title: Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
abstract: Accurate protein identification in large-scale proteomics experiments relies upon a detailed, accurate protein catalogue, which is derived from predictions of open reading frames based on genome sequence data. Integration of mass spectrometry-based proteomics data with computational proteome predictions from environmental metagenomic sequences has been challenging because of the variable overlap between proteomic datasets and corresponding short-read nucleotide sequence data. In this study, we have benchmarked several strategies for increasing microbial peptide spectral matching in metaproteomic datasets using protein predictions generated from matched metagenomic sequences from the same human fecal samples. Additionally, we investigated the impact of mass spectrometry-based filters (high mass accuracy, delta correlation), and de novo peptide sequencing on the number and robustness of peptide-spectrum assignments in these complex datasets. In summary, we find that high mass accuracy peptide measurements searched against non-assembled reads from DNA sequencing of the same samples significantly increased identifiable proteins without sacrificing accuracy.
authors: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors: Brandi L
authors: BL
authors: Cantarel
authors: Alison R
authors: AR
authors: Erickson
authors: Nathan C
authors: NC
authors: VerBerkmoes
authors: Brian K
authors: BK
authors: Erickson
authors: Patricia A
authors: PA
authors: Carey
authors: Chongle
authors: C
authors: Pan
authors: Manesh
authors: M
authors: Shah
authors: Emmanuel F
authors: EF
authors: Mongodin
authors: Janet K
authors: JK
authors: Jansson
authors: Claire M
authors: CM
authors: Fraser-Liggett
authors: Robert L
authors: RL
authors: Hettich
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000378:metabolism*; D030562:Databases, Protein; D017753:Ecosystem; D005260:Female; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D010455:Peptides / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012111:Residence Characteristics; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid
chemical_list: D010455:Peptides