Supplementary Figure 5: Examples of high-quality annotated pseudo-MS/MS spectra showing 4/34 phosphorylation sites in osteopontin identified using PIQED. Osteopontin is overexpressed in a variety of cancers.
From: PIQED: automated identification and quantification of protein modifications from DIA-MS data
(A) Annotated spectra for pSer-219 showing the presence of phosphate neutral loss on all y-ions and a prominent fragment ion corresponding to fragmentation n-terminal of proline. (B) Annotated spectra for a peptide containing pSer-310 from the Osteopontin C-terminal, which has a nearly-complete b-ion series. (C) Annotated spectra for a peptide containing pSer-308 and pSer-310 from the Osteopontin c-terminal, which also contains a nearly complete b-ion series and neutral losses of one or two phosphoric acids starting at b7 and b9, respectively. The spectra in (B) and (C) also contain unlabeled fragment ions that correspond to a neutral loss of water from one of the unmodified serine residues.
