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Genomic insights into the Ixodes scapularis tick vector of Lyme disease
TLDR
Insights from genome analyses into parasitic processes unique to ticks, including host ‘questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival are reported. Expand
A refined method to calculate false discovery rates for peptide identification using decoy databases.
TLDR
It is demonstrated that by analyzing as a whole the joint distribution of matches obtained after performing a separate database search, and applying the competition strategy, it is possible to make a more accurate calculation of false discovery rates. Expand
Ultra fast trypsin digestion of proteins by high intensity focused ultrasound.
TLDR
Proteolytic digestion of proteins in seconds under an ultrasonic field provided by high-intensity focused ultrasound (HIFU) has been achieved and greatly reduces the time needed for protein digestion, is of easy implementation, environmental friendly, and economic. Expand
Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST.
TLDR
This work has used as a model the nuclear proteome from Jurkat cells and presents a processing algorithm that allows accurate predictions of random matching distributions, based on the two SEQUEST scores Xcorr and DeltaCn, and demonstrates that the score distributions are highly dependent on database size and precursor mass window. Expand
Statistical Model to Analyze Quantitative Proteomics Data Obtained by 18O/16O Labeling and Linear Ion Trap Mass Spectrometry
TLDR
This work presents the largest quantitative proteomics study to date on the short term effects of VEGF on human umbilical vein endothelial cells by 18O/16O labeling and a random effects model was developed including four different sources of variance at the spectrum-fitting, scan, peptide, and protein levels. Expand
Systems Biology of Tissue-Specific Response to Anaplasma phagocytophilum Reveals Differentiated Apoptosis in the Tick Vector Ixodes scapularis
TLDR
The results showed tissue-specific differences in tick response to infection and revealed differentiated regulation of apoptosis pathways, which will contribute to characterize gene regulation in ticks. Expand
Expression of Heat Shock and Other Stress Response Proteins in Ticks and Cultured Tick Cells in Response to Anaplasma spp. Infection and Heat Shock
TLDR
The complexity of the stress response in ticks is illustrated and a function for the HSPs and other SRPs during Anaplasma spp. Expand
General statistical framework for quantitative proteomics by stable isotope labeling.
TLDR
This work presents a generally applicable model that accurately explains the behavior of data obtained using current SIL approaches, including (18)O, iTRAQ, and SILAC labeling, and different MS instruments, and decomposes the total technical variance into the spectral, peptide, and protein variance components. Expand
High-sensitivity analysis of specific peptides in complex samples by selected MS/MS ion monitoring and linear ion trap mass spectrometry: application to biological studies.
TLDR
Results were obtained by selecting an appropriate combination of scans according to the purpose of each one of these research scenarios, which include highly specific identification of proteins present in low amounts, characterization and relative quantification of post-translational modifications such as phosphorylation and S-nitrosylation and species-specific peptide identification. Expand
De novo mass spectrometry sequencing and characterization of species-specific peptides from nucleoside diphosphate kinase B for the classification of commercial fish species belonging to the family
TLDR
A rapid and effective classification method, based in the detection of these biomarker peptides using the selective ion reaction monitoring (SIRM) scan mode in mass spectrometry, is proposed. Expand
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