Fragment ion analysis

14 methods · 2003–2026

Fragment ion analysis: Work on the fragment ions themselves before any sequence is proposed: charge state, isotope pattern and series assignment, which is what a sequencing algorithm downstream has to assume it already has.

Work on the fragment ions themselves before any sequence is proposed: charge state, isotope pattern and series assignment, which is what a sequencing algorithm downstream has to assume it already has.

The earliest of its 14 methods is Hot ECD w-ion Leu/Ile discrimination (2003); 13 more have followed.

Methods 14
Papers describing them 14
Authors 47
Active 2003-06-01 to 2026-01-27
Kinds adjacent (11), algorithm (3)
Acquisition DDA (13)

Methods (14)

Oldest first, by the paper that describes each one.

  • Hot ECD w-ion Leu/Ile discrimination (2003): Uses secondary side-chain losses in hot electron capture dissociation, formed through a gamma-lactam ring, to tell isoleucine from leucine, which ordinary de novo sequencing cannot do.
  • c1 ions from Gln-containing peptides (2004): Shows that peptides with glutamine at position two give an abundant c1 ion under low-energy CID, which helps assign the N-terminal two residues during de novo sequencing.
  • Neutral-loss specificity for de novo (2007): Shows from 20,000 high-resolution spectra that ammonia loss from b ions reliably flags Q, N, H, K and R, a constraint for de novo sequencing.
  • PFIA (2007): Peptide Fragment Ion Analyser for interpreting tandem MS data and de novo peptide sequencing.
  • Ion trap spectrum sequence information analysis (2008): Measures from 400,000 identified spectra how many complementary b/y ions and how much sequence an LTQ spectrum carries for de novo sequencing.
  • PXleS (2014): Predictor for Xle Sites: combines leucine aminopeptidase and chymotrypsin selectivity experiments with germline frequencies in a logistic regression that calls Leu or Ile at ambiguous sites in de novo sequenced mAbs, at 96% accuracy.
  • MS3 w-ion Leu/Ile discrimination (2014): Separates the isomeric residues leucine and isoleucine during de novo sequencing by instrument rather than by inference: multistage ETD isolates the primary odd-electron z-dot ions and HCD then drives radical-site fragmentation into w-ions, whose masses differ between the two isomers and which come out as the most intense peaks in the spectrum. Demonstrated on six natural non-tryptic peptides of 15 to 37 residues from Rana ridibunda frog skin secretion, resolving all 22 Leu/Ile positions.
  • CID vs HCD for natural peptide de novo (2014): Compares low-energy CID and HCD for de novo sequencing of natural non-tryptic peptides with disulfide bonds and proline residues.
  • Nanoflow LCMSn Leu/Ile discrimination (2017): Uses multistage fragmentation on nanoflow LC to distinguish leucine from isoleucine in mAb peptides online, for de novo antibody sequencing.
  • Adjacent y-ion intensity-ratio scoring feature (2017): A scoring feature from intensity ratios of adjacent y-ions, learned from the NIST library, that improved Novor and X!Tandem.
  • Hydrogen atom attachment phosphopeptide sequencing (2018): Radical fragmentation by hydrogen atom attachment on a MALDI instrument, which keeps the labile phosphate in place while cleaving the backbone, so tryptic phosphopeptides can be sequenced de novo and their phosphosites located.
  • Sodiated amide peptide dissociation (2020): Studies how sodiated C-terminally amidated peptides fragment under CID and PSD, as a basis for de novo sequencing of small natural peptides.
  • Continuous digestion MS3 Leu/Ile discrimination (2022): Combines continuous enzymatic digestion, to expose Leu/Ile at peptide N-termini, with a combined verification score over multiple MS3 spectra, resolving 67 of 68 Leu/Ile sites in trastuzumab.
  • Log-transformed mass domain de novo sequencing (2026): Bypasses averagine-based deconvolution by working directly in natural log-transformed m/z space, where charge-state spacing is mass-invariant and therefore supplies an intrinsic internal-calibration reference on both FT-ICR and Orbitrap. Isotopologue pairing in that domain then supports de novo sequencing of intact proteins.

Papers describing them (14)

Authors (47)

Albert T. Lebedev, Alexander Makarov, Chao Yang, Chloe N. Poston, Christine Enjalbal, Daiki Asakawa, Dhanashri Bagal, Eddie Kast, Egor A. Vorontsov, Elodie Logerot, Eugen Damoc, Frank Kjeldsen, Hidenori Takahashi, Jagannath Swaminathan, Jesus A. Gutierrez, Jianhui Liu, Jinsam You, John E. Hale, Jürgen Cox, Koichi Tanaka, Konstantin A. Artemenko, Krishna Saketh Kamadana, Lihua Zhang, Lissa C. Anderson, Matthias Mann, Michael D. Knierman, Michael L. Nielsen, Mikhail M. Savitski, Nathan K. Kaiser, Nina C. Hubner, Ping Cao, Richard E. Higgs, Robert Siegel, Roman A. Zubarev, Shinichi Iwamoto, Tatiana Yu. Samgina, Tiancong Wang, Valentina Gelfanova, Varatharajan Sabareesh, Vladimir Gorshkov, Weijie Zhang, Xian Mallory, Yichu Shan, Young Jin Lee, Young Moo Lee, Yukui Zhang, Zhen Liang

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