Dataset Information

Improved detection of quantitative differences using a combination of spectral counting and MS/MS total ion current.

ABSTRACT: Label-free quantitative strategies are commonly used in shotgun proteomics to detect differences in protein abundance between biological sample groups. Here, we have employed a combination of two such approaches, spectral counting (SpC) and average MS/MS total ion current (MS(2) TIC), for the analysis of rat kidney mitochondria in response to metabolic acidosis. In total, 49 proteins were observed to be significantly altered in response to metabolic acidosis (p-value < 0.05). Of these, 32 proteins were uniquely observed as significantly different by SpC, 14 by MS(2) TIC, and only 3 by both approaches. Western blot analysis was performed on a subset of these proteins to validate the observed abundance differences. This study illustrates the utility and ease of combining these two label-free quantitative approaches to increase the number of detected protein abundance differences in the shotgun analysis of complex biological samples.

SUBMITTER: Freund DM

PROVIDER: S-EPMC3834011 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Improved detection of quantitative differences using a combination of spectral counting and MS/MS total ion current.

Freund Dana M DM Prenni Jessica E JE

Journal of proteome research 20130312 4

Label-free quantitative strategies are commonly used in shotgun proteomics to detect differences in protein abundance between biological sample groups. Here, we have employed a combination of two such approaches, spectral counting (SpC) and average MS/MS total ion current (MS(2) TIC), for the analysis of rat kidney mitochondria in response to metabolic acidosis. In total, 49 proteins were observed to be significantly altered in response to metabolic acidosis (p-value < 0.05). Of these, 32 protei ...[more]

PMID: 23445521

Similar Datasets

Project description:ObjectiveEvaluation of image characteristics at ultra-low radiation dose levels of a first-generation dual-source photon-counting computed tomography (PCCT) compared to a dual-source dual-energy CT (DECT) scanner.MethodsA multi-energy CT phantom was imaged with and without an extension ring on both scanners over a range of radiation dose levels (CTDIvol 0.4-15.0 mGy). Scans were performed in different modes of acquisition for PCCT with 120 kVp and DECT with 70/Sn150 kVp and 100/Sn150 kVp. Various tissue inserts were used to characterize the precision and repeatability of Hounsfield units (HUs) on virtual mono-energetic images between 40 and 190 keV. Image noise was additionally investigated at an ultra-low radiation dose to illustrate PCCT's ability to remove electronic background noise.ResultsOur results demonstrate the high precision of HU measurements for a wide range of inserts and radiation exposure levels with PCCT. We report high performance for both scanners across a wide range of radiation exposure levels, with PCCT outperforming at low exposures compared to DECT. PCCT scans at the lowest radiation exposures illustrate significant reduction in electronic background noise, with a mean percent reduction of 74% (p value ~ 10-8) compared to DECT 70/Sn150 kVp and 60% (p value ~ 10-6) compared to DECT 100/Sn150 kVp.ConclusionsThis paper reports the first experiences with a clinical dual-source PCCT. PCCT provides reliable HUs without disruption from electronic background noise for a wide range of dose values. Diagnostic benefits are not only for quantification at an ultra-low dose but also for imaging of obese patients.Key pointsPCCT scanners provide precise and reliable Hounsfield units at ultra-low dose levels. The influence of electronic background noise can be removed at ultra-low-dose acquisitions with PCCT. Both spectral platforms have high performance along a wide range of radiation exposure levels, with PCCT outperforming at low radiation exposures.

Dataset Information

Improved detection of quantitative differences using a combination of spectral counting and MS/MS total ion current.

Publications

Improved detection of quantitative differences using a combination of spectral counting and MS/MS total ion current.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets