Monte Carlo bottom-up evaluation of the uncertainty of complex sample preparation: Elemental determination in sediments

2021 ◽  
pp. 338732
Author(s):  
Vanessa Morgado ◽  
Carla Palma ◽  
Ricardo J.N. Bettencourt da Silva
2021 ◽  
Author(s):  
Yan Chen ◽  
Nurgul Kaplan Lease ◽  
Jennifer Gin ◽  
Tad Ogorzalek ◽  
Paul D. Adams ◽  
...  

Manual proteomic sample preparation methods limit sample throughput and often lead to poor data quality when thousands of samples must be analyzed. Automated workflows are increasingly used to overcome these issues for some (or even all) of the sample preparation steps. Here, we detail three optimised step-by-step protocols to: (A) lyse Gram-negative bacteria and fungal cells; (B) quantify the amount of protein extracted; and (C) normalize the amount of protein and set up tryptic digestion. These protocols have been developed to facilitate rapid, low variance sample preparation of hundreds of samples, be easily implemented on widely-available Beckman-Coulter Biomek automated liquid handlers, and allow flexibility for future protocol development. By using this workflow 50 micrograms of peptides for 96 samples can be prepared for tryptic digestion in under an hour. We validate these protocols by analyzing 47 E. coli and R. toruloides samples and show that this modular workflow provides robust, reproducible proteomic samples for high-throughput applications. The expected results from these protocols are 94 peptide samples from Gram-negative bacterial and fungal cells prepared for bottom-up quantitative proteomic analysis without the need for desalting column cleanup and with peptide variance (CVs) below 15%.


2014 ◽  
Vol 2014 ◽  
pp. 1-6
Author(s):  
Caio B. Wetterich ◽  
Emery C. Lins ◽  
José Belasque ◽  
Luis G. Marcassa

Observation of climacteric-like behavior in citrus leaves depends on the detection of ethylene. However, such detection requires a gas chromatographer and complex sample preparation procedures. In this work, fluorescence spectroscopy was investigated as a diagnostic technique for climacteric-like behavior in citrus leaves. Our results indicate that the chlorophyll fluorescence presents a time evolution consistent with the ethylene evolution. Therefore, fluorescence spectroscopy may be used to observe the climacteric-like behavior in citrus leaves.


2014 ◽  
Vol 81 (5) ◽  
pp. 1610-1615 ◽  
Author(s):  
Anthony G. Dodge ◽  
Kelvin Carrasquillo ◽  
Luis Rivera ◽  
Lei Xu ◽  
Lawrence P. Wackett ◽  
...  

ABSTRACTAbrin is a toxic protein produced by the ornamental plantAbrus precatorius, and it is of concern as a biothreat agent. The small coextracting moleculeN-methyl-l-tryptophan (l-abrine) is specific to members of the genusAbrusand thus can be used as a marker for the presence or ingestion of abrin. Current methods for the detection of abrin orl-abrine in foods and other matrices require complex sample preparation and expensive instrumentation. To develop a fast and portable method for the detection ofl-abrine in beverages and foods, theEscherichia coliproteinsN-methyltryptophan oxidase (MTOX) and tryptophanase were expressed and purified. The two enzymes jointly degradedl-abrine to products that included ammonia and indole, and colorimetric assays for the detection of those analytes in beverage and food samples were evaluated. An indole assay using a modified version of Ehrlich's/Kovac's reagent was more sensitive and less subject to negative interferences from components in the samples than the Berthelot ammonia assay. The two enzymes were added into food and beverage samples spiked withl-abrine, and indole was detected as a degradation product, with the visual lower detection limit being 2.5 to 10.0 μM (∼0.6 to 2.2 ppm)l-abrine in the samples tested. Results could be obtained in as little as 15 min. Sample preparation was limited to pH adjustment of some samples. Visual detection was found to be about as sensitive as detection with a spectrophotometer, especially in milk-based matrices.


2006 ◽  
Vol 106 (7) ◽  
pp. 597-602 ◽  
Author(s):  
Yusuke Ominami ◽  
Quoc Ngo ◽  
Nobuhiko P. Kobayashi ◽  
Kevin Mcilwrath ◽  
Konrad Jarausch ◽  
...  

Proteomes ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 14 ◽  
Author(s):  
Emmalyn J. Dupree ◽  
Madhuri Jayathirtha ◽  
Hannah Yorkey ◽  
Marius Mihasan ◽  
Brindusa Alina Petre ◽  
...  

Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future.


Lab on a Chip ◽  
2019 ◽  
Vol 19 (20) ◽  
pp. 3490-3498 ◽  
Author(s):  
Jan Leipert ◽  
Andreas Tholey

The combination of digital microfluidics and magnetic beads for removal of polymer surfactants enables sensitive LC-MS-based microproteomics analyses down to 100 mammalian cells.


SPARK ◽  
2018 ◽  
Author(s):  
Cezar Augusto Bizzi ◽  
Erico Marlon de Moraes Flores ◽  
Marcia Foster Mesko

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