3.1. General results
The validation results are given in Table 3. It is appropriate to
compare these to corresponding values of the previous research
for the small library of literature spectra. The principal value was
73% TP [12]. Here the corresponding result is 75% for the literature
sublibrary (Table 3) that is very close to the previous value. Two
other sublibraries are new in the second version.
The experimental sublibrary includes 54 ESI and MALDI product-
ion mass spectra recorded in our laboratory for 6–7 cyclic peptides.
This implies 7.7 replicate spectra available per a compound.
The last value is relatively high one that is essential for obtaining
true search results. Indeed, it is known that both the TPR and the
mean MF usually tend to rise with the number of replicate
‘unknown’ and reference spectra acquired for a unique compound
[10, p.186; 11]. It is explained by increasing a probability of matching
spectra of the same compounds. Searches performed only for
the spectral subset under consideration, i.e. when both test and
reference spectra were experimental, led to 100% TP (Table 3).
The average MF in these searches is within the range of 590–648
that is higher than the average value of 396 for the 1st rank spectra
in all the test searches.
Both ESI and MALDI fragment spectra are obviously closer to
each other in every of the two groups than between groups. The
spectral resemblance seems to be due to a similarity in experimental
conditions which are rather similar within the groups although
collision energy and partly laser shots/power are not the same.
Also, ESI product-ion mass spectra match rather well with MALDI
ones and vice versa. As the result, in all the test searches reference
spectra of these two groups may substitute for one another, retaining
high outcome of 86–95% initial TP obtained for both groups
without their elimination.
It should be supplemented that MALDI product-ion spectra are
very seldom to be entered in mass spectral libraries. To our best
knowledge, the only exclusion is the group of MALDI ToF–ToF spectra
obtained by means of high-energy collision-induced dissociation
and incorporated in MassBank [38]. Our library is the first
one containing MALDI LIFT ToF/ToF spectra (see also [39]).
Another part of the library is ‘one-dimension’ spectra. Searches
performed only within this type of data resulted in the low rate of
36% TP. We explain this low value by frequent false matching many
‘one-dimension’ spectra of different compounds because of the
same m/z of many fragment ions with the same 100% intensity of
their peaks.
Basic validation results refer to the sum of sublibraries and
searches in the entire library. The overall TPR of 70% is not very
high one. The rate is diminished due to the unconventional contribution
of defective/‘one-dimension’ data. Without that, the correct
results that are the 1st rank above-threshold matches appeared in
88% of cases (Table 3). However, incorporation of ‘one-dimension’
subset into only reference spectra set increases the rate of TP from
88% to 91% (Table 3). We think that this effect is due to rising total
probability of spectral match of the same compounds with increasing
the number of replicate spectra (see below). It is also clear that
here probable false matches
3.1. General resultsThe validation results are given in Table 3. It is appropriate tocompare these to corresponding values of the previous researchfor the small library of literature spectra. The principal value was73% TP [12]. Here the corresponding result is 75% for the literaturesublibrary (Table 3) that is very close to the previous value. Twoother sublibraries are new in the second version.The experimental sublibrary includes 54 ESI and MALDI product-ion mass spectra recorded in our laboratory for 6–7 cyclic peptides.This implies 7.7 replicate spectra available per a compound.The last value is relatively high one that is essential for obtainingtrue search results. Indeed, it is known that both the TPR and themean MF usually tend to rise with the number of replicate‘unknown’ and reference spectra acquired for a unique compound[10, p.186; 11]. It is explained by increasing a probability of matchingspectra of the same compounds. Searches performed only forthe spectral subset under consideration, i.e. when both test andreference spectra were experimental, led to 100% TP (Table 3).The average MF in these searches is within the range of 590–648that is higher than the average value of 396 for the 1st rank spectrain all the test searches.Both ESI and MALDI fragment spectra are obviously closer toeach other in every of the two groups than between groups. Thespectral resemblance seems to be due to a similarity in experimentalconditions which are rather similar within the groups althoughcollision energy and partly laser shots/power are not the same.Also, ESI product-ion mass spectra match rather well with MALDIones and vice versa. As the result, in all