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Comparison of data analysis parameters and MS/MS fragmentation techniques for quantitative proteome analysis using isobaric peptide termini labeling (IPTL)

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Abstract

Isobaric peptide termini labeling (IPTL) is a quantification method which permits relative quantification using quantification points distributed throughout the whole tandem mass spectrometry (MS/MS) spectrum. It is based on the complementary derivatization of peptide termini with different isotopes resulting in isobaric peptides. Here, we use our recently developed software package IsobariQ to investigate how processing and data analysis parameters can improve IPTL data. Deisotoping provided cleaner MS/MS spectra and improved protein identification and quantification. Denoising should be used with caution because it may remove highly regulated ion pairs. An outlier detection algorithm on the ratios within every individual MS/MS spectrum was beneficial in removing false-positive quantification points. MS/MS spectra using IPTL typically contain two peptide series with complementary labels resulting in lower Mascot ion scores than non-labeled equivalent peptides. To avoid this penalty, the two chemical modifications for IPTL were specified as variables including satellite neutral losses of tetradeuterium with positive loss for the heavy isotopes and negative loss for the light isotopes. Thus, the less dominant complementary ion series were not considered for the scoring, which improved the ion scores significantly. In addition, we showed that IPTL was suitable for fragmentation by electron transfer dissociation (ETD) and higher energy collisionally activated dissociation (HCD) besides the already reported collision-induced dissociation (CID). Notably, ETD and HCD data can be identified and quantified using IsobariQ. ETD outperformed CID and HCD only for charge states ≥4+ but yielded in total fewer protein identifications and quantifications. In contrast, the high-resolution information of HCD fragmented peptides provided most identification and quantification results using the same scan speed.

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Abbreviations

CID:

Collision-induced dissociation

ETD:

Electron transfer dissociation

HCD:

Higher energy collisionally activated dissociation

ICAT:

Isotope-coded affinity tagging

ICPL:

Isotope-coded protein labeling

IPTL:

Isobaric peptide termini labeling

iTRAQ:

Isobaric tagging for relative and absolute quantification

LC:

Liquid chromatography

MS:

Mass spectrometry

MS/MS:

Tandem mass spectrometry

SILAC:

Stable isotope labeling with amino acid in cell culture

STLC:

S-Trityl-l-cysteine

TMT:

Tandem mass tagging

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Acknowledgments

We would like to thank Yue Xuan (Thermo Fisher Scientific, Bremen, Germany) and Olav Mjaavatten and Frode Berven (PROBE, Bergen, Norway) for performing the measurements on their LTQ-Orbitrap Velos Pro instruments.

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Authors and Affiliations

  1. The Biotechnology Centre of Oslo, University of Oslo, 0317, Oslo, Norway

    Christian J. Koehler, Magnus Ø. Arntzen & Bernd Thiede

  2. NEPAF, Devonshire Building, Newcastle upon Tyne, NE1 7RU, UK

    Achim Treumann

Authors
  1. Christian J. Koehler
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  2. Magnus Ø. Arntzen
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  3. Achim Treumann
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  4. Bernd Thiede
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Corresponding author

Correspondence to Bernd Thiede.

Additional information

Christian J. Koehler and Magnus Ø. Arntzen contributed equally to this work.

Published in the topical issue Quantitative Mass Spectrometry in Proteomics with guest editors Bernhard Kuster and Marcus Bantscheff.

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Koehler, C.J., Arntzen, M.Ø., Treumann, A. et al. Comparison of data analysis parameters and MS/MS fragmentation techniques for quantitative proteome analysis using isobaric peptide termini labeling (IPTL). Anal Bioanal Chem 404, 1103–1114 (2012). https://doi.org/10.1007/s00216-012-5949-z

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