TY - JOUR
T1 - Large-Scale Label-Free Quantitative Mapping of the Sputum Proteome
AU - The U-Biopred Study Group
AU - Burg, Dominic
AU - Schofield, James P. R.
AU - Brandsma, Joost
AU - Staykova, Doroteya
AU - Folisi, Caterina
AU - Bansal, Aruna
AU - Nicholas, Ben
AU - Xian, Yang
AU - Rowe, Anthony
AU - Corfield, Julie
AU - Wilson, Susan
AU - Ward, Jonathan
AU - Lutter, Rene
AU - Fleming, Louise
AU - Shaw, Dominick E.
AU - Bakke, Per S.
AU - Caruso, Massimo
AU - Dahlen, Sven-Erik
AU - Fowler, Stephen J.
AU - Hashimoto, Simone
AU - Horváth, Ildikó
AU - Howarth, Peter
AU - Krug, Norbert
AU - Montuschi, Paolo
AU - Sanak, Marek
AU - Sandström, Thomas
AU - Singer, Florian
AU - Sun, Kai
AU - Pandis, Ioannis
AU - Auffray, Charles
AU - Sousa, Ana R.
AU - Adcock, Ian M.
AU - Chung, Kian Fan
AU - Sterk, Peter J.
AU - Djukanović, Ratko
AU - Skipp, Paul J.
PY - 2018
Y1 - 2018
N2 - Analysis of induced sputum supernatant is a minimally invasive approach to study the epithelial lining fluid and, thereby, provide insight into normal lung biology and the pathobiology of lung diseases. We present here a novel proteomics approach to sputum analysis developed within the U-BIOPRED (unbiased biomarkers predictive of respiratory disease outcomes) international project. We present practical and analytical techniques to optimize the detection of robust biomarkers in proteomic studies. The normal sputum proteome was derived using data-independent HDMSE applied to 40 healthy nonsmoking participants, which provides an essential baseline from which to compare modulation of protein expression in respiratory diseases. The "core" sputum proteome (proteins detected in ≥40% of participants) was composed of 284 proteins, and the extended proteome (proteins detected in ≥3 participants) contained 1666 proteins. Quality control procedures were developed to optimize the accuracy and consistency of measurement of sputum proteins and analyze the distribution of sputum proteins in the healthy population. The analysis showed that quantitation of proteins by HDMSE is influenced by several factors, with some proteins being measured in all participants' samples and with low measurement variance between samples from the same patient. The measurement of some proteins is highly variable between repeat analyses, susceptible to sample processing effects, or difficult to accurately quantify by mass spectrometry. Other proteins show high interindividual variance. We also highlight that the sputum proteome of healthy individuals is related to sputum neutrophil levels, but not gender or allergic sensitization. We illustrate the importance of design and interpretation of disease biomarker studies considering such protein population and technical measurement variance.
AB - Analysis of induced sputum supernatant is a minimally invasive approach to study the epithelial lining fluid and, thereby, provide insight into normal lung biology and the pathobiology of lung diseases. We present here a novel proteomics approach to sputum analysis developed within the U-BIOPRED (unbiased biomarkers predictive of respiratory disease outcomes) international project. We present practical and analytical techniques to optimize the detection of robust biomarkers in proteomic studies. The normal sputum proteome was derived using data-independent HDMSE applied to 40 healthy nonsmoking participants, which provides an essential baseline from which to compare modulation of protein expression in respiratory diseases. The "core" sputum proteome (proteins detected in ≥40% of participants) was composed of 284 proteins, and the extended proteome (proteins detected in ≥3 participants) contained 1666 proteins. Quality control procedures were developed to optimize the accuracy and consistency of measurement of sputum proteins and analyze the distribution of sputum proteins in the healthy population. The analysis showed that quantitation of proteins by HDMSE is influenced by several factors, with some proteins being measured in all participants' samples and with low measurement variance between samples from the same patient. The measurement of some proteins is highly variable between repeat analyses, susceptible to sample processing effects, or difficult to accurately quantify by mass spectrometry. Other proteins show high interindividual variance. We also highlight that the sputum proteome of healthy individuals is related to sputum neutrophil levels, but not gender or allergic sensitization. We illustrate the importance of design and interpretation of disease biomarker studies considering such protein population and technical measurement variance.
UR - https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85047084957&origin=inward
UR - https://www.ncbi.nlm.nih.gov/pubmed/29737851
U2 - https://doi.org/10.1021/acs.jproteome.8b00018
DO - https://doi.org/10.1021/acs.jproteome.8b00018
M3 - Review article
C2 - 29737851
SN - 1535-3893
VL - 17
SP - 2072
EP - 2091
JO - Journal of proteome research
JF - Journal of proteome research
IS - 6
ER -