Biotechnology Bulletin ›› 2021, Vol. 37 ›› Issue (8): 307-318.doi: 10.13560/j.cnki.biotech.bull.1985.2021-0183
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WANG Zhi-bo1,2(), WANG Dao-ping2, MIAO Lan1,3, LI Ying1, PAN Ying-hong2(), LIU Jian-xun1,3()
Received:
2021-02-09
Online:
2021-08-26
Published:
2021-09-10
Contact:
PAN Ying-hong,LIU Jian-xun
E-mail:wzb19950916@163.com;panyinghong@caas.cn;liujx0324@sina.com
WANG Zhi-bo, WANG Dao-ping, MIAO Lan, LI Ying, PAN Ying-hong, LIU Jian-xun. Comparative Study on Methods of Analyzing Proteome in Blood Samples[J]. Biotechnology Bulletin, 2021, 37(8): 307-318.
Fig. 2 Comparison of mass spectrometry results of blood samples prepared by 3 pre-processing methods A:Protein identification numbers and duplication rates of three repeated sample preparations for plasma(P),serum(SK)with high-abundance proteins remained,and serum(SR)with high-abundance proteins removed. B:The average number of proteins,peptides,PSMs and MS/MS spectrum for SK and SR. **:P<0.01. C:Principal component analysis of protein quantification
Fig. 3 Comparison of mass spectrometry results of serum proteins with different enzymatic digestion methods A:Average number of identified proteins,peptides and PSMs. *:P<0.05,and **:P<0.01. B:Comparison of percentage of missed enzymatic cleavage sites. C:Protein identification number and duplication rate of 3 repeated sample preparations. D:Sequence coverage of protein. E:Principal component analysis of protein quantification
Fig. 4 Comparison of DDA and DIA data indices A:Average number of identified proteins in 3 technical repeats,*:P<0.05. B:Missing value matrix of protein quantification in 3 technical repeats,the red area represents missing values. C:Comparison of protein qualitative repeatability by 3 technical repeats. D:The statistics in coefficient of variation of the protein(peptides)peak intensity
蛋白 Protein | DIA* | PRM** |
---|---|---|
A0A0G2JSK1 | 0.163 | IFSQQADLSR,0.045;KIFSQQADLSR,0.064;DTLPHEDQGKGR,0.123 |
A0A0G2JVP4 | 0.030 | ESATVTCLVK,0.058;TFPTLR,0.0732;DLPSPQK,0.128 |
A0A0G2JV1 | 0.083 | HMEASLQEFKASPR,0.077;AVYLPNCDR,0.090;ISELKAEAVK,0.520 |
A0A0G2K4K2 | 0.867 | LWIYDTSK,0.502 |
A0A0G2K531 | 0.209 | QAALGAR,0.029;LFWEPMKIHDIR,0.460;NSCPPTAELLGSPGR,0.480 |
A0A0G2K7X7 | 0.283 | CVGSAFETQSCNPER,0.019;ILPLTICK,0.019;ACGACPIWSK,0.032 |
A0A0G2K896 | 0.217 | SSTFQLFGSPHGK,0.013;WCIVSDHEATK,0.059;VKWCAVGQQER,0.063 |
B0BNN4 | 0.157 | SISCDEIPGQQSR,0.023;LCTPLLPK,0.031;HCYDIHNCVLK,0.129 |
B2RYM3 | 0.052 | ELAAQTIK,0.024;ANLSSQILK,0.031;IADHKLSTFKADVR,0.049 |
B5DEH7 | 0.114 | ANPGNFPWQAFTNIHGR,0.053;LPIADR,0.122;GLTVHLK,0.248 |
D3ZAB3 | 0.711 | LMIYGATNLEDGVPSR,0.140 |
D3ZAE6 | 1.732 | YLQGNTVQLR,0.085;QLDEGLFGR,0.450 |
F1LWD0 | 0.867 | ANSYTTEYNPSVK,0.033 |
F1LWS4 | 1.292 | NGYLYHENIRR,0.227;SYFPVPIGK,0.333;QCVFHYVENGESSYWQR,0.375 |
F1LWW1 | 0.902 | VTISCR,1.485 |
F1LXY6 | 0.040 | APEWLGFIR,0.037;ANGYTTEYNPSVK,0.040;AEDTATYYCAR,0.062 |
F1LYU4 | 1.732 | ASNLASGIPAR,0.020 |
G3V7L3 | 0.193 | TNVIQLR,0.019;CGTYGIYTK,0.066;LPITSLEK,0.080 |
G3V7N9 | 0.055 | VITNVNDNYEPR,0.022;TVNSALRPNQAIR,0.057;TVNSALRPNQAIRFEK,0.146 |
G3V7P2 | 0.250 | TLQEAVDSLKK,0.296 |
G3V7P5 | 1.076 | WQSLPR,0.011;SCDVPVFENAK,0.022;IDHGSIKLPR,0.026 |
Table 1 Quantitative analysis on the coefficient of variation of protein from DIA and corresponding peptides from PRM in 3 repeats
蛋白 Protein | DIA* | PRM** |
---|---|---|
A0A0G2JSK1 | 0.163 | IFSQQADLSR,0.045;KIFSQQADLSR,0.064;DTLPHEDQGKGR,0.123 |
A0A0G2JVP4 | 0.030 | ESATVTCLVK,0.058;TFPTLR,0.0732;DLPSPQK,0.128 |
A0A0G2JV1 | 0.083 | HMEASLQEFKASPR,0.077;AVYLPNCDR,0.090;ISELKAEAVK,0.520 |
A0A0G2K4K2 | 0.867 | LWIYDTSK,0.502 |
A0A0G2K531 | 0.209 | QAALGAR,0.029;LFWEPMKIHDIR,0.460;NSCPPTAELLGSPGR,0.480 |
A0A0G2K7X7 | 0.283 | CVGSAFETQSCNPER,0.019;ILPLTICK,0.019;ACGACPIWSK,0.032 |
A0A0G2K896 | 0.217 | SSTFQLFGSPHGK,0.013;WCIVSDHEATK,0.059;VKWCAVGQQER,0.063 |
B0BNN4 | 0.157 | SISCDEIPGQQSR,0.023;LCTPLLPK,0.031;HCYDIHNCVLK,0.129 |
B2RYM3 | 0.052 | ELAAQTIK,0.024;ANLSSQILK,0.031;IADHKLSTFKADVR,0.049 |
B5DEH7 | 0.114 | ANPGNFPWQAFTNIHGR,0.053;LPIADR,0.122;GLTVHLK,0.248 |
D3ZAB3 | 0.711 | LMIYGATNLEDGVPSR,0.140 |
D3ZAE6 | 1.732 | YLQGNTVQLR