Studying the fragmentation behavior of peptides with arginine phosphorylation and its influence on phospho-site localization
Article first published online: 18 FEB 2013
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Special Issue: Analysis of Post-translational Modifications
Volume 13, Issue 6, pages 945–954, March 2013
How to Cite
Schmidt, A., Ammerer, G. and Mechtler, K. (2013), Studying the fragmentation behavior of peptides with arginine phosphorylation and its influence on phospho-site localization. Proteomics, 13: 945–954. doi: 10.1002/pmic.201200240
- Issue published online: 11 MAR 2013
- Article first published online: 18 FEB 2013
- Accepted manuscript online: 21 NOV 2012 08:02AM EST
- Manuscript Accepted: 1 OCT 2012
- Manuscript Revised: 10 SEP 2012
- Manuscript Received: 12 JUN 2012
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Figure S1. Correct pArg site assignment from MSA-CID and ETD data from in vitro phosphorylation of ClpC by McsB.
Figure S2. Occurrence of dominant neutral loss of H3PO4 upon CID-MS/MS of peptides with pArg
Figure S3. A-D Neutral loss without OH-moieties for neutral loss. Interestingly, intact modification on b-ions is preserved starting from b7, which is the tyrosine residue, that might take part in the neutral loss formation instead of the C-terminus.
Figure S4. High-resolution orbitrap-ETD MS/MS spectrum of PepR_01
Figure S5. Formation of neutral loss species at different activation parameters
Figure S6. CID-MS3 spectra of PepR_04 (pHis) and PepR_05 (pSer) and corresponding y-ion distributions
Figure S7. Ambiguous Phospho-Site Localization of CID-Data
Figure S8 A. Chemically different OH-moieties serve as phospho-acceptors for gas phase rearrangement. Figure S8B CID-MS3-y-ion distribution. Figure S8C Annotated CID-MS3 spectra of peptides PepR_10 to PepR_14
Figure S9. The amidated C-terminus of Pep_11 and Glu12 on Peptide PEP_13 act as phospho-acceptor site under CID conditions.
Figure S10. HCD spectra of PEP_01 and PEP_05
Table TS1. Phosphopeptides of McsB and CtsR resulting from five different enzymatic cleavages.
Table S2. Charge state dependency of phospho-site localization by phosphoRS from CID, MSA-CID, HCD and ETD-MS/MS data for 1% FDR and 2% FDR on the peptide spectrum match level
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