In retrospect, one of the first reports that was presented on the ability to mapa protein expression in human blood plasma, was made with 2D gel electrophoresiswith intact proteins, in contrast to the protein digest protocol, followed byLC-MS, that is the most commonly used separation and mass spectrometry platformof today [22].
Presumptive Campylobacter isolates were confirmed and the species identified using a polymerase chain reaction (PCR) amplification/restriction digest protocol described previously (Engvall et al. 2002).
The in solution digest protocol based on the detergent RapiGest included a step of protein precipitation for lipid removal through centrifugation prior to trypsin treatment.
This restriction digest protocol has been used successfully in previous works (De Smet et al, 1996; Sigalotti et al, 2002) and has been found to result consistently in complete digestion of the genomic DNA by HpaII restriction enzyme.
All solution samples within a set of samples were analyzed identically and in a quantitative manner (i.e. sample volume, digest protocol, injection amount, and LC/MS/MS analysis).
Pseudosite integration donor vectors (Fig. 6B,C) were cloned via standard PCR and restriction digest protocols (all enzymes from NEB).
Gel slices were handled with a standard in-gel digest protocol (http://donatello.ucsf.edu/ingel.html).html
This relatively aggressive digest protocol was needed to improve the yield of peptides from Ub and TRIM5α proteins.
The HiCUP pipeline includes additional filters when following the double-digest protocol, since the start of every read should now correspond to a cut site (in contrast to sonication, which is essentially a random fragmentation process).
ScrF I digests were performed upon the positive control degenerate PCR products and it was shown that the sub-family centred PCR-restriction digest protocol was capable of producing a diagnostic Kir isoform-specific duplex banding pattern in agreement with that predicted from the published human sequences (Fig. 5).
The low number of hits may be due to the fact that Gal/GalNAc lectin is a glycoprotein which is more difficult to digest using the common digestion protocol.
