Enhancing TOF/TOF-based de Novo Sequencing Capability for High Throughput Protein Identification with Amino Acid-Coded Mass Tagging

peer-reviewed · Journal of Proteome Research · 2005

peer-reviewed · Journal of Proteome Research · 2005. Wenqing Shui et al. Because of the intrinsic physical properties of single- or double-charged ions, MALDI-based CID on these…

Date	2005-02-01
Type	peer-reviewed
Venue	Journal of Proteome Research
Publisher	American Chemical Society (ACS)
Contribution	algorithm
DOI	10.1021/pr049850u
Citations (OpenAlex)	19
Venue 2-year citedness	3.83

Abstract

Because of the intrinsic physical properties of single- or double-charged ions, MALDI-based CID on these peptide precursor ions tends to be incomplete, resulting in a large number of MS/MS spectra unassigned or ambiguously identified. Consequently, the TOF/TOF high throughput capability may not be fully explored and utilized. Here, we describe a novel method for de novo sequence assignment of those MALDI TOF/TOF MS/MS spectra with incomplete or weak fragment ion series. In this approach, the deuterium-labeled lysine and leucine precursors were used in parallel to mass-tag the proteome of a metastatic human hepatocellular carcinoma (HCC) cell line during in vivo cell culturing. These stable isotope precursor markers not only position at terminal but at internal MS/MS fragment ions with the characteristic isotope pattern induced by multiple mass tagging in parallel. This enhanced signal specificity evidently resolved ambiguities in those sparse poor-quality TOF/TOF spectra by providing critical sequential links among MS/MS fragment ions. Our data-dependent approach was able to reduce many false-positives in current genome sequence-based peptide sequencing. With developing new algorithms accordingly, our approach is amenable for automation that will lead to more comprehensive and reliable identification for proteomes.

Authors

1. Wenqing Shui · Fudan University, Los Alamos National Laboratory
2. Yinkun Liu · Fudan University, Los Alamos National Laboratory
3. Huizhi Fan · Fudan University, Los Alamos National Laboratory
4. Huimin Bao · Fudan University, Los Alamos National Laboratory
5. Shufang Liang · Fudan University, Los Alamos National Laboratory
6. Pengyuan Yang · Fudan University, Los Alamos National Laboratory
7. Xian Chen · Los Alamos National Laboratory

Methods and tools

• Amino acid-coded mass tagging: Codes amino acids by mass before MALDI TOF/TOF so that incomplete CID of singly and doubly charged precursors still yields assignable series, recovering spectra that would otherwise go unidentified and making the instrument’s throughput usable for de novo work.

Cites (5)

• De novo sequencing of peptides using MALDI/TOF-TOF (2002) crossref
• De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging (2002) crossref
• Derivatization procedures to facilitate de novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry (2000) crossref
• Quantitation and Facilitated de Novo Sequencing of Proteins by Isotopic N-Terminal Labeling of Peptides with a Fragmentation-Directing Moiety (2000) crossref
• Rapid de novo peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer (1997) crossref

Cited by (2)

• De novo sequencing of peptides by MS/MS (2010) crossref
• De novo peptide sequencing using exhaustive enumeration of peptide composition (2006) crossref

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