CoChat
Sign Up
Cited by 41Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsClinical Laboratory Practices and Quality Control

Simultaneous Phenotyping and Quantification of α-1-Antitrypsin by Liquid Chromatography–Tandem Mass Spectrometry

Open access
Chen, Yuhong, Snyder, Melissa R, Zhu, Yi, Tostrud, Linda J, Benson, Linda M, Katzmann, Jerry A, Bergen, H Robert·2011·Clinical Chemistry
DOI 10.1373/clinchem.2011.163006PMC PMC3275912
Open this paper in CoChat — free account

Abstract

BACKGROUND: α-1-Antitrypsin (A1AT) deficiency results from a genetic disorder at 2 common loci. Diagnosis requires quantification of A1AT and subsequent identification of the specific variant. The current algorithm of laboratory testing for the diagnosis of A1AT deficiency uses a combination of quantification (nephelometry), genotyping, and/or phenotyping. We developed a multiple reaction monitoring liquid chromatography–tandem mass spectrometry (LC-MS/MS) method for simultaneous quantification of A1AT and identification of the 2 most common deficiency alleles present in 95% of the patients with A1AT deficiency. METHODS: Serum samples (n = 40) were digested with trypsin, and appropriate 13C/15N-labeled standard peptides were added. We performed LC-MS/MS analysis with a 0.5- by 150-mm C18 column and H2O:acetonitrile:n-propanol:formic acid (A:98:1:1:0.2 and B:10:80:10:0.2; flow 12 μL/min) mobile phase in positive ion mode on a TSQ Quantum triple quadrupole MS system. We measured the A1AT concentration by comparison to a calibration curve and determined the phenotype by the presence or absence of variant peptides. We compared the results to the current phenotyping assay by isoelectric focusing (IEF) and the immunonephelometry quantitative assay. RESULTS: For A1AT allele detection, in 39 of 40 samples the LC-MS/MS results were identical to those obtained by IEF gel electrophoresis. The single discrepant result was rerun by IEF at a lower dilution, and the results were in concordance. The A1AT quantification by LC-MS/MS also compared favorably with nephelometry. CONCLUSIONS: The LC-MS/MS method correlates well with current phenotyping and nephelometric assays and has the potential to improve the laboratory diagnosis of genetic A1AT deficiency.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1373/clinchem.2011.163006

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • LC-MS/MS is suitable for highly multiplexed protein quantification and isoform differentiation, including apolipoproteins.

    “LC-MS/MS has proven suitable for multiplexed quantification and phenotyping of apolipoproteins.”

    From Automated multiplex LC-MS/MS assay for quantifying serum apolipoproteins A-I, B, C-I, C-II, C-III, and E with qualitative apolipoprotein E phenotyping (2016) · cites this paper as [12]

    The Discussion describes a multiplexed LC-MS/MS assay that simultaneously quantifies and phenotypes α-1-antitrypsin by detecting its S and Z variants. It does not demonstrate highly multiplexed quantification of multiple proteins or phenotyping of apolipoproteins. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 31

