R of Title Loaded From File retrovirus infection homolog isoformNP_001011700.2 mitochondrial coiled-coil domain protein 1 precursorNP_001092926.2 neuropeptide W preproproteinNP_076938.2 modulator of retrovirus infection homolog isoform3 Serum Antibody Repertoire ProfilingNP_000396.2 ganglioside GM2 activator isoform 1 precursorNP_065117.1 claudinNP_997394.1 uncharacterized protein C9orfNP_114103.2 voltage-dependent calcium channel gamma-6 subunit isoform cNP_942567.1 probable alpha-ketoglutarate-dependent dioxygenase ABH6 isoformNP_443183.1 deoxynucleotidyl-transferase terminal-interacting proteinNP_665814.1 voltage-dependent calcium channel gamma-6 subunit isoform bNP_001090.2 prostatic acid phosphatase isoform PAP precursorNP_005182.1 T-lymphocyte activation antigen CD80 precursorNP_001010905.1 UPF0762 protein Title Loaded From File C6orf58 precursorNP_001127666.1 prostatic acid phosphatase isoform TM-PAP precursorProteins selected for PAP3 antiserumNP_149101.1 gamma-glutamylaminecyclotransferaseNP_001165160.1 AMME syndrome candidate gene 1 protein isoformNP_001025046.1 regulator of G-protein signaling 7-binding proteinNP_060436.4 vacuolar protein sorting-associated protein 37CNP_113633.2 AMMECR1-like proteinNP_003921.2 src kinase-associated phosphoproteinSerum Antibody Repertoire ProfilingMajor epitope score The table shows the top candidate antigens selected for 16985061 the antibodies of the PAP1, PAP2 and PAP3 antisera by sorting the data generated by processing the results of BLAST database search for the corresponding peptide sequences. doi:10.1371/journal.pone.0067181.tfor the large number of peptides against large number of proteins. These analyses identified all the peptides in the list with matches to selected proteins. The proteins were then ranked according to the final score that was calculated as the sum of the scores for the all peptides with matches against the protein divided by the length of the protein. Such analyses ranked the PAP isoforms NP_001090.2 and NP_001127666.1 at the 4th and the 7th positions, respectively (Table S2A and Table 1). The Blast2seq analysis for the 500 PAP1 peptides against PAP NP_001090.2 or NP_001127666.1 isoforms identified 48 peptides with matches to the PAP protein. 23148522 Out of 48 peptides, 20 were related to the sequence NFTLPSWA located at the amino acid positions 220?27 of the PAP protein. Figure 1 shows the location of peptide matches on the sequence of the NP_001090.2 PAP variant. Three other proteins, that were ranked higher than the NP_001090.2 PAP isoform also contained the sequences related to the NFTLPSWA sequence and had multiple matches to related peptides. However, the sum of scores for the peptides related to the NFTLPSWA sequence of the PAP isoforms was the highest among the sums of scores for the related epitopes in other proteins (Table 1). The list of top 500 candidate peptides for the PAP2 serum was significantly enriched with peptides with homology to the PAP proteins sequence. The BLAST search against human refseq_protein for the first most abundant 120 peptides of the PAP2 list contained 7 peptides that retrieved the PAP protein isoforms with the maximal score 18.5. Out of 500 peptides of the PAP2 list analyzed by the blast2seq, 136 peptides matched the PAP isoforms, of which 110 peptides were related to the NFTLPSWA sequence, which was the same sequence related to the peptides for the PAP1 sample. Besides 2 isoforms of the PAP protein, there were 490 other proteins that had multiple matches to different peptides. After ran.R of retrovirus infection homolog isoformNP_001011700.2 mitochondrial coiled-coil domain protein 1 precursorNP_001092926.2 neuropeptide W preproproteinNP_076938.2 modulator of retrovirus infection homolog isoform3 Serum Antibody Repertoire ProfilingNP_000396.2 ganglioside GM2 activator isoform 1 precursorNP_065117.1 claudinNP_997394.1 uncharacterized protein C9orfNP_114103.2 voltage-dependent calcium channel gamma-6 subunit isoform cNP_942567.1 probable alpha-ketoglutarate-dependent dioxygenase ABH6 isoformNP_443183.1 deoxynucleotidyl-transferase terminal-interacting proteinNP_665814.1 voltage-dependent calcium channel gamma-6 subunit isoform bNP_001090.2 prostatic acid phosphatase isoform PAP precursorNP_005182.1 T-lymphocyte activation antigen CD80 precursorNP_001010905.1 UPF0762 protein C6orf58 precursorNP_001127666.1 prostatic acid phosphatase isoform TM-PAP precursorProteins selected for PAP3 antiserumNP_149101.1 gamma-glutamylaminecyclotransferaseNP_001165160.1 AMME syndrome candidate gene 1 protein isoformNP_001025046.1 regulator of G-protein signaling 7-binding proteinNP_060436.4 vacuolar protein sorting-associated protein 37CNP_113633.2 AMMECR1-like proteinNP_003921.2 src kinase-associated phosphoproteinSerum Antibody Repertoire ProfilingMajor epitope score The table shows the top candidate antigens selected for 16985061 the antibodies of the PAP1, PAP2 and PAP3 antisera by sorting the data generated by processing the results of BLAST database search for the corresponding peptide sequences. doi:10.1371/journal.pone.0067181.tfor the large number of peptides against large number of proteins. These analyses identified all the peptides in the list with matches to selected proteins. The proteins were then ranked according to the final score that was calculated as the sum of the scores for the all peptides with matches against the protein divided by the length of the protein. Such analyses ranked the PAP isoforms NP_001090.2 and NP_001127666.1 at the 4th and the 7th positions, respectively (Table S2A and Table 1). The Blast2seq analysis for the 500 PAP1 peptides against PAP NP_001090.2 or NP_001127666.1 isoforms identified 48 peptides with matches to the PAP protein. 23148522 Out of 48 peptides, 20 were related to the sequence NFTLPSWA located at the amino acid positions 220?27 of the PAP protein. Figure 1 shows the location of peptide matches on the sequence of the NP_001090.2 PAP variant. Three other proteins, that were ranked higher than the NP_001090.2 PAP isoform also contained the sequences related to the NFTLPSWA sequence and had multiple matches to related peptides. However, the sum of scores for the peptides related to the NFTLPSWA sequence of the PAP isoforms was the highest among the sums of scores for the related epitopes in other proteins (Table 1). The list of top 500 candidate peptides for the PAP2 serum was significantly enriched with peptides with homology to the PAP proteins sequence. The BLAST search against human refseq_protein for the first most abundant 120 peptides of the PAP2 list contained 7 peptides that retrieved the PAP protein isoforms with the maximal score 18.5. Out of 500 peptides of the PAP2 list analyzed by the blast2seq, 136 peptides matched the PAP isoforms, of which 110 peptides were related to the NFTLPSWA sequence, which was the same sequence related to the peptides for the PAP1 sample. Besides 2 isoforms of the PAP protein, there were 490 other proteins that had multiple matches to different peptides. After ran.