the test searches referencespectra of these two groups may substitute for one another, retaininghigh outcome of 86–95% initial TP obtained for both groupswithout their elimination.It should be supplemented that MALDI product-ion spectra arevery seldom to be entered in mass spectral libraries. To our bestknowledge, the only exclusion is the group of MALDI ToF–ToF spectraobtained by means of high-energy collision-induced dissociationand incorporated in MassBank [38]. Our library is the firstone containing MALDI LIFT ToF/ToF spectra (see also [39]).Another part of the library is ‘one-dimension’ spectra. Searchesperformed only within this type of data resulted in the low rate of36% TP. We explain this low value by frequent false matching many‘one-dimension’ spectra of different compounds because of thesame m/z of many fragment ions with the same 100% intensity oftheir peaks.Basic validation results refer to the sum of sublibraries andsearches in the entire library. The overall TPR of 70% is not veryhigh one. The rate is diminished due to the unconventional contributionof defective/‘one-dimension’ data. Without that, the correctresults that are the 1st rank above-threshold matches appeared in88% of cases (Table 3). However, incorporation of ‘one-dimension’subset into only reference spectra set increases the rate of TP from88% to 91% (Table 3). We think that this effect is due to rising totalprobability of spectral match of the same compounds with increasingthe number of replicate spectra (see below). It is also clear thathere probable false matches
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3.1. General results
The validation results are given in Table 3. It is appropriate to
compare these to corresponding values of the previous research
for the small library of literature spectra. The principal value was
73% TP [12]. Here the corresponding result is 75% for the literature
sublibrary (Table 3) that is very close to the previous value. Two
other sublibraries are new in the second version.
The experimental sublibrary includes 54 ESI and MALDI product-
ion mass spectra recorded in our laboratory for 6–7 cyclic peptides.
This implies 7.7 replicate spectra available per a compound.
The last value is relatively high one that is essential for obtaining
true search results. Indeed, it is known that both the TPR and the
mean MF usually tend to rise with the number of replicate
‘unknown’ and reference spectra acquired for a unique compound
[10, p.186; 11]. It is explained by increasing a probability of matching
spectra of the same compounds. Searches performed only for
the spectral subset under consideration, i.e. when both test and
reference spectra were experimental, led to 100% TP (Table 3).
The average MF in these searches is within the range of 590–648
that is higher than the average value of 396 for the 1st rank spectra
in all the test searches.
Both ESI and MALDI fragment spectra are obviously closer to
each other in every of the two groups than between groups. The
spectral resemblance seems to be due to a similarity in experimental
conditions which are rather similar within the groups although
collision energy and partly laser shots/power are not the same.
Also, ESI product-ion mass spectra match rather well with MALDI
ones and vice versa. As the result, in all the test searches reference
spectra of these two groups may substitute for one another, retaining
high outcome of 86–95% initial TP obtained for both groups
without their elimination.
It should be supplemented that MALDI product-ion spectra are
very seldom to be entered in mass spectral libraries. To our best
knowledge, the only exclusion is the group of MALDI ToF–ToF spectra
obtained by means of high-energy collision-induced dissociation
and incorporated in MassBank [38]. Our library is the first
one containing MALDI LIFT ToF/ToF spectra (see also [39]).
Another part of the library is ‘one-dimension’ spectra. Searches
performed only within this type of data resulted in the low rate of
36% TP. We explain this low value by frequent false matching many
‘one-dimension’ spectra of different compounds because of the
same m/z of many fragment ions with the same 100% intensity of
their peaks.
Basic validation results refer to the sum of sublibraries and
searches in the entire library. The overall TPR of 70% is not very
high one. The rate is diminished due to the unconventional contribution
of defective/‘one-dimension’ data. Without that, the correct
results that are the 1st rank above-threshold matches appeared in
88% of cases (Table 3). However, incorporation of ‘one-dimension’
subset into only reference spectra set increases the rate of TP from
88% to 91% (Table 3). We think that this effect is due to rising total
probability of spectral match of the same compounds with increasing
the number of replicate spectra (see below). It is also clear that
here probable false matches
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