NDLI: Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation

Content Provider	PubMed Central
Author	Brown, Robert Stuart, Scott A. Houel, Stephane Ahn, Natalie G. Old, William M.
Abstract	Collision-induced dissociation (CID) remains the predominant mass spectrometry based method for identifying phosphorylation sites in complex mixtures. Unfortunately, the gas-phase reactivity of phosphoester bonds results in MS/MS spectra dominated by phosphoric acid (H3PO4) neutral loss events, suppressing informative peptide backbone cleavages. To understand the major drivers of H3PO4 neutral loss, we performed robust non-parametric statistical analysis of local and distal sequence effects on the magnitude and variability of neutral loss, using a collection of over 35,000 unique phosphopeptide MS/MS spectra. In contrast to peptide amide dissociation pathways, which are strongly influenced by adjacent amino acid side chains, we find that neutral loss of H3PO4 is affected by both proximal and distal sites, most notably basic residues and the peptide N-terminal primary amine. Previous studies have suggested that protonated basic residues catalyze neutral loss through direct interactions with the phosphate. In contrast, we find that nearby basic groups decrease neutral loss regardless of mobility class, an effect only seen by stratifying spectra by charge-mobility. The most inhibitory bases are those immediately N-terminal to the phosphate, presumably due to steric hindrances in catalyzing neutral loss. Further evidence of steric effects is shown by the presence of proline which can dramatically reduce the presence of neutral loss when between the phosphate and a possible charge donor. In mobile proton spectra the N-terminus is the strongest predictor of high neutral loss, with proximity to the N-terminus essential for peptides to exhibit the highest levels of neutral loss.
Related Links	http://dx.doi.org/10.1007/s13361-015-1109-y
Ending Page	1142
Page Count	15
Starting Page	1128
File Format	PDF
ISSN	10440305
e-ISSN	18791123
Journal	Journal of the American Society for Mass Spectrometry
Issue Number	7
Volume Number	26
Language	English
Publisher Date	2015-07-01
Access Restriction	Open
Subject Keyword	Spectroscopy Structural Biology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Spectroscopy Structural Biology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Erratum to: Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss During Collision Induced Dissociation

Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation

Erratum to: Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss During Collision Induced Dissociation

Surface-Induced Dissociation Shows Potential to be More Informative than Collision-Induced Dissociation for Structural Studies of Large Systems

Investigation of neutral loss during collision induced dissociation of peptide ions.

Electron Capture, Collision-Induced, and Electron Capture-Collision Induced Dissociation in Q-TOF

Peroxide Bond Driven Dissociation of Hydroperoxy-Cholesterol Esters Following Collision Induced Dissociation

Peptide Scrambling During Collision-Induced Dissociation is Influenced by N -terminal Residue Basicity

Surface-induced dissociation shows potential to be more informative than collision-induced dissociation for structural studies of large systems

Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation

Similar Documents

Erratum to: Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss During Collision Induced Dissociation

Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation

Erratum to: Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss During Collision Induced Dissociation

Surface-Induced Dissociation Shows Potential to be More Informative than Collision-Induced Dissociation for Structural Studies of Large Systems

Investigation of neutral loss during collision induced dissociation of peptide ions.

Electron Capture, Collision-Induced, and Electron Capture-Collision Induced Dissociation in Q-TOF

Peroxide Bond Driven Dissociation of Hydroperoxy-Cholesterol Esters Following Collision Induced Dissociation

Peptide Scrambling During Collision-Induced Dissociation is Influenced by N -terminal Residue Basicity

Surface-induced dissociation shows potential to be more informative than collision-induced dissociation for structural studies of large systems

Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation