We compared the performance
of MS Amanda
based on four data sets: an HCD HeLa sample, a synthetic peptide library,
a histone data set, and a CID HeLa sample. The HCD HeLa sample, published
by Michalski et al.,30 (link) consists of three
replicate measurements of tryptic peptides derived from one human
cancer cell line. The synthetic peptide library, as described by Marx
et al.,31 (link) is composed of more than 200 000
phosphorylated and nonphosphorylated peptides. Performance comparisons
were based on provided HCD and ETD data. The histone data set is composed
of four different preparations, namely, Histone II-A from calf thymus
(Sigma), Histone III-S from calf thymus (Sigma), Histone IV from Xenopus laevis, recombinantly expressed in Escherichia coli (Upstate), and Core Histones from
chicken erythrocytes (Millipore). The published CID HeLa sample32 (link) covers three replicates measured with a 1 h
gradient (1 μg).
of MS Amanda
based on four data sets: an HCD HeLa sample, a synthetic peptide library,
a histone data set, and a CID HeLa sample. The HCD HeLa sample, published
by Michalski et al.,30 (link) consists of three
replicate measurements of tryptic peptides derived from one human
cancer cell line. The synthetic peptide library, as described by Marx
et al.,31 (link) is composed of more than 200 000
phosphorylated and nonphosphorylated peptides. Performance comparisons
were based on provided HCD and ETD data. The histone data set is composed
of four different preparations, namely, Histone II-A from calf thymus
(Sigma), Histone III-S from calf thymus (Sigma), Histone IV from Xenopus laevis, recombinantly expressed in Escherichia coli (Upstate), and Core Histones from
chicken erythrocytes (Millipore). The published CID HeLa sample32 (link) covers three replicates measured with a 1 h
gradient (1 μg).