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Samples were extracted via dried filter spot technique in a 96-well plate format, which is well suitable for high-throughput analysis.
The sample preparation included: I) protein precipitation by placing a 20 µL sample volume on the filter spot, and precipitation by 200 µL Naïve; II) hydrolysis by 100 µL of 0.35 M KOH in 95% ethanol for 2 hrs; III) a washing step (3×200 µL H2O) to remove hydrolysis reagent; and, finally, IV) extraction by means of 100 µL aqueous methanol.
Stringent criteria were applied to filter spot intensity data.
Specifically, gel image filter, spot detection, background subtraction and spot matching were performed.
Samples were extracted via dried filter spot technique and measured by LC-ESI-MS/MS with an ABSciex 4000 QTrapTM tandem mass spectrometry instrument (AB Sciex, Darmstadt, Germany).
Proteins considered not significant when setting the DIA exclusion filter spot volume limit to 200.000 a.u. where ATP synthase beta chain (P06576), smooth muscle actin (P62736), fast myosin light chain 3 alkali (P06741), myotilin (Q9UBF9) and creatine kinase M-type (P06732).
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Genomic DNA was extracted from filter spots using the chelex procedure [36].
In brief, internal standards and a 20 µL sample volume placed onto the filter spots were extracted and simultaneously protein precipitated with aqueous methanol.
Samples were added on filter spots placed in a 96- solvinert well plate (internal standards were placed and dried down under nitrogen before), fixed above a 96 deep well plate (capture plate).
Reactions were carried out at 37°C for 2hr and terminated by heating at 85°C for 5 min. [14C]CO2 was trapped with Whatman 3-mm paper filter spotted wit 10 µl of 10% w/v KOH and quantified by scintillation counter.
After incubation, the filter spots were dried again using an evaporator.
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