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. Author manuscript; available in PMC: 2011 Feb 5.
Published in final edited form as: J Proteome Res. 2010 Feb 5;9(2):990–996. doi: 10.1021/pr900885k

Table 1.

Neuropeptides identified from the sea urchin radial nerve tissue by combined database search and hybrid approach.

Protein/EST Id Description Sequence Ptm Mascot ProtDBa Rescueb Custom DB based on Maldi/Qtof MSc Detail IggyPepd Masco t score Mascot score threshold delta mass charge
XP_001176287 hypothetical protein R.GFETPASSRIN.S √ -/√ 43 35 0.0151 2
XP_001176287 hypothetical protein R.GFETPASSRINS.R √ √/√ 46 37 0.0314 2
XP_001176287 hypothetical protein R.GFRVLPQLNDDD.N √ √/- 40 39 0.2654 2
XP_001176287 hypothetical protein R.GFRVLPQLNDDDN.- √ √/√ 73 39 0.0251 2
XP_001176287 hypothetical protein A.EDGMELTHDEQPLNAMEI.R √ √ √/- 26 37 0.3249 2
XP_001176287 hypothetical protein R.SPQDEQIDLRYLLQNFLDNRDT.R √ √/- 48 27 0.4845 2
XP_785647 similar to pedal peptide precursor protein K.GFNSGAMEPLGAGFF.K √ √/√ 30 26 0.036 2
XP_785647 similar to pedal peptide precursor protein K.GFHNGAMEPLKSGFL.K √ √/√ 51 31 0.0990 2
XP_785647 similar to pedal peptide precursor protein K.RFLTGALEPLSSGFI.K √ √/√ 56 36 0.0269 2
XP_785647 similar to pedal peptide precursor protein K.GFNTGAMEPLGSGFI.K √ √ -/√ 11 24 0.0157 2
XP_785647 similar to pedal peptide precursor protein R.FLTGALEPLSSGFI.K √ -/√ 42 27 0.0811 2
XP_785647 similar to pedal peptide precursor protein K.DFNTGAMEPLGSGFI.K √ √ -/√ 11 22 0.0239 2
XP_785647 similar to pedal peptide precursor protein K.GFHAGAMEPLSSGFIDG.K Am √ √/√ 85 34 0.3258 2
XP_785647 similar to pedal peptide precursor protein R.GFYNGAMEPLSAGFHQG.K Am √ √/- 69 32 0.3522 2
XP_785647 similar to pedal peptide precursor protein K.GFNSGAMEPLGSGFI.K √ √/√ 36 33 0.0871 2
XP_785647 similar to pedal peptide precursor protein R.GFYNGAMEPLSAGFHQG.K Am √ √/√ 69 31 0.3426 2
XP_001175944 hypothetical protein S.LQFETTQDRVPA.K √ √/√ 87 44 0.2271 2
XP_001175944 hypothetical protein C.SLQFETTQDRVPA.K √ √/√ 80 46 0.2941 2
XP_799858 hypothetical protein K.APVYSGAKPIM.- √ √/√ 62 52 0.2208 2
XP_799858 hypothetical protein R.SINSYLPGDMVRHVS.K √ √/- 39 26 0.0071 2
XP_799858 hypothetical protein R.SLKNRQLFTQTRNKY.S √ √ √/- 18 31 0.5412 4
XP_001175555 hypothetical protein L.YEEPIRQEGGD.K √ -/- √ 35 29 0.0221 2
XP_001199000 similartoarginine/serine-richsplicingfactor4 T.SIKADGEVTEDVDK.R √ √ -/√ 21 34 0.0383 2
XP_001199000 similartoarginine/serine-richsplicingfactor4 R.ANMFRSRLRGNG.K Am √ √ -/√ 9 24 0.0445 2
XP_001199000 similartoarginine/serine-richsplicingfactor4 R.ANYFRGRGRKPG.K Am √ √ -/√ 11 28 0.035 2
XP_001199000 similartoarginine/serine-richsplicingfactor4 R.ANMFRSRLRGKG.K Am √ √ √/√ 18 25 0.0454 2
