关于pFind结果文件pFind.protein的几个问题

[daimantianxingguangzhishi]

zyl.spectra.xlsx zly-Filtered.spectra.xlsx zyl.protein.xlsx

1.pFind.protein文件表头第一行中Have_Distinct_Pep一列只显示该蛋白质是否含有protein-unique peptide，请问从哪里可以看到该独特肽段的序列具体是什么？

2.pFind.protein文件表头第二行中Proteins显示不完全，只能显示11个蛋白质。在pFind_Filtered.spectra和pFind.spectra文件中，同一个File_Name的肽段指向了更多的蛋白质。请问如何在pFind.protein文件中导出全部蛋白？ 如：我们的数据zyl.protein.xlsx中，肽段20210110-S13.22095.22095.2.0.dta在pFind.protein文件的proteins显示11个蛋白： col1_Philantomba_maxwellii__Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Cephalophinae_Philantomba/col1_Capra_ibex__2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Caprinae__Capra/col1_Bos_grunniens_Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Bovinae__Bos/col1_Aepyceros_melampus_Meillour_2020_MSMS_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Aepycerotinae__Aepyceros/col1_Capra_hircus_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Caprinae__Capra/col1_Connochaetes_taurinus__Janzen_2021_MSMS_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Alcelaphinae/col1_Sylvicapra_grimmia__Janzen_2021_MSMS_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Cephalophinae_Sylvicapra/col1_Cephalophus_harveyi__Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Cephalophinae_Cephalophus/col1_Aepyceros_melampus__Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Aepycerotinae__Aepyceros/col1_Raphicerus_campestris/col1_Madoqua_kirkii/； 而该肽段在PBuild和pFind_Filtered.spectra文件中的proteins显示更多的蛋白： col1_Philantomba_maxwellii__Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Cephalophinae_Philantomba/col1_Capra_ibex__2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Caprinae__Capra/col1_Bos_grunniens_Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Bovinae__Bos/col1_Aepyceros_melampus_Meillour_2020_MSMS_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Aepycerotinae__Aepyceros/col1_Capra_hircus_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Caprinae__Capra/col1_Connochaetes_taurinus__Janzen_2021_MSMS_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Alcelaphinae/col1_Sylvicapra_grimmia__Janzen_2021_MSMS_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Cephalophinae_Sylvicapra/col1_Cephalophus_harveyi__Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Cephalophinae_Cephalophus/col1_Aepyceros_melampus__Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Aepycerotinae__Aepyceros/col1_Raphicerus_campestris/col1_Madoqua_kirkii/col1_Eudorcas_thomsonii/col1_Bubalus_bubalis_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Bovinae__Bubalus/col1_Bos_mutus_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Bovinae__Bos/col1_Oreotragus_oreotragus/col1_Litocranius_walleri/col1_Procapra_przewalskii/col1_Bos_indicus_x_Bos_taurus_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Bovinae__Bos/col1_Oryx_gazella__Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Hippotraginae_Oryx/col1_Rupicapra_rupicapra_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Caprinae__Rupicapra/col1_Neotragus_moschatus/col1_Pantholops_hodgsonii_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Antilopinae__Pantholops/col1_Bos_indicus_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Bovinae__Bos/col1_Nanger_granti/col1_Saiga_tatarica_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Antilopinae__Saiga/col1_Ourebia_ourebi/col1_Bison_bison_bison_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Bovinae__Bison/col1_Cyncerus_caffer_Africanbuffalo_Janzen_2021_MSMS_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Bovinae__Syncerus/col1_Damaliscus_lunatus__Janzen_2021_MSMS_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Alcelaphinae/col1_Aepyceros_melampus_2019_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Aepycerotinae__Aepyceros/col1_Capra_ibex__Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Caprinae__Capra/col1_Ovis_aries_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Caprinae__Ovis/col1_Alcelaphus_buselaphus__Janzen_2021_MSMS_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Alcelaphinae/col1_Bos_taurus_2019Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae__Bovinae__Bos/。

3.我们观察到，同一肽段可能来源于target蛋白和decoy蛋白（REV_），而系统将其标识为target肽段报导，意思是该肽段属于target和decoy数据库的共有肽段吗？是根据什么做出target/decoy判断的？ 如：我们的数据zyl.protein.xlsx中，我们鉴定到一个肽段GAPGLPGPR（File_Name:20210110-S13.8873.8873.2.0.dta），显示为target，其proteins包含多个target蛋白和decoy蛋白，例如我们可以同时在pFind.protein文件中的target蛋白（如protein group: col1_Cephalophus_harveyi__Janzen_2021_DNA_Mammalia__Eutheria__Laurasiatheria__Cetartiodactyla__Ruminantia__Pecora__Bovidae_Cephalophinae_Cephalophus）和decoy蛋白（如protein group: REV_col1_Antidorcas）中找到该肽段的报导。这说明该肽段可能来源于target蛋白和decoy蛋白（REV_），意思是该肽段属于target和decoy数据库的共有肽段吗？pFind将其标识为target报导，是根据什么做出target/decoy判断的？

4.由于我们的数据库中部分蛋白在某些位点为未知氨基酸，我们鉴定到了一些序列中包含“X”的肽段，这里X指的是任意氨基酸吗？能否显示鉴定到的肽段的实际序列？ 如：我们的数据zyl.protein.xlsx中，根据数据库蛋白序列“…XXXXXX.XXXXXXGFSGLDGAKGDAGPAGPK.GEPGSP…”（其中两个间隔符“.”之间的为匹配到肽段的序列）鉴定到肽段XXXXXXGFSGLDGAKGDAGPAGPK（File_Name:20210110-S13.23333.23333.3.0.dta）。