TY - JOUR
T1 - Improving the identification rate of data independent label-free quantitative proteomics experiments on non-model crops: A case study on apple fruit
AU - Buts, Kim
AU - Michielssens, Servaas
AU - Hertog, Maarten L.A.T.M.
AU - Hayakawa, Eisuke
AU - Cordewener, Jan
AU - America, Antoine H.P.
AU - Nicolai, Bart M.
AU - Carpentier, Sebastien C.
PY - 2014/6/13
Y1 - 2014/6/13
N2 - Complex peptide extracts from non-model crops are troublesome for proper identification and quantification. To increase the identification rate of label free DIA experiments of Braeburn apple a new workflow was developed where a DDA database was constructed and linked to the DIA data. At a first level, parent masses found in DIA were searched in the DDA database based on their mass to charge ratio and retention time; at a second level, masses of fragmentation ions were compared for each of the linked spectrum. Following this workflow, a tenfold increase of peptides was identified from a single DIA run. As proof of principle, the designed workflow was applied to determine the changes during a storage experiment, achieving a two-fold identification increase in the number of significant peptides. The corresponding protein families were divided into nine clusters, representing different time profiles of changes in abundances during storage. Up-regulated protein families already show a glimpse of important pathways affecting aging during long-term storage, such as ethylene synthesis, and responses to abiotic stresses and their influence on the central metabolism. Biological significance: Proteomics research on non-model crops causes additional difficulties in identifying the peptides present in, often complex, samples. This work proposes a new workflow to retrieve more identifications from a set of quantitative data, based on linking DIA and DDA data at two consecutive levels. As proof of principle, a storage experiment on Braeburn apple resulted in twice as much identified storage related peptides. Important proteins involved in central metabolism and stress are significantly up-regulated after long term storage. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
AB - Complex peptide extracts from non-model crops are troublesome for proper identification and quantification. To increase the identification rate of label free DIA experiments of Braeburn apple a new workflow was developed where a DDA database was constructed and linked to the DIA data. At a first level, parent masses found in DIA were searched in the DDA database based on their mass to charge ratio and retention time; at a second level, masses of fragmentation ions were compared for each of the linked spectrum. Following this workflow, a tenfold increase of peptides was identified from a single DIA run. As proof of principle, the designed workflow was applied to determine the changes during a storage experiment, achieving a two-fold identification increase in the number of significant peptides. The corresponding protein families were divided into nine clusters, representing different time profiles of changes in abundances during storage. Up-regulated protein families already show a glimpse of important pathways affecting aging during long-term storage, such as ethylene synthesis, and responses to abiotic stresses and their influence on the central metabolism. Biological significance: Proteomics research on non-model crops causes additional difficulties in identifying the peptides present in, often complex, samples. This work proposes a new workflow to retrieve more identifications from a set of quantitative data, based on linking DIA and DDA data at two consecutive levels. As proof of principle, a storage experiment on Braeburn apple resulted in twice as much identified storage related peptides. Important proteins involved in central metabolism and stress are significantly up-regulated after long term storage. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
KW - Data independent acquisition
KW - Label free quantification
KW - Non-model crop
KW - Plant proteomics
U2 - 10.1016/j.jprot.2014.02.015
DO - 10.1016/j.jprot.2014.02.015
M3 - Article
C2 - 24565695
AN - SCOPUS:84901826910
SN - 1874-3919
VL - 105
SP - 31
EP - 45
JO - Journal of Proteomics
JF - Journal of Proteomics
ER -