XP_001199000 similartoarginine/serine-richsplicingfactor4 R.DDPDAAEALVPGGDLSEE.K √ √ √/√ 19 33 0.0311 2
XP_001199000 similartoarginine/serine-richsplicingfactor4 R.DDPDAALVDEFMDEE.K √ √/√ 42 29 0.0316 2
ABU55286 GnRH-like tetrapeptide R.QFVGGELIPSPEL.R pQ √ -/√ 29 27 0.0256 2
AAC26833 thymosin beta N.TLPTKETIEQEKTA.- √ -/- √ 43 25 0.0113 2
XP_001175484 hypothetical protein A.APAPYFDEDAMDLMDPVFNFKDDSAV.K √ -/- 25 22 0.523 2
XP_001186882 similar to LFRFa precursor R.PHGGSAFVFG.R Am √ √ -/- 25 42 0.1743 2
XP_001186882 similar to LFRFa precursor R.DWAPREQDFANAAEESGPY.K √ √ -/- 23 27 0.3151 2
XP 001175691 hypothetical protein R.GAAENALDEQEIYEIIESLEHAM.S √ -/- 35 34 0.4755 3
New_Precursor_GSTPEDIA R.GSTPEDIAELVSRN.R √/√ 92 49 0.2919 2
New_Precursor_GSTPEDIA Q.QKQDLAAILDQLHNTYQM.A pQ √/√ 70 57 0.4383 2
CD294941 New_Precursor_FGGANEPM K.NFGGSMEPMQSGFY.K √ √/- 18 32 0.2296 2
CD294941 New_Precursor_FGGANEPM K.NFGSGLNMEPMQSGFY.K -/√ 35 34 0.017 2
CD294941 New_Precursor_FGGANEPM R.FGGANEPMRSGFF.K √/√ 86 50 0.298 2
CD294941 New_Precursor_FGGANEPM R.FGSGLDSMQSGFY.K √ -/√ 21 25 0.0326 2
CD294941 New_Precursor_FGGANEPM R.FGSGSLEPMSSGFY.K √ -/√ 24 35 0.2291 2
CD294941 New_Precursor_FGGANEPM R.FGSMNMEPLVSGFY.K √/√ 45 33 0.2724 2
CD294941 New_Precursor_FGGANEPM T.LPIEDKDGLDIEDQE.E -/√ 54 32 0.0481 2
CD294941 New_Precursor_FGGANEPM T.LPIEDKDGLDIEDQEE.A √/√ 53 40 0.2881 2
CD294941 New_Precursor_FGGANEPM T.LPIEDKDGLDIEDQEEAE.K -/√ 54 27 0.0303 2
New_Precursor_GYPRNSVV R.GYPRNSVVADPVL.R √/√ 57 40 0.2945 2
New_Precursor_DAGPAWYG R.DAGPHAWYGTGMFG.K Am √/- 40 30 0.2646 2
New_Precursor_LPANLARE S.LPANLARE.R √ 0.0076 2
New_Precursor_LYDALKNA R.LYDALKNAQV.K √ 0.017 2
a

Neuropeptides identified with a Mascot database search against the NCBI Sea Urchin protein database containing 44039 sequences.

b

Neuropeptides having a Mascot score below the threshold are “rescued” based on multiple criteria: 1) one or more de novo derived tags coincide with the Mascot sequence or the peptide is exclusively found with IggyPep, 2) the precursor protein received a good Mascot score, 3) manual inspection of Δmass, fragmentation pattern, and error distribution between experimental and predicted fragment ions. Only peptides that meet the neuropeptide precursor characteristics (basic cleavage patterns, leading signal peptide) are considered for “rescuing”.

c

Neuropeptides identified with a Mascot database search against a custom database, compiled using all open reading frames sharing overlap with the chromosome locations where de novo derived tags map (IggyPep batch mode).Data shown for both Maldi TOF-TOF and ESI-Qtof spectra.

d

Neuropeptides identified from high quality unassigned spectra using the IggyPep web interface (www.iggypep.org) after manual or automatic de novo sequencing (IggyPep detailed mode).