides.
 Glycan are cleaved from the stationary phase by PNGase F.
@@ -29,7 +29,7 @@ We direct readers to several reviews on glycopeptide enrichment strategies [@DOI
 ### Phosphoproteomics  
 Protein phosphorylation, a hallmark of protein regulation, dictates protein interactions, signaling, and cellular viability. 
 This post-translational modification (PTM) involves the installation of a negatively charged phosphate moiety (PO 4-) onto the hydroxyl side-chain of serine (Ser, S), threonine (Thr, T), and tyrosine (Tyr, Y), residues on target proteins. 
-Protein kinases catalyze the transfer of PO 4- group from ATP to the nucleophile (OH) group of serine, threonine, and tyrosine residues, while protein phosphatases catalyze the removal of PO 4 -. 
+Protein kinases catalyze the transfer of PO 4- group from ATP to the nucleophile (OH) group of serine, threonine, and tyrosine residues, while protein phosphatases catalyze the removal of PO4-. 
 Phosphorylation changes the charge of a protein, often altering protein conformation and therefore function [@PMID:26473910]. 
 Protein phosphorylation is one of the major PTMs that alters the stability, subcellular location, enzymatic activity complex formation, degradation of protein, and cell signaling of protein with a diverse role in cells [@PMID:31819260, @PMID:35227377]. 
 Phosphorylation can regulate almost all cellular processes, including metabolism, growth, division, differentiation, apoptosis, and signal transduction pathways [@PMID:28656226]. 
@@ -91,8 +91,8 @@ A novel phosphopeptide enrichment technique using sequential enrichment with mag
 •	Do not use milk as a blocking agent when western blotting for phosphorylation because milk contains the phosphoprotein casein and can lead to a higher background due to non-specific binding.  
 
 ### Antibody enrichments of modifications  
-Western blot analysis is used to detect the PTMs in a protein by using antibodies [@PMID:25059473]. 
-As an extension of this, pan-PTM antibodies have been used to isolate peptides bearing the PTM of interest [@PMID:8633009]. 
+Western blot analysis is used to detect the PTMs in a protein through the use of antibodies [@PMID:25059473]. 
+As an extension, pan-PTM antibodies have been used to isolate peptides bearing the PTM of interest [@PMID:8633009]. 
 One benefit of this approach is that peptides are less likely to experience non-specific binding than proteins [@PMID:19743430]. 
 Initially peptide immunoaffinity precipitation was developed to enrich for phosphotyrosine-containing peptides. 
 This protocol was initially designed to enrich for phosphotyrosine-containing peptides [@PMID:15592455]. 
@@ -104,10 +104,11 @@ Anti-O-GlcNAc monoclonal antibody enables enrichment from O-GlcNAcylated peptide
 These antibodies have high sensitivity and specificity toward O-GlcNAc-modified peptides and do not identify O-GalNAc or GlcNAc in extended glycans [@PMID:34678516].
 
 ### Abundant protein depletion (Blood samples)
-The range abundances of proteins in the blood/plasma proteome exceeds 10 orders of magnitude. 
-Due to this wide dynamic range, detection of proteins with medium and low abundance by proteomic analyses is difficult [@PMID:20677825]. 
-Identifying protein biomarkers from biological samples such as blood is often obstructed by proteins present at higher concentrations. 
-The removal of these high abundant proteins enables the detection of less abundant and unique proteins. 
+Many plasma proteomics studies involve the analysis of untreated, unenriched plasma (i.e., neat plasma) [@DOI:10.1021/acs.jproteome.7b00623; @DOI:10.1016/j.cels.2020.10.003].
+However, the abundance range of proteins in the blood/plasma proteome exceeds 10 orders of magnitude. 
+Due to this wide dynamic range, detection of proteins with medium and low abundance by proteomic analyses is difficult [@PMID:20677825], and identifying protein biomarkers from biological samples such as blood is often obstructed by proteins present at higher concentrations. 
+In fact, the top 14 most abundant proteins in human plasma constitute over 99% of the total protein mass.
+The removal of these high-abundant proteins enables the detection of less abundant and unique proteins. 
 The ability to deplete abundant proteins with specificity, reproducibility, and selectivity is extremely important in proteomic studies [@PMID:16052628].
 
 The following are some of the methods used for abundant protein depletion:  
@@ -138,7 +139,7 @@ It is extremely simple and cost-effective.
 However, it is less specific with a risk of protein loss, difficulty in protein resolubilization as well as time consuming [@PMID:31617391].
 
 #### New technologies: 
-Newer methods of highly abundant protein depletion are based on the interaction between polymers such as bacterial cellulose nanofibers [@PMID:30219335], cryogels [@PMID:30999704; @PMID:23668981] and nanomaterials [@DOI:10.1016/j.procbio.2010.07.007].  
+Newer methods of highly abundant protein depletion are based on the interaction between polymers such as bacterial cellulose nanofibers [@PMID:30219335], cryogels [@PMID:23668981], and nanomaterials [@DOI:10.1016/j.procbio.2010.07.007].  
 These techniques are highly specific, relatively cheap, and very stable. 
 They can also be reused since they have larger binding capacity and less cross-reactivity [@PMID:31617391].
-
+Protein enrichment/depletion strategies which make use of protein coronas [@DOI:10.1038/s41467-020-17033-7; @DOI:10.1101/2023.08.28.555225] or extracellular vesicle enrichment [@DOI:10.1101/2023.06.10.544439] are enabling researchers to probe deeper into the plasma, serum, lymph, and cerebrospinal fluid proteomes.