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 Pipeline mzML/mzXML (conversion options-Centroid all scans) Add mzXML files Add Tandem Parameters (tandem.params配置参数文件) Add sequence database (待搜索fasta文件) Convert output files to pepXML
0.009
0.031
3.444444444
0.045
0.103
2.288888889
寻找全蛋白
全蛋白
protein
sp|P06733|ENOA_ HUMAN sp|P14618|KPYM_ HUMAN sp|P04406|G3P_HU MAN sp|P68104|EF1A1_ HUMAN sp|P10809|CH60_H UMAN sp|Q05639|EF1A2_ HUMAN sp|P09211|GSTP1_ HUMAN sp|P00558|PGK1_H UMAN sp|P12277|KCRB_ HUMAN sp|P63261|ACTG_ HUMAN sp|P09104|ENOG_ HUMAN sp|P11142|HSP7C_ HUMAN
0.02
0.012
0.6
0.014
0.007
0.5
Argininosuccinate synthase sp|P00966|ASSY_HUMAN OS=Homo sapiens GN=ASS1 PE=1 SV=2 sp|P02768|ALBU_HUMA Serum albumin OS=Homo sapiens N GN=ALB PE=1 SV=2
聚类分析（MeV）
Pathway分析（DAVID）
T-TH P05787 P21333 P00966 P31949 P48643 P78371 P25398 P35579 P68363 P10809
Thank you！
sp|O60869|EDF1_HUMA N
Endothelial differentiation-related factor 1 OS=Homo sapiens GN=EDF1 PE=1 SV=1
0.013
0.006
0.461538462
Tubulin-specific chaperone A sp|O75347|TBCA_HUMA OS=Homo sapiens GN=TBCA PE=1 N SV=3 sp|P00390|GSHR_HUMA N Glutathione reductase, mitochondrial OS=Homo sapiens GN|HNRDL_HU MAN
1
9.3
5
差异表达蛋白筛选流程（Knime）
差异表达蛋白
protein sp|A6NHG4|DDTL_HUMA N protein description Twist1 0.028 0.009 Twist1/Hsp90 0.017 0.005 Result 0.607142857 0.555555556 UDP-glucose 6-dehydrogenase sp|O60701|UGDH_HUMA OS=Homo sapiens GN=UGDH PE=1 N SV=1
18.9
6
GQVLNSDELQELYEGLR+TVS TLHHVLQR+VLSIQSHVIR+VV PLADIITPNQFEAELLSGR
LMCPQEIVDYIADKK+LSVNS HFMK
5
1
15.4
4
6
sp|O14745|NHRF1_HU MAN
1
14.5
5
KGPSGYGFNLHSDK+LLVVDP ETDEQLQK+LVEVNGENVEK +MSADAAAGAPLPR DAASVDK+DLTEYLSR+FGEV VDCTLK+GFGFVLFK+VFVGG LSPDTSEEQIK
protein description
percent tot indep coverage spectra
27.1 18.6 13 9
peptides
PFLELDTNLPANR+SHSAHFF EFLTK+VPAGLEK DIELVMSQANVSR+NILFVITK PDVYK+SPASDTYIVFGEAK GFTIPEAFR+IGNCPFSQR+KF LDGNELTLADCNLLPK+LHIV QVVCK
entry no.
1 2
protein
sp|A6NHG4|DDTL_HUM AN sp|E9PAV3|NACAM_HU MAN sp|O00299|CLIC1_HUM AN sp|O00764|PDXK_HUM AN sp|O14561|ACPM_HUM AN
protein probability
1 1
Add *.tandem.pep.xml Output *.tandem.interact.pep.xml
Analysis Peptides
TPP(home)-TandemDatabase Search(Run X!tandem)
搜库软件（X!Tandem）
Run PSMs 肽匹配数
X!Tandem输出结果
3
1
Chloride intracellular channel protein 1 OS=Homo sapiens GN=CLIC1 PE=1 SV=4
18.7
8
4
1
Pyridoxal kinase OS=Homo sapiens GN=PDXK PE=1 SV=1
Acyl carrier protein, mitochondrial OS=Homo sapiens GN=NDUFAB1 PE=1 SV=3 Na(+)/H(+) exchange regulatory cofactor NHERF1 OS=Homo sapiens GN=SLC9A3R1 PE=1 SV=4 Heterogeneous nuclear ribonucleoprotein D-like OS=Homo sapiens GN=HNRNPDL PE=1 SV=3
Heat treatment
1 0.522205207 0.483920368 0.413476263 0.378254211 0.359877489 0.327718224 0.292496172 0.264931087 0.263399694 0.232771822 0.21898928
寻找共定量蛋白
Control
1 0.545189504 0.288629738 0.583090379 0.556851312 0 0.402332362 0.411078717 0.27696793 0.32361516 0 0.274052478
Twist1
1 0.434504792 0.365814696 0.321086262 0.17571885 0 0.271565495 0.333865815 0.260383387 0.231629393 0 0.110223642
Twist1/HSP90
1 0.444940476 0.363095238 0.416666667 0.424107143 0.383928571 0.214285714 0.203869048 0.239583333 0.21875 0 0.186011905
HSP90
1 0.488405797 0.369565217 0.41884058 0.337681159 0.353623188 0.244927536 0.242028986 0.22173913 0.262318841 0 0.173913043