In this manual verification the mass error, the presence of fragment ion series and the expected prevalence of C-terminus containing ions (Y-type) in the high mass range were all taken into account.
As the C isotope is stable and the natural abundance is 0.011 [ 28], the experimental error of some fragments, which were slightly higher than the natural C abundance, might be large.
In truth, the rhythm of fragment and frustration, of erasure and error and slow emergence of form, was familiar.
X! Tandem parameters included: pre-cursor mass error of 10 ppm, fragment ion mass tolerance of 0.3 Da, tryptic cleavage specificity with up to three missed cleavages for probing labeling efficiency and up to one missed cleavage when applying the labeling technique to tumor samples.
These artificial indels originated mostly from homopolymeric regions or other sequencing errors of different pyrosequence reads from the same fragment.
In the absence of errors, we expect the fragment sizes c1,…, c n from an in silico digest of the sequence to be in one-to-one correspondence and identical to a subsequence of fragment sizes o j,…, o j + n − 1 of the optical map fragments o1, …, o m.
The NF probability of fragment f i is composed of the probability of the individual haplotypes and the probability of the SNP fragment given the haplotypes: where α is a error term to deal with sequencing and PHASE errors.
It is defined as: Error(v ) = ∑ i ∈ fragments (fragmen t i (v ) - measure d i ) 2 σ 2 where measured i is the measured fractional enrichment of fragment i, fragment i v) is the computed fractional enrichment of fragment i as a function of the flux distribution v, and α = 0 :014 is the standard deviation of the fragments as calculated from experimental replicates.
The algorithm, as the original percolator algorithm [104], is based on a semi-supervised SVM approach, and is able to discriminate between correct and incorrect identifications by assigning weights to a number of features such as: Mascot score, precursor mass error, fragment mass error, number of variable modifications used in the search, etc.
On the other hand, high quality images should be prepared for the purpose of precise detection of fragments and reduce errors.
