Computational Detection of Phosphopantetheine Modified Peptides via Tandem Mass Spectrometry by Anand Patel

SciVee ◽  
2009 ◽  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Modified Peptides

scholarly journals Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis

2020 ◽  
Author(s):  
Nicholas Riley ◽  
Stacy Malaker ◽  
Carolyn Bertozzi
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Peptide Fragments ◽  
Terminal Residue ◽  
Bacterial Enzyme ◽  
N Terminus ◽  
Modified Peptides ◽  
Potential Benefits

<p>The recently described O-glycoprotease OpeRATOR presents exciting opportunities for O-glycoproteomics. This bacterial enzyme purified from <i>Akkermansia (Sp). muciniphila</i> cleaves N-terminally to serine and threonine residues that are modified with (preferably asialylated) O-glycans. This <a>provides orthogonal cleavage relative to canonical proteases (e.g., trypsin) for improved O-glycopeptide characterization with tandem mass spectrometry (MS/MS). O-glycopeptides with a modified N-terminal residue, such as those generated by OpeRATOR, present several potential benefits, perhaps the most notable being <i>de facto</i> O-glycosite localization without the need of glycan-retaining fragments in MS/MS spectra. Indeed, O-glycopeptides modified exclusively at the N-terminus would enable O-glycoproteomic methods to rely solely on collision-based fragmentation rather than electron-driven dissociation because glycan-retaining peptide fragments would not be required for localization. The caveat is that modified peptides would need to reliably contain only a single O-glycosite. </a>Here we use methods that combine collision- and electron-based fragmentation to characterize the number of <i>O-</i>glycosites that are present in <i>O-</i>glycopeptides derived from OpeRATOR digestion of four known <i>O-</i>glycoproteins. Our data show that over 50% of <i>O-</i>glycopeptides generated from combined digestion using OpeRATOR and trypsin contain multiple <i>O-</i>glycosites, indicating that collision-based fragmentation alone is not sufficient. Electron-based dissociation methods are necessary to capture the <i>O-</i>glycopeptide diversity present in OpeRATOR digestions. </p>

scholarly journals Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis

2020 ◽  
Author(s):  
Nicholas Riley ◽  
Stacy Malaker ◽  
Carolyn Bertozzi
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Peptide Fragments ◽  
Terminal Residue ◽  
Bacterial Enzyme ◽  
N Terminus ◽  
Modified Peptides ◽  
Potential Benefits

<p>The recently described O-glycoprotease OpeRATOR presents exciting opportunities for O-glycoproteomics. This bacterial enzyme purified from <i>Akkermansia (Sp). muciniphila</i> cleaves N-terminally to serine and threonine residues that are modified with (preferably asialylated) O-glycans. This <a>provides orthogonal cleavage relative to canonical proteases (e.g., trypsin) for improved O-glycopeptide characterization with tandem mass spectrometry (MS/MS). O-glycopeptides with a modified N-terminal residue, such as those generated by OpeRATOR, present several potential benefits, perhaps the most notable being <i>de facto</i> O-glycosite localization without the need of glycan-retaining fragments in MS/MS spectra. Indeed, O-glycopeptides modified exclusively at the N-terminus would enable O-glycoproteomic methods to rely solely on collision-based fragmentation rather than electron-driven dissociation because glycan-retaining peptide fragments would not be required for localization. The caveat is that modified peptides would need to reliably contain only a single O-glycosite. </a>Here we use methods that combine collision- and electron-based fragmentation to characterize the number of <i>O-</i>glycosites that are present in <i>O-</i>glycopeptides derived from OpeRATOR digestion of four known <i>O-</i>glycoproteins. Our data show that over 50% of <i>O-</i>glycopeptides generated from combined digestion using OpeRATOR and trypsin contain multiple <i>O-</i>glycosites, indicating that collision-based fragmentation alone is not sufficient. Electron-based dissociation methods are necessary to capture the <i>O-</i>glycopeptide diversity present in OpeRATOR digestions. </p>

scholarly journals Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis

2020 ◽  
Author(s):  
Nicholas Riley ◽  
Stacy Malaker ◽  
Carolyn Bertozzi
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Peptide Fragments ◽  
Terminal Residue ◽  
Bacterial Enzyme ◽  
N Terminus ◽  
Modified Peptides ◽  
Potential Benefits

<p>The recently described O-glycoprotease OpeRATOR presents exciting opportunities for O-glycoproteomics. This bacterial enzyme purified from <i>Akkermansia (Sp). muciniphila</i> cleaves N-terminally to serine and threonine residues that are modified with (preferably asialylated) O-glycans. This <a>provides orthogonal cleavage relative to canonical proteases (e.g., trypsin) for improved O-glycopeptide characterization with tandem mass spectrometry (MS/MS). O-glycopeptides with a modified N-terminal residue, such as those generated by OpeRATOR, present several potential benefits, perhaps the most notable being <i>de facto</i> O-glycosite localization without the need of glycan-retaining fragments in MS/MS spectra. Indeed, O-glycopeptides modified exclusively at the N-terminus would enable O-glycoproteomic methods to rely solely on collision-based fragmentation rather than electron-driven dissociation because glycan-retaining peptide fragments would not be required for localization. The caveat is that modified peptides would need to reliably contain only a single O-glycosite. </a>Here we use methods that combine collision- and electron-based fragmentation to characterize the number of <i>O-</i>glycosites that are present in <i>O-</i>glycopeptides derived from OpeRATOR digestion of four known <i>O-</i>glycoproteins. Our data show that over 50% of <i>O-</i>glycopeptides generated from combined digestion using OpeRATOR and trypsin contain multiple <i>O-</i>glycosites, indicating that collision-based fragmentation alone is not sufficient. Electron-based dissociation methods are necessary to capture the <i>O-</i>glycopeptide diversity present in OpeRATOR digestions. </p>

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