  1. [1]Lee WL Downey GP Leukocyte elastase: Physiological functions and role in acute lung injury Am J Respir Crit Care Med 2001 164 896 904 11549552
  2. [2]Carrell RW Cell toxicity and conformational disease Trends Cell Biol 2005 15 574 80 16202603
  3. [3]Carrell RW Lomas DA Alpha1-antitrypsin deficiency--a model for conformational diseases N Engl J Med 2002 346 45 53 11778003
  4. [4]Lomas DA Parfrey H Alpha1-antitrypsin deficiency. 4: Molecular pathophysiology Thorax 2004 59 529 35 15170041 PMC1747018
  5. [5]Perlmutter DH Joslin G Nelson P Schasteen C Adams SP Fallon RJ Endocytosis and degradation of alpha 1-antitrypsin-protease complexes is mediated by the serpin-enzyme complex (sec) receptor J Biol Chem 1990 265 16713 6 2211587
  6. [6]Brantly M Efficient and accurate approaches to the laboratory diagnosis of alpha1-antitrypsin deficiency: The promise of early diagnosis and intervention Clin Chem 2006 52 2180 1 17138849
  7. [7]Brantly M Nukiwa T Crystal RG Molecular basis of alpha-1-antitrypsin deficiency Am J Med 1988 84 13 31 3289385
  8. [8]Stoller JK Alpha1-antitrypsin deficiency Thorax 2004 59 92 3 14760142 PMC1746941
  9. [9]Curiel DT Chytil A Courtney M Crystal RG Serum alpha 1-antitrypsin deficiency associated with the common s-type (glu264----val) mutation results from intracellular degradation of alpha 1-antitrypsin prior to secretion J Biol Chem 1989 264 10477 86 2567291
  10. [10]Long GL Chandra T Woo SL Davie EW Kurachi K Complete sequence of the cdna for human alpha 1-antitrypsin and the gene for the s variant Biochemistry 1984 23 4828 37 6093867
  11. [11]Nukiwa T Satoh K Brantly ML Ogushi F Fells GA Courtney M Crystal RG Identification of a second mutation in the protein-coding sequence of the z type alpha 1-antitrypsin gene J Biol Chem 1986 261 15989 94 3491072
  12. [12]Lomas DA Evans DL Finch JT Carrell RW The mechanism of z alpha 1-antitrypsin accumulation in the liver Nature 1992 357 605 7 1608473
  13. [13]Needham M Stockley RA Alpha 1-antitrypsin deficiency. 3: Clinical manifestations and natural history Thorax 2004 59 441 5 15115878 PMC1746985
  14. [14]Roche D Mesner A Al Nakib M Leonard F Beaune P Automated determination of serum alpha1-antitrypsin by antitryptic activity measurement Clin Chem 2009 55 513 8 19168554
  15. [16]Kueppers F Determination of alpha1-antitrypsin phenotypes by isoelectric focusing in polyacrylamide gels J Lab Clin Med 1976 88 151 5 1084381
  16. [17]Braun A Meyer P Cleve H Roscher AA Rapid and simple diagnosis of the two common alpha 1-proteinase inhibitor deficiency alleles pi*z and pi*s by DNA analysis Eur J Clin Chem Clin Biochem 1996 34 761 4 8891530
  17. [18]von Ahsen N Oellerich M Schutz E Use of two reporter dyes without interference in a single-tube rapid-cycle pcr: Alpha(1)-antitrypsin genotyping by multiplex real-time fluorescence pcr with the lightcycler Clin Chem 2000 46 156 61 10657370
  18. [19]Snyder MR Katzmann JA Butz ML Wiley C Yang P Dawson DB Diagnosis of alpha-1-antitrypsin deficiency: An algorithm of quantification, genotyping, and phenotyping Clin Chem 2006 52 2236 42 17053153
  19. [20]Bergen HR 3rd Zeldenrust SR Butz ML Snow DS Dyck PJ Dyck PJ Identification of transthyretin variants by sequential proteomic and genomic analysis Clin Chem 2004 50 1544 52 15217993
  20. [21]Lacey JM Bergen HR Magera MJ Naylor S O'Brien JF Rapid determination of transferrin isoforms by immunoaffinity liquid chromatography and electrospray mass spectrometry Clin Chem 2001 47 513 8 11238305
  21. [22]Bondar OP Barnidge DR Klee EW Davis BJ Klee GG Lc-ms/ms quantification of zn-alpha2 glycoprotein: A potential serum biomarker for prostate cancer Clin Chem 2007 53 673 8 17317883
  22. [23]Carr SA Anderson L Protein quantitation through targeted mass spectrometry: The way out of biomarker purgatory? Clin Chem 2008 54 1749 52 18957555 PMC2848668
  23. [25]Hortin GL A new era in protein quantification in clinical laboratories: Application of liquid chromatography-tandem mass spectrometry Clin Chem 2007 53 543 4 17405946
  24. [26]Cox DW Scriver CR Beaudet AL Sly WS Valle D Alpha-1-antitrypsin deficiency Metabolic & molecular bases of inherited disease 3 New York, NY McGraw-Hill, Inc 1995 4125 58
  25. [27]Cowden DI Fisher GE Weeks RL A pilot study comparing the purity, functionality and isoform composition of alpha-1-proteinase inhibitor (human) products Curr Med Res Opin 2005 21 877 83 15969888
  26. [28]Bornhorst JA Procter M Meadows C Ashwood ER Mao R Evaluation of an integrative diagnostic algorithm for the identification of people at risk for alpha1-antitrypsin deficiency Am J Clin Pathol 2007 128 482 90 17709323
  27. [29]Mahadeva R Chang WS Dafforn TR Oakley DJ Foreman RC Calvin J Heteropolymerization of s, i, and z alpha1-antitrypsin and liver cirrhosis J Clin Invest 1999 103 999 1006 10194472 PMC408255
  28. [31]Siepen JA Keevil EJ Knight D Hubbard SJ Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics J Proteome Res 2007 6 399 408 17203985 PMC2664920
  29. [32]Yen CY Russell S Mendoza AM Meyer-Arendt K Sun S Cios KJ Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: Protease cleavage and scx elution rules from data mining of ms/ms spectra Anal Chem 2006 78 1071 84 16478097
  30. [33]Monigatti F Berndt P Algorithm for accurate similarity measurements of peptide mass fingerprints and its application J Am Soc Mass Spectrom 2005 16 13 21 15653359
  31. [34]Keil B Specificity of proteolysis New Your Springer-Verlag 1992

