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#MS/MS

2 public questions tagged with this topic.

Mass Spectroscopy

A shift of 98 Da less than expected in MS/MS means:

Phosphorylation adds 80 Da, but under collision-induced dissociation phosphorylated serine and threonine frequently undergo beta-elimination of phosphoric acid H3PO4 with mass 97.9769 Da, rounded to 98 Da loss from precursor or product ions. Observation of peak 98 Da lower than predicted molecular weight signals neutral loss of phosphate, indicating presence of phosphopeptide that lost H3PO4 during fragmentation. This diagnostic loss distinguishes phosphorylated peptides from unmodified counterparts and contrasts with oxidation or deamination shifts. Recognition of -98 Da loss supports phospho

Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.

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X Ray, IR Spectroscopy

What indicates peptide phosphorylation in MS/MS?

Protein phosphorylation attaches phospho group HPO3 to serine, threonine or tyrosine hydroxyls via kinase action, adding monoisotopic mass 79.966 Da, approximated as 80 Da shift on intact peptide. Tandem mass spectra retain this increment on modified b- and y-ions, enabling site localization. Under low-energy collision-induced dissociation, phosphopeptides often undergo neutral loss of phosphoric acid H3PO4, 98 Da, creating dehydroalanine marker. In contrast, oxidation adds 16 Da and acetylation adds 42 Da. Detecting +80 Da precursor and characteristic fragment ions reliably identifies regulat

Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.

View Details