Abstract
The analysis of bronchoalveolar lavage fluid (BALF) using mass spectrometry-based metabolomics can provide insight into lung diseases, such as asthma. However, the important step of compound identification is hindered by the lack of a small molecule database that is specific for BALF. Here we describe prototypic, small molecule databases derived from human BALF samples (n=117). Human BALF was extracted into lipid and aqueous fractions and analyzed using liquid chromatography mass spectrometry. Following filtering to reduce contaminants and artifacts, the resulting BALF databases (BALF-DBs) contain 11,736 lipid and 658 aqueous compounds. Over 10% of these were found in 100% of samples. Testing the BALF-DBs using nested test sets produced a 99% match rate for lipids and 47% match rate for aqueous molecules. Searching an independent dataset resulted in 45% matching to the lipid BALF-DB compared to<25% when general databases are searched. The BALF-DBs are available for download from MetaboLights. Overall, the BALF-DBs can reduce false positives and improve confidence in compound identification compared to when general databases are used.
Highlights
Background and summaryBronchoalveolar lavage fluid (BALF) can be a valuable biospecimen for the diagnoses and study of lung diseases, including chronic obstructive pulmonary disease (COPD) and asthma
We describe the assembly of a prototypic, human bronchoalveolar lavage fluid (BALF)-specific small molecule database
COPDGene was approved by the institutional review board at each participating center; all subjects were enrolled from January 2008 to April 2011 and provided written informed consent
Summary
Bronchoalveolar lavage fluid (BALF) can be a valuable biospecimen for the diagnoses and study of lung diseases, including chronic obstructive pulmonary disease (COPD) and asthma. A comprehensive database of compounds that have been observed in a specific sample type, such as BALF, can better streamline compound identification This concept is beginning to be realized through efforts at the Human Metabolome Database (HMDB) which supports some biofluid-specific databases, such as for serum[9], cerebral spinal fluid[10], and urine[11]. Improved compound identification is being addressed through the Model Organism Metabolomes (MOM) task group of the Metabolomics Society[13] and through efforts towards a tissue-specific Drosophila melanogaster Atlas[14] While each of these constitutes a step forward in improving confidence in compound identification, to our knowledge, a small molecule database that is specific for use in unbiased LC/MS-based BALF metabolomics studies will be a first-of-its-kind. We describe the assembly of a prototypic, human BALF-specific small molecule database
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