Cited by

Sorted by citations

Authors
Chen, Y., Snyder, M. R., Zhu, Y., Tostrud, L. J., Benson, L. M., Katzmann, J. A., & Bergen, H. R.
Affiliations
  • Division of Clinical Pharmacology, Department of Molecular and Experimental Therapeutics
  • Division of Clinical Biochemistry & Immunology, Department of Laboratory Medicine & Pathology
  • Mayo Proteomics Research Center, and
  • Mayo Clinic (US)
ORCID
Venue
Clinical Chemistry
Publisher
Oxford University Press (OUP)
Published
2011-08-01
Volume
57
Issue
8
Pages
1161-1168
ISSN
  • 0009-9147 (ISSN-L)
  • 1530-8561
DOI
10.1373/clinchem.2011.163006
PMC
PMC3275912
OpenAlex
W2169213915
Cited by
41
References
1
Citations by year
2025: 1 · 2023: 1 · 2022: 1 · 2021: 2 · 2020: 4 · 2019: 3 · 2018: 3 · 2017: 4 · 2016: 7 · 2015: 4 · 2014: 3 · 2013: 4 · 2012: 3
FWCI
1.51
Type
journal article
Language
en
Open access
Licence
academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
Locations
  • Clinical Chemistry (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • NIH (T32 GM08685)
  • Arlene Kogod Center on Aging
  • Noaber Foundation
  • Ted Nash Foundation
  • Mayo Clinic Research Committee
  • David Woods Kemper Memorial Foundation
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Health Sciences › Medicine › Physiology › Clinical Laboratory Practices and Quality Control
Keywords
alpha-1 antitrypsin deficiency, multiple reaction monitoring, isoelectric focusing, nephelometry, genetic variant identification, trypsin digestion
MeSH terms
Alleles, alpha 1-Antitrypsin, Chromatography, Liquid, Heterozygote, Homozygote, Humans, Immunoassay, Isoelectric Focusing, Nephelometry and Turbidimetry, Phenotype, alpha 1-Antitrypsin Deficiency, Tandem Mass Spectrometry

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review