Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry

@article{Zhang2003IdentificationAQ,
  title={Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry},
  author={Hui Zhang and Xiao-Jun Li and Daniel B. Martin and Ruedi Aebersold},
  journal={Nature Biotechnology},
  year={2003},
  volume={21},
  pages={660-666}
}
Quantitative proteome profiling using stable isotope protein tagging and automated tandem mass spectrometry (MS/MS) is an emerging technology with great potential for the functional analysis of biological systems and for the detection of clinical diagnostic or prognostic marker proteins. Owing to the enormous complexity of proteomes, their comprehensive analysis is an as-yet-unresolved technical challenge. However, biologically or clinically important information can be obtained if specific… 
Chemical methods for glycoprotein discovery.
Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site–specific stable isotope tagging
TLDR
A protocol for isotope-coded glycosylation site–specific tagging (IGOT), a method for the large-scale identification of N-linked glycoproteins from complex biological samples, is described here.
Stable isotope labeling of N-glycosylated peptides by enzymatic deglycosylation for mass spectrometry-based glycoproteomics.
TLDR
A protocol for peptide-N-glycanase-mediated (18)O labeling of N-glycosylated peptides, termed "isotope-coded glycosylation site-specific tagging," is described, which facilitates the identification of hundreds to thousands of N -glycoproteins, coupled with their sites of gly cosylation, from a complex biological mixture.
Targeting the human glycoproteome New enrichment protocols and mass spectrometric analyses reveal unique and novel glycosylation sites
TLDR
A targeted O-glycoproteomics approach was developed, allowing for sequence analysis of preferred O- glycosylation sites of glycoproteins, and the applicability of the sialic acid capture-and-release strategy was further demonstrated for human urine, a technically more challenging biological fluid.
Analysis of N-glycoproteins using genomic N-glycosite prediction.
TLDR
The results showed that over three times the quantity of N-deglycopeptide assignments from the same mass spectrometry data could be produced in ovarian cancer cell lines compared to a MS/MS fragmentation method.
Mass spectrometry–based detection and quantification of plasma glycoproteins using selective reaction monitoring
TLDR
The present protocol includes the development and optimization of SRM assays associated with each peptide of interest and the qualification of assays in the biological matrix to establish the limits of detection and quantification.
Modification-Specific Proteomic Analysis of Glycoproteins in Human Body Fluids by Mass Spectrometry
TLDR
This chapter describes some general strategies for the enrichment of glycoproteins and glycopeptides with an emphasis on proteomic analysis of N-glycosylated proteins in body fluids and other complex samples.
Multiplexed Targeted Mass Spectrometry-Based Assays for the Quantification of N-Linked Glycosite-Containing Peptides in Serum.
TLDR
It is shown that 43 selected N-linked glycosite-containing peptides identified in prostate cancer tissue studies carried out in the authors' group were detected in the sera of prostate cancer patients within the quantitative range of the developed PRM assays, demonstrating that the assays can be used for the high throughput and reproducible quantification of a panel of formerly N- linked glycosite - containing peptides.
Quantitative glycomics using liquid phase separations coupled to mass spectrometry.
TLDR
A critical review of analytical quantitation approaches using liquid phase separations coupled to mass spectrometry for released glycans of biopharmaceutical and biomedical significance is presented.
Solid-phase extraction of N-linked glycopeptides
TLDR
A protocol for solid-phase extraction of N-linked glycopeptides and subsequent identification of N -linked glycosylation sites (N-glycosites) by tandem mass spectrometry is described.
...
...

References

SHOWING 1-10 OF 51 REFERENCES
Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
TLDR
The method and the new software tools to support it are well suited to the large-scale, quantitative analysis of membrane proteins and other classes of proteins that have been refractory to standard proteomics technology.
Simplification of complex peptide mixtures for proteomic analysis: Reversible biotinylation of cysteinyl peptides
TLDR
An affinity selection method to capture cysteinyl peptides and thereby simplify the mixture and was applied to the analysis of a protein fraction obtained from isolated mitochondria treated with atractyloside.
Abundance ratio-dependent proteomic analysis by mass spectrometry.
TLDR
A novel approach to quantitative proteomics is described, based on a highly accurate algorithm for the automated quantification of chromatographically fractionated, isotope-coded affinity-tagged peptides and MALDI quadrupole time-of-flight tandem mass spectrometry for their identification.
Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer.
TLDR
The effectiveness of this approach is demonstrated in the quantification and identification of peptides from a control mixture of proteins of known relative concentrations and also in the comparative analysis of protein expression in Saccharomyces cerevisiae grown on two different carbon sources.
Proteome analysis using selective incorporation of isotopically labeled amino acids
Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome
TLDR
A method for enriching phosphoserine/threonine-containing proteins from crude cell extracts and for subsequently identifying the phosphoproteins and sites of phosphorylation is described, which involves chemical replacement of the phosphate moieties by affinity tags and should be of widespread utility for defining signaling pathways and control mechanisms that involve phosphorylated or dephosphorylation of serine/Threonine residues.
Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype
TLDR
Results indicate that activity-based probes compatible with whole-proteome analysis can be developed for numerous enzyme classes and applied to identify enzymes associated with discrete pathological states.
Direct analysis of protein complexes using mass spectrometry
We describe a rapid, sensitive process for comprehensively identifying proteins in macromolecular complexes that uses multidimensional liquid chromatography (LC) and tandem mass spectrometry (MS/MS)
Accurate quantitation of protein expression and site-specific phosphorylation.
TLDR
The present method is general and affords a quantitative description of cellular differences at the level of protein expression and modification, thus providing information that is critical to the understanding of complex biological phenomena.
Approaching complete peroxisome characterization by gas‐phase fractionation
TLDR
The utility of gas‐phase fractionation in the m/z dimension to increase proteome coverage and reproducibility of peptide ion selection by direct microliquid chromatography/electrospray ionization‐tandem mass spectrometry is examined and the two types of GPF are proposed as GPFm/z and GPFRI.
...
...