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Analytical and Bioanalytical Chemistry

, Volume 396, Issue 3, pp 1223–1247 | Cite as

Precipitation and selective extraction of human serum endogenous peptides with analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides

  • Declan Williams
  • Suzanne Ackloo
  • Peihong Zhu
  • Peter Bowden
  • Kenneth R. Evans
  • Christina L. Addison
  • Chris Lock
  • John G. Marshall
Original Paper

Abstract

The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization and liquid chromatography–electrospray ionization–tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments. The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors, and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation. Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations, and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using the Paragon algorithm.

Keywords

Bioanalytical methods Mass spectrometry/ICP–MS Amino acids/peptides 

Abbreviations

AEBSF

4-(2-Aminoethyl) benzenesulfonyl fluoride

CBBR

Coomassie brilliant blue R-250

CHCA

α-Cyano-4-hydroxycinnamic acid

CID

Collision-induced dissociation

Da

Dalton

DEAE

Diethylaminoethyl

DTT

Dithiothreitol

ESI

Electrospray ionization

GPM

Global proteome machine

ITIH4

Inter-alpha (globulin) inhibitor H4

MALDI

Matrix-assisted laser desorption/ionization

MS

Mass spectrometry

MS/MS

Tandem mass spectrometry

PBS

Phosphate-buffered saline

NCBI

National Center for Biotechnology Information

PPM

Part per million

PMSF

Phenylmethanesulfonyl fluoride

Qq-TOF

Quadrupole-quadrupole time of flight

RCF

Relative centrifugal force

SDS-PAGE

Sodium dodecyl sulfate polyacrylamide gel electrophoresis

TFE

Trifluoroethanol

Tris

Tris(hydroxymethyl)aminomethane

Supplementary material

216_2009_3345_MOESM1_ESM.pdf (383 kb)
ESM 1 Precipitation and selective extraction of human serum endogenous peptides analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides (PDF 383 kb)

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Declan Williams
    • 1
  • Suzanne Ackloo
    • 2
    • 3
  • Peihong Zhu
    • 3
  • Peter Bowden
    • 1
  • Kenneth R. Evans
    • 3
  • Christina L. Addison
    • 4
  • Chris Lock
    • 2
  • John G. Marshall
    • 1
    • 3
  1. 1.Department of Chemistry and Biology, Faculty of Engineering and Applied ScienceRyerson UniversityTorontoCanada
  2. 2.MDS Analytical TechnologiesConcordCanada
  3. 3.Ontario Cancer Biomarker Network (OCBN)TorontoCanada
  4. 4.Cancer TherapeuticsOttawa Health Research InstituteOttawaCanada

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