Dataset Information

Using iRT, a normalized retention time for more targeted measurement of peptides.

ABSTRACT: Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments.

SUBMITTER: Escher C

PROVIDER: S-EPMC3918884 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Using iRT, a normalized retention time for more targeted measurement of peptides.

Escher Claudia C Reiter Lukas L MacLean Brendan B Ossola Reto R Herzog Franz F Chilton John J MacCoss Michael J MJ Rinner Oliver O

Proteomics 20120401 8

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. ...[more]

PMID: 22577012

Similar Datasets

Project description:The retention of participants in studies is important for the validity of research. We updated our prior systematic review (2005) to assess retention strategies for in-person follow-up in health care studies.We searched PubMed, Cumulative Index of Nursing and Allied Health Literature, Cochrane Controlled Trials Register, Cochrane Methodology Register, and Embase (August 2013) for English-language reports of studies that described retention strategies for in-person follow-up in health care studies. We abstracted each retention strategy, and two authors independently classified each retention strategy with one of the themes developed in our prior review.We identified 88 studies (67 newly identified studies), six of which were designed to compare retention strategies, whereas the remainder described retention strategies and retention rates. There were 985 strategies abstracted from the descriptive studies (617 from new studies), with a median (interquartile range) number of strategies per study of 10 (7 to 17) and a median (interquartile range) number of themes per study of 6 (4 to 7). Financial incentives were used in 47 (57%) of the descriptive studies. We classified 28% of the strategies under the theme of "contact and scheduling methods," with 83% of the identified studies using at least one strategy within this theme. The number of strategies used was positively correlated with retention rate (P = 0.027), but the number of themes was not associated with retention rate (P = 0.469).The number of studies describing retention strategies has substantially increased since our prior review. However, the lack of comparative studies and the heterogeneity in the types of strategies, participant population and study designs, prohibits synthesis to determine the types of cohort retention strategies that were most effective. However, using a larger number of retention strategies, across five or six different themes, appears to retain more study participants.

Project description:Rationale: miRNA therapeutics have gained attention during the past decade. These oligonucleotide treatments can modulate the expression of miRNAs in vivo and could be used to correct the imbalance of gene expression found in human diseases such as obesity, metabolic syndrome and atherosclerosis. The in vivo efficacy of current anti-miRNAs technologies hindered by physiological and cellular barriers to delivery into targeted cells and the nature of miRNAs that allows one to target an entire pathway that may lead to deleterious off-target effects. For these reasons, novel targeted delivery systems to inhibit miRNAs in specific tissues will be important for developing effective therapeutic strategies for numerous diseases including atherosclerosis. Objective: To explore the application of anti-miR-33 (miR-33-5p) conjugated pH Low-Insertion Peptides (pHLIP) constructs for the specific targeting of macrophages located in vascular lesions in the regression of atherosclerosis. Methods and Results: The anti-miR-33 conjugated pHLIP constructs are preferentially delivered to atherosclerotic plaques macrophages. The inhibition of miR-33 using pHLIP-directed macrophage targeting improves atherosclerosis regression by increasing collagen content and decreased lipid accumulation within vascular lesions. Single cell RNA sequencing analysis revealed higher expression of fibrotic genes (Col2a1, Col3a1, Col1a2, Fn1, etc) and tissue inhibitor of metalloproteinase 3 (Timp3), and downregulation of matrix metallopeptidase 12 (Mmp12) in macrophages from atherosclerotic lesions targeted by pHLIP- anti-miR-33. Conclusions: This study provides proof of principle for the application of pHLIP for treating advanced atherosclerosis via pharmacological inhibition of miR-33 in macrophages that avoids the deleterious effects in other metabolic tissues. This may open new therapeutic opportunities for atherosclerosis-associated cardiovascular diseases via selective delivery of other protective miRNAs.

Dataset Information

Using iRT, a normalized retention time for more targeted measurement of peptides.

Publications

Using iRT, a normalized retention time for more targeted measurement of peptides.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets