Ionisation bias undermines the use of matrix-assisted laser desorption/ionisation for estimating peptide deamidation: synthetic peptide studies demonstrate electrospray ionisation gives more reliable response ratios

TY - JOUR

T1 - Ionisation bias undermines the use of matrix-assisted laser desorption/ionisation for estimating peptide deamidation

T2 - synthetic peptide studies demonstrate electrospray ionisation gives more reliable response ratios

AU - Simpson, Joanna P.

AU - Fascione, Martin

AU - Bergström, Ed

AU - Wilson, Julie

AU - Collins, Matthew J.

AU - Penkman, Kirsty E.H.

AU - Thomas-Oates, Jane

PY - 2019

Y1 - 2019

N2 - Rationale: Although mass spectrometry (MS) is routinely used to determine deamination in peptide mixtures, the effects of the choice of ionisation source have not yet been investigated. In particular, matrix-assisted laser desorption/ionisation (MALDI) has become a popular tool with which to measure levels of glutamine deamidation in ancient proteins. Here we use model synthetic peptides to rigorously compare MALDI and electrospray ionisation (ESI). Methods: We used two synthetic peptides, with glutamine (Q) in one substituted for glutamic acid (E) in the other, to investigate the suitability of MALDI and ESI sources for the assessment of deamidation in peptides using MS. We also compared measurements of the same Q- and E-containing peptide mixtures using two different mass analysers (time-of-flight (TOF) and Fourier transform ion cyclotron resonance (FT-ICR)). Results: When standard mixtures of the Q- and E-containing peptides were analysed using MALDI, under-representation of the E-containing peptide was observed. This observation was consistent between analyses carried out using either TOF or FT-ICR-MS. When the same mixtures were analysed using ESI FT-ICR-MS, no ionisation bias was observed. Conclusions: MALDI may not be a suitable ionisation method for the determination of deamidation in peptide mixtures. However, ESI was successfully used to determine the ratio in known mixtures of Q- and E-containing peptides. These preliminary observations warrant further investigation into ionisation bias when measuring deamidation in other peptide sequences.

AB - Rationale: Although mass spectrometry (MS) is routinely used to determine deamination in peptide mixtures, the effects of the choice of ionisation source have not yet been investigated. In particular, matrix-assisted laser desorption/ionisation (MALDI) has become a popular tool with which to measure levels of glutamine deamidation in ancient proteins. Here we use model synthetic peptides to rigorously compare MALDI and electrospray ionisation (ESI). Methods: We used two synthetic peptides, with glutamine (Q) in one substituted for glutamic acid (E) in the other, to investigate the suitability of MALDI and ESI sources for the assessment of deamidation in peptides using MS. We also compared measurements of the same Q- and E-containing peptide mixtures using two different mass analysers (time-of-flight (TOF) and Fourier transform ion cyclotron resonance (FT-ICR)). Results: When standard mixtures of the Q- and E-containing peptides were analysed using MALDI, under-representation of the E-containing peptide was observed. This observation was consistent between analyses carried out using either TOF or FT-ICR-MS. When the same mixtures were analysed using ESI FT-ICR-MS, no ionisation bias was observed. Conclusions: MALDI may not be a suitable ionisation method for the determination of deamidation in peptide mixtures. However, ESI was successfully used to determine the ratio in known mixtures of Q- and E-containing peptides. These preliminary observations warrant further investigation into ionisation bias when measuring deamidation in other peptide sequences.

U2 - 10.1002/rcm.8441

DO - 10.1002/rcm.8441

M3 - Journal article

C2 - 30908787

AN - SCOPUS:85066498192

SN - 0951-4198

VL - 33

SP - 1049

EP - 1057

JO - Rapid Communications in Mass Spectrometry

JF - Rapid Communications in Mass Spectrometry

IS - 12

ER -