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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

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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.

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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

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Author notes

  1. Suzanne Ackloo

    Present address: Ontario Cancer Biomarker Network (OCBN), 101 College Street, Toronto, ON, M5G 1L7, Canada

Authors and Affiliations

  1. Department of Chemistry and Biology, Faculty of Engineering and Applied Science, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada

    Declan Williams, Peter Bowden & John G. Marshall

  2. MDS Analytical Technologies, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada

    Suzanne Ackloo & Chris Lock

  3. Ontario Cancer Biomarker Network (OCBN), 101 College Street, Toronto, ON, M5G 1L7, Canada

    Peihong Zhu, Kenneth R. Evans & John G. Marshall

  4. Cancer Therapeutics, Ottawa Health Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada

    Christina L. Addison

Authors
  1. Declan Williams
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  2. Suzanne Ackloo
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  3. Peihong Zhu
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  4. Peter Bowden
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  8. John G. Marshall
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Correspondence to John G. Marshall.

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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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Williams, D., Ackloo, S., Zhu, P. et al. 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. Anal Bioanal Chem 396, 1223–1247 (2010). https://doi.org/10.1007/s00216-009-3345-0

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  • DOI: https://doi.org/10.1007/s00216-009-3345-0

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