Chemical labeling assisted
20 methods · 1997–2024
Chemical labeling assisted: Isotopic or mass-coded labels introduced before the mass spectrometer, so one ion series can be told from the other by a known mass shift instead of by inference. The problem is eased in the sample, not the algorithm.
Isotopic or mass-coded labels introduced before the mass spectrometer, so one ion series can be told from the other by a known mass shift instead of by inference. The problem is eased in the sample, not the algorithm.
The earliest of its 20 methods is Rapid QTOF de novo sequencing (1997); 19 more have followed.
| Methods | 20 |
| Papers describing them | 24 |
| Authors | 104 |
| Active | 1997-06-15 to 2024-10-22 |
| Kinds | adjacent (17), algorithm (3) |
| Acquisition | DDA (20) |
Methods (20)
Oldest first, by the paper that describes each one.
- Rapid QTOF de novo sequencing (1997): Nanoelectrospray, isotopic-labeling, and quadrupole/time-of-flight workflow for rapid de novo peptide sequencing.
- 18O ion trap de novo sequencing (1998): Ion-trap de novo peptide sequencing method using 18O labeling to distinguish fragment ion series.
- Isotopic N-terminal labeling de novo sequencing (2000): Isotopic N-terminal labeling with a fragmentation-directing moiety for protein quantitation and facilitated de novo sequencing.
- Differential methyl esterification labeling (2001): Labels peptide carboxyl groups with d0- or d3-methanol so that mixed samples give quantitation and isotope-paired fragment ions that support automated de novo sequencing.
- MCAT (2002): Mass-coded abundance tagging strategy for de novo peptide sequencing and quantitative profiling of complex protein mixtures.
- Amino acid-coded mass tagging (2002): 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.
- 15N-labeled 2D mass spectra (2004): Overlays spectra of 15N-labeled and unlabeled peptides so each ion carries its nitrogen count, adding discriminating power for identification and de novo interpretation.
- Isotope-coded N-terminal sulfonation (ICenS) (2004): Labels peptides with light or 13C6 heavy 4-sulfophenyl isothiocyanate so the same derivatization yields y-ion dominated spectra for de novo sequencing and isotope pairs for quantification.
- Dual-labeling (guanidination/amidination) de novo sequencing (2005): Derivatizes peptides by guanidination and amidination so mass-coded labels distinguish N- and C-terminal fragment ions and promote informative fragmentation for de novo sequencing.
- Reductive methylation de novo sequencing (2005): Reductive isotopic methylation strategy for de novo sequencing of neuropeptides.
- Validator (18O pair picking) (2009): Finds 16O/18O-labeled peptide pairs and compares their fragmentation, validating Mascot results and, in Validator 3, deriving peptides from labeled y-ion pairs independently of the search engine.
- Dimethyl isotope labeling de novo sequencing (2010): Dimethyl isotope labeling-assisted workflow for de novo peptide sequencing.
- Asp-Pro linker 18O OBOC peptide sequencing (2012): Releases one-bead-one-compound hexapeptides through an acid-labile Asp-Pro linker in partly 18O water, so N- and C-terminal ions can be told apart during de novo sequencing.
- Stable isotope N-phosphorylation labeling (SIPL) (2012): Labels peptide N-termini and lysines with light or heavy phosphoryl groups in a one-pot reaction, improving ionization, strengthening fragment series and giving isotope signatures that ease de novo sequencing and relative quantification.
- NeuCode y-ion annotation (2013): Two lysine isotopologues differing by 36 mDa are embedded metabolically, so every C-terminal fragment appears as a resolvable doublet and N-terminal ones do not. An algorithm reads that signature to label y-type ions at 93.2% accuracy, which among other uses lifts correct de novo identifications with PepNovo+ by 34%.
- Simplified 18O labeling de novo sequencing (2014): Adds H2 18O and trypsin directly to the digest so 18O is incorporated at peptide C-termini, marking y-ions to ease de novo sequencing without extra drying steps.
- Isotopic differentiation protocol (IDP) (2015): Forms light and deuterated methyl esters at the C-terminus or acetamides at the N-terminus so that mass shifts between isotopologues pick out C- and N-terminal ion series for de novo sequencing.
- NIPTL-Novo (2017): Non-isobaric peptide termini labeling assisted peptide de novo sequencing.
- Mirror-image trypsin D-protein sequencing (2024): A chemically synthesized D-trypsin digests mirror-image proteins into peptides that can be sequenced by LC-MS/MS, used to sequence D-proteins and read data stored in a long D-peptide.
- R-met C-terminal labeling de novo sequencing (2024): Labels the peptide C-terminus and Asp/Glu carboxyl groups with arginine methyl ester so non-tryptic peptides fragment well, and EThcD then resolves isobaric ambiguities for bottom-up de novo protein sequencing.
Papers describing them (24)
- Rapid de novo peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer (1997, Rapid Communications in Mass Spectrometry, peer-reviewed)
- De novo peptide sequencing in an ion trap mass spectrometer with 18O labeling (1998, Rapid Communications in Mass Spectrometry, peer-reviewed)
- Quantitation and Facilitated de Novo Sequencing of Proteins by Isotopic N-Terminal Labeling of Peptides with a Fragmentation-Directing Moiety (2000, Analytical Chemistry, peer-reviewed)
- Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation (2001, Rapid Communications in Mass Spectrometry, peer-reviewed)
- De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging (2002, Nature Biotechnology, peer-reviewed)
- Use of Deuterium-Labeled Lysine for Efficient Protein Identification and Peptide de Novo Sequencing (2002, Analytical Chemistry, peer-reviewed)
- Precise peptide sequencing and protein quantification in the human proteome through in vivo lysine-specific mass tagging (2003, Journal of the American Society for Mass Spectrometry, peer-reviewed)
- De Novo Peptide Sequencing by Nanoelectrospray Tandem Mass Spectrometry Using Triple Quadrupole and Quadrupole/Time-of-Flight Instruments (2003, Mass Spectrometry of Proteins and Peptides, peer-reviewed)
- “De Novo” Sequencing of Peptides Recovered from In-Gel Digested Proteins by Nanoelectrospray Tandem Mass Spectrometry (2003, Molecular Biotechnology, peer-reviewed)
- Two-Dimensional Mass Spectra Generated from the Analysis of 15N-Labeled and Unlabeled Peptides for Efficient Protein Identification and de novo Peptide Sequencing (2004, Journal of Proteome Research, peer-reviewed)
- Isotope‐coded N‐terminal sulfonation of peptides allows quantitative proteomic analysis with increased de novo peptide sequencing capability (2004, Rapid Communications in Mass Spectrometry, peer-reviewed)
- Enhancing TOF/TOF-based de Novo Sequencing Capability for High Throughput Protein Identification with Amino Acid-Coded Mass Tagging (2005, Journal of Proteome Research, peer-reviewed)
- Peptide de Novo Sequencing Facilitated by a Dual-Labeling Strategy (2005, Analytical Chemistry, peer-reviewed)
- De Novo Sequencing of Neuropeptides Using Reductive Isotopic Methylation and Investigation of ESI QTOF MS/MS Fragmentation Pattern of Neuropeptides with N-Terminal Dimethylation (2005, Analytical Chemistry, peer-reviewed)
- Rapid Validation of Mascot Search Results via Stable Isotope Labeling, Pair Picking, and Deconvolution of Fragmentation Patterns (2009, Molecular & Cellular Proteomics, peer-reviewed)
- Dimethyl isotope labeling assisted de novo peptide sequencing (2010, Journal of the American Society for Mass Spectrometry, peer-reviewed)
- Introducing an Asp-Pro Linker in the Synthesis of Random One-Bead-One-Compound Hexapeptide Libraries Compatible with ESI-MS Analysis (2012, ACS Combinatorial Science, peer-reviewed)
- Stable Isotope N-Phosphorylation Labeling for Peptide de Novo Sequencing and Protein Quantification Based on Organic Phosphorus Chemistry (2012, Analytical Chemistry, peer-reviewed)
- Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra (2013, Molecular & Cellular Proteomics, peer-reviewed)
- A Simplified Method for Peptide De Novo Sequencing Using 18 O Labeling (2014, European Journal of Mass Spectrometry, peer-reviewed)
- Isotopic Differentiation Protocol, a Selective Extraction of C- and N-Terminal Ions in ESI-Ms/Ms De Novo Peptide Sequencing (2015, Natural Products Chemistry & Research, peer-reviewed)
- NIPTL-Novo: Non-isobaric peptide termini labeling assisted peptide de novo sequencing (2017, Journal of Proteomics, peer-reviewed)
- Mirror-image trypsin digestion and sequencing of D-proteins (2024, Nature Chemistry, peer-reviewed)
- Enhancing De Novo Protein Sequencing through the C-Terminal Labeling Strategy: Resolving Isobaric Ambiguities by Electron-Transfer/Higher Energy Collision Dissociation (EThcD) (2024, Analytical Chemistry, peer-reviewed)