pFind3
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pFindStudio
how to do label-free quantification and I cannot find the value from pBulid and the result files. I am wondering if the pfind is capable to do LFQ, and if...
在运行时报错内容如下 Process 1: [pParse] - pParse writes logs in E:\pFind3\data\.proc1\pParsePlusLog.txt Process 2: [pParse] - pParse writes logs in E:\pFind3\data\.proc2\pParsePlusLog.txt Process 3: [pParse] - pParse writes logs in E:\pFind3\data\.proc3\pParsePlusLog.txt Process 1:...
您好，请问thermo Astral数据如何用pfind搜库，用.raw+HCD-FTMS会报错，提示[pFind] ALERT: Invalid_msmspath1_Path: [D:\DKYF\QC\DDA\K562_QC_DDA_A_24min_20231127_1_HCDIT.pf2]
如题，pfind生成的mgf文件中，同一个scan对应多个TITLE，TITLE=peptide_20231113223937.13694.13694.2.0.dta; TITLE=peptide_20231113223937.13694.13694.2.1.dta; TITLE=peptide_20231113223937.13694.13694.2.2.dta。这些TITLE的PEPMASS不同，但子离子完全一致。另外，同一个scan，在pfind生成的mgf文件和msconvert生成的mgf文件中，离子峰数目是不同的，请问是什么原因？
In the article: _J. Am. Soc. Mass Spectrom._ 2019， 30， 8， 1396–1405. a DIA mode was used. But where is it in the newest pFind3 version?
[zyl.spectra.xlsx](https://github.com/pFindStudio/pFind3/files/13260323/zyl.spectra.xlsx) [zly-Filtered.spectra.xlsx](https://github.com/pFindStudio/pFind3/files/13260324/zly-Filtered.spectra.xlsx) [zyl.protein.xlsx](https://github.com/pFindStudio/pFind3/files/13260325/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）。
**1.我们发现即使在勾选open search后，是否添加某些不常见的Variable Modification依然能够显著影响ID rate，理论上这种情况是否很少见？** 如：对我们的古生物样品来说，勾选open search后，Variable Modification不添加Oxidation[P]的ID rate仅有0.3%，而添加Oxidation[P]后达到9.3%（Oxidation[P]修饰在Display All中选择）。 _搜库前Open Search和Variable Modification的设置如下图所示：_  _搜库后结果对比如下图所示（上为不添加Oxidation[P]，下为添加Oxidation[P]）：_     **2.在Identification中将FDR≤1%设为Spectra水平开始搜库，搜库完成后的Summary会自动写作“FDR Less than 1% at Peptides Level”而非Spectra Level。** _搜库前的设置如下图所示，设置为Spectra Level：_  _搜库完成后的Summary如下图所示，自动变为Peptide...
根据说明，pFind.spectra文件表头中Specificity列应为：0: non-specific; 1: C端特异性酶切; 2: N端特异性酶切; 3:两端都特异性酶切。我们发现我们样品得到的结果文件pFind.spectra似乎不符合上述取值规律：样品elastase酶切（酶切位点是AVSGLI的C端），搜库参数为Non-Specific，在pFind_Filtered.spectra、pFind.protein文件中所有肽段的Specificity均为0（non-specific），但pFind.spectra文件共27677个PSM中，却显示存在Specificity为1的肽段252个（例如：A.YRRFYGPV.-、R.RFYGPV.-、K.EQPPQPLFSFDFGA.S；其中两个间隔符“.”之间的为匹配的PSM，前后各为DataBase中蛋白被匹配段前后的氨基酸），Specificity为2的肽段289个（例如：G.APGVPGPA.G、-.MGPQGAR.R、M.GEGPVGEPPPL.Q）。尽管这些肽段全部因为q value>0.01而被筛去，以Non-Specific为搜库参数时是否应该所有肽段的Specificity都为0？
Hi, I'm a new user of pFind. When I try to search raw file, it stopped at the beginning and the report indicated an alert as follow. Please anyone tell...
