King the top 100 proteins identified in the first step of analysis

King the top 100 proteins identified in the first step of analysis using the blast2seq, the PAP isoforms occupied the 12th and the 15th positions (Table S2B and Table 1). The proteins that were ranked higher than the PAP isoforms all had the sequences related to the NFTLPSWA sequence. The higher final scores of these proteins were caused by the input from peptides that have matches to these sequences. As was the case for the PAP1 serum, the sum of scores for the PAP2 peptides related to the NFTLPSWA sequence of the PAP isoforms was higher than the sum of scores for the peptides that have matches to the related sequences in other proteins. The BLAST search of the first 120 peptides of the PAP3 500 peptide list also contained PAP isoforms as well as 444 proteins that had multiple matches to different peptides with the threshold maximal score 18.5. After ranking the top 100 proteins identified in the first step of analysis using the blast2seq, the PAP isoforms occupied the 8th and the 12th positions (Table S2C and Table 1). Out of 500 peptides of the PAP3 list, the 69 and 70 peptides had the matches to the two respective PAP isoforms, of which 48 peptides were related to the amino acids 336?42 QHEPYPL sequence of the PAP protein. The proteins that were ranked higher than the longest NP_001127666.1 PAP isoform also contained the motifs related to the QHEPYPL sequence. The sum of the scores for the QHEPYPL epitope of the PAP isoforms was ranked as 5th among the similar AN 3199 epitopes in other proteins. Validating the SAS Results of Mouse Sera Profiling by Bioinformatics Analyses. The BLAST-based analysis of serum antibody Pentagastrin Repertoire described above can identify the linear epitopes but will miss mimotopes that mimic the non-linear protein or carbohydrate epitopes. To identify all the motifs recognized by serum antibodies that represent linear and non-linear epitopes we analyzed the lists857.906.876.906.Final score3.0 2.616484 476.2 0.0164 3 NP_001180318.1 putative E3 ubiquitin-protein ligase UNKL isoform 142.2.2.Sum of overall scores2.2.3.1127.1159.1044.1169.481.Initial score0.478.0.0.0.Initial number of matches0.0.0.Protein length(aa)NP_004995.1 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit186 8, mitochondrial precursorNP_001127666.1 prostatic acid phosphatase isoform TM-PAP precursoNP_001504.2 maleylacetoacetate isomerase isoformNP_665878.2 maleylacetoacetate isomerase isoformNP_001090.2 prostatic acid phosphatase isoform PAPNP_005986.2 T-box transcription factor TBXProteins selected for PAP1 antiserumTable 1. Cont.RankNP_061867.1 F-box only proteinNP_078870.1 pantothenate kinase0.1764.618.2.1024.243.Serum Antibody Repertoire ProfilingFigure 1. Epitope profile of the PAP protein generated by PAP1 mouse antiserum. (A) The NP_001090.2 PAP variant amino acid sequence and the 40 matching peptides with the highest match scores generated by bl2seq program are shown. The sequences of the protein matching to peptides and the corresponding peptide sequences that match to protein are underlined. B. The graphic shows the distribution of the total score of the peptide matching over the sequence of the PAP protein. doi:10.1371/journal.pone.0067181.gof peptides using MEME software available online http://meme. sdsc.edu/meme/cgi-bin/meme.cgi. Figure 2 shows the three motifs identified by MEME for the each PAP antiserum. For the PAP1, PAP2 and PAP3 antisera, the most represented motifs were related to the NFTLPSWA and QHEPYPL sequences of the PAP pr.King the top 100 proteins identified in the first step of analysis using the blast2seq, the PAP isoforms occupied the 12th and the 15th positions (Table S2B and Table 1). The proteins that were ranked higher than the PAP isoforms all had the sequences related to the NFTLPSWA sequence. The higher final scores of these proteins were caused by the input from peptides that have matches to these sequences. As was the case for the PAP1 serum, the sum of scores for the PAP2 peptides related to the NFTLPSWA sequence of the PAP isoforms was higher than the sum of scores for the peptides that have matches to the related sequences in other proteins. The BLAST search of the first 120 peptides of the PAP3 500 peptide list also contained PAP isoforms as well as 444 proteins that had multiple matches to different peptides with the threshold maximal score 18.5. After ranking the top 100 proteins identified in the first step of analysis using the blast2seq, the PAP isoforms occupied the 8th and the 12th positions (Table S2C and Table 1). Out of 500 peptides of the PAP3 list, the 69 and 70 peptides had the matches to the two respective PAP isoforms, of which 48 peptides were related to the amino acids 336?42 QHEPYPL sequence of the PAP protein. The proteins that were ranked higher than the longest NP_001127666.1 PAP isoform also contained the motifs related to the QHEPYPL sequence. The sum of the scores for the QHEPYPL epitope of the PAP isoforms was ranked as 5th among the similar epitopes in other proteins. Validating the SAS Results of Mouse Sera Profiling by Bioinformatics Analyses. The BLAST-based analysis of serum antibody repertoire described above can identify the linear epitopes but will miss mimotopes that mimic the non-linear protein or carbohydrate epitopes. To identify all the motifs recognized by serum antibodies that represent linear and non-linear epitopes we analyzed the lists857.906.876.906.Final score3.0 2.616484 476.2 0.0164 3 NP_001180318.1 putative E3 ubiquitin-protein ligase UNKL isoform 142.2.2.Sum of overall scores2.2.3.1127.1159.1044.1169.481.Initial score0.478.0.0.0.Initial number of matches0.0.0.Protein length(aa)NP_004995.1 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit186 8, mitochondrial precursorNP_001127666.1 prostatic acid phosphatase isoform TM-PAP precursoNP_001504.2 maleylacetoacetate isomerase isoformNP_665878.2 maleylacetoacetate isomerase isoformNP_001090.2 prostatic acid phosphatase isoform PAPNP_005986.2 T-box transcription factor TBXProteins selected for PAP1 antiserumTable 1. Cont.RankNP_061867.1 F-box only proteinNP_078870.1 pantothenate kinase0.1764.618.2.1024.243.Serum Antibody Repertoire ProfilingFigure 1. Epitope profile of the PAP protein generated by PAP1 mouse antiserum. (A) The NP_001090.2 PAP variant amino acid sequence and the 40 matching peptides with the highest match scores generated by bl2seq program are shown. The sequences of the protein matching to peptides and the corresponding peptide sequences that match to protein are underlined. B. The graphic shows the distribution of the total score of the peptide matching over the sequence of the PAP protein. doi:10.1371/journal.pone.0067181.gof peptides using MEME software available online http://meme. sdsc.edu/meme/cgi-bin/meme.cgi. Figure 2 shows the three motifs identified by MEME for the each PAP antiserum. For the PAP1, PAP2 and PAP3 antisera, the most represented motifs were related to the NFTLPSWA and QHEPYPL sequences of the PAP pr.

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