蛋白质组学数据数据处理流程

1、蛋白质组学数据处理流程Veyron质谱数据 raw data文件转换成mzXML文件Analysis PipelinemzML/mzXML(conversion options-Centroid all scans)TPP(home)-Tandem-Database Search(Run X!tandem)Add mzXML filesAdd Tandem Parameters(tandem.params配置参数文件)Add sequence database(待搜索fasta文件)Convert output files to pepXMLAnalysisPeptidesAdd *.tand

2、em.pep.xmlOutput *.eract.pep.xmlRun PSMs肽匹配数搜库软件（X!Tandem）entry teinprotein probabilityprotein descriptionpercent coveragetot indep spectrapeptides1sp|A6NHG4|DDTL_HUMAN127.113PFLELDTNLPANR+SHSAHFFEFLTK+VPAGLEK2sp|E9PAV3|NACAM_HUMAN118.69DIELVMSQANVSR+NILFVITKPDVYK+SPASDTYIVFGEAK3sp|O

3、00299|CLIC1_HUMAN1Chloride intracellular channel protein 1 OS=Homo sapiens GN=CLIC1 PE=1 SV=418.78GFTIPEAFR+IGNCPFSQR+KFLDGNELTLADCNLLPK+LHIVQVVCK4sp|O00764|PDXK_HUMAN1Pyridoxal kinase OS=Homo sapiens GN=PDXK PE=1 SV=118.96GQVLNSDELQELYEGLR+TVSTLHHVLQR+VLSIQSHVIR+VVPLADIITPNQFEAELLSGR5sp|O14561|ACPM

4、_HUMAN1Acyl carrier protein, mitochondrial OS=Homo sapiens GN=NDUFAB1 PE=1 SV=315.44LMCPQEIVDYIADKK+LSVNSHFMK6sp|O14745|NHRF1_HUMAN1Na(+)/H(+) exchange regulatory cofactor NHE-RF1 OS=Homo sapiens GN=SLC9A3R1 PE=1 SV=414.55KGPSGYGFNLHSDK+LLVVDPETDEQLQK+LVEVNGENVEK+MSADAAAGAPLPR7sp|O14979|HNRDL_HUMAN1

5、Heterogeneous nuclear ribonucleoprotein D-like OS=Homo sapiens GN=HNRNPDL PE=1 SV=39.35DAASVDK+DLTEYLSR+FGEVVDCTLK+GFGFVLFK+VFVGGLSPDTSEEQIKX!Tandem输出结果输出结果差异表达蛋白筛选流程（Knime）差异表达蛋白proteinprotein descriptionTwist1Twist1/Hsp90Resultsp|A6NHG4|DDTL_HUMAN0.0280.0170.607142857sp|O60701|UGDH_HUMANUDP-glucos

6、e 6-dehydrogenase OS=Homo sapiens GN=UGDH PE=1 SV=10.0090.0050.555555556sp|O60869|EDF1_HUMANEndothelial differentiation-related factor 1 OS=Homo sapiens GN=EDF1 PE=1 SV=10.0130.0060.461538462sp|O75347|TBCA_HUMANTubulin-specific chaperone A OS=Homo sapiens GN=TBCA PE=1 SV=30.020.0120.6sp|P00390|GSHR_

7、HUMANGlutathione reductase, mitochondrial OS=Homo sapiens GN=GSR PE=1 SV=20.0140.0070.5sp|P00966|ASSY_HUMANArgininosuccinate synthase OS=Homo sapiens GN=ASS1 PE=1 SV=20.0090.0313.444444444sp|P02768|ALBU_HUMANSerum albumin OS=Homo sapiens GN=ALB PE=1 SV=20.0450.1032.288888889寻找全蛋白全蛋白proteinControlTwi

8、st1Twist1/HSP90HSP90Heat treatmentsp|P06733|ENOA_HUMAN11111sp|P14618|KPYM_HUMAN0.5451895040.4345047920.4449404760.4884057970.522205207sp|P04406|G3P_HUMAN0.2886297380.3658146960.3630952380.3695652170.483920368sp|P68104|EF1A1_HUMAN0.5830903790.3210862620.4166666670.418840580.413476263sp|P10809|CH60_HU

9、MAN0.5568513120.175718850.4241071430.3376811590.378254211sp|Q05639|EF1A2_HUMAN000.3839285710.3536231880.359877489sp|P09211|GSTP1_HUMAN0.4023323620.2715654950.2142857140.2449275360.327718224sp|P00558|PGK1_HUMAN0.4110787170.3338658150.2038690480.2420289860.292496172sp|P12277|KCRB_HUMAN0.276967930.2603833870.2395833330.221739130.264931087sp|P63261|ACTG_HUMAN0.323615160.2316293930.218750.2623188410.263399694sp|P09104|ENOG_HUMAN00000.232771822sp|P11142|HSP7C_HUMAN0.2740524