In-Source Collision-Induced Dissociation (CID) Improves Higher-Energy Collisional Dissociation (HCD)-Dependent Fragmentation of ADP-Ribosyl Peptides

IF 1.8 3区化学 Q4 BIOCHEMICAL RESEARCH METHODS

Rapid Communications in Mass Spectrometry Pub Date : 2024-12-04 DOI:10.1002/rcm.9961

Taku Kasai, Yuto Nakamura, Masanori Aikawa, Sasha A. Singh

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引用次数: 0

Abstract

Rationale

ADP-ribosylation is a posttranslational modification whose higher-energy collisional dissociation (HCD) products are dominated by complete or partial modification losses, complicating peptide sequencing and acceptor site localization efforts. We tested whether in-source collision-induced dissociation (CID) performed on a quadrupole-Orbitrap could convert ADPr to the smaller phosphoribose-H₂O derivative to facilitate HCD-dependent peptide sequencing.

Methods

ADP-ribosyl (ADPr) peptides derived from the human macrophage-like cell line THP-1 were analyzed on a quadrupole-Orbitrap. We monitored the dissociation of ADPr (+ 541.061 Da) to phosphoribosyl-H₂O (+ 193.997 Da) peptides while varying the source and high-field asymmetric waveform ion mobility mass spectrometry (FAIMS) compensation voltages. Xcorr and ptmRS were used to evaluate peptide sequencing and acceptor site confidence, respectively. Phosphoribosyl-H₂O acceptor sites were compared with those determined by electron-transfer higher-energy collision dissociation (EThcD), performed on a quadrupole-ion trap-Orbitrap.

Results

In-source CID of ADPr peptides to their phosphoribosyl-H₂O derivatives increased with increasing source voltage (up to 50 V), as judged by monitoring the corresponding modification loss ([adenosine monophosphate/AMP]⁺) and the number of identified phosphoribosyl-H₂O peptide identifications. The average Xcorr increased from 1.36 (ADPr) to 2.26 (phosphoribosyl-H₂O), similar to that achieved with EThcD for ADPr peptides (2.29). The number of high-confidence acceptor sites (> 95%) also increased, from 31% (ADPr) to 70% (phosphoribosyl-H₂O), which was comparable to EThcD (70%).

Conclusions

In-source CID converts ADP-ribosyl to phosphoribosyl-H₂O peptides that are more amenable to HCD-dependent peptide sequencing, providing an alternative method for acceptor site determination when ETD-based methods are not available.

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来源期刊

Rapid Communications in Mass Spectrometry 化学-分析化学

CiteScore

4.10

自引率

5.00%

发文量

219

审稿时长

2.6 months

期刊介绍： Rapid Communications in Mass Spectrometry is a journal whose aim is the rapid publication of original research results and ideas on all aspects of the science of gas-phase ions; it covers all the associated scientific disciplines. There is no formal limit on paper length ("rapid" is not synonymous with "brief"), but papers should be of a length that is commensurate with the importance and complexity of the results being reported. Contributions may be theoretical or practical in nature; they may deal with methods, techniques and applications, or with the interpretation of results; they may cover any area in science that depends directly on measurements made upon gaseous ions or that is associated with such measurements.