TY - JOUR
T1 - Database-independent de novo metaproteomics of complex microbial communities
AU - Kleikamp, Hugo B.C.
AU - Pronk, Mario
AU - Tugui, Claudia
AU - Guedes da Silva, Leonor
AU - Abbas, Ben
AU - Lin, Yue Mei
AU - van Loosdrecht, Mark C.M.
AU - Pabst, Martin
PY - 2021
Y1 - 2021
N2 - Metaproteomics has emerged as one of the most promising approaches for determining the composition and metabolic functions of complete microbial communities. Conventional metaproteomics approaches rely on the construction of protein sequence databases and efficient peptide-spectrum-matching algorithms, an approach that is intrinsically biased towards the content of the constructed sequence database. Here, we introduce a highly efficient, database-independent de novo metaproteomics approach and systematically evaluate its quantitative performance using synthetic and natural microbial communities comprising dozens of taxonomic families. Our work demonstrates that the de novo sequencing approach can vastly expand many metaproteomics applications by enabling rapid quantitative profiling and by capturing unsequenced community members that otherwise remain inaccessible for further interpretation. Kleikamp et al., describe a novel de novo metaproteomics pipeline (NovoBridge) that enables rapid community profiling without the need for constructing protein sequence databases.
AB - Metaproteomics has emerged as one of the most promising approaches for determining the composition and metabolic functions of complete microbial communities. Conventional metaproteomics approaches rely on the construction of protein sequence databases and efficient peptide-spectrum-matching algorithms, an approach that is intrinsically biased towards the content of the constructed sequence database. Here, we introduce a highly efficient, database-independent de novo metaproteomics approach and systematically evaluate its quantitative performance using synthetic and natural microbial communities comprising dozens of taxonomic families. Our work demonstrates that the de novo sequencing approach can vastly expand many metaproteomics applications by enabling rapid quantitative profiling and by capturing unsequenced community members that otherwise remain inaccessible for further interpretation. Kleikamp et al., describe a novel de novo metaproteomics pipeline (NovoBridge) that enables rapid community profiling without the need for constructing protein sequence databases.
KW - de novo peptide sequencing
KW - metaproteomics
KW - microbial communities
UR - http://www.scopus.com/inward/record.url?scp=85105753228&partnerID=8YFLogxK
U2 - 10.1016/j.cels.2021.04.003
DO - 10.1016/j.cels.2021.04.003
M3 - Article
AN - SCOPUS:85105753228
VL - 12
SP - 375-383.e5
JO - Cell Systems
JF - Cell Systems
SN - 2405-4712
IS - 5
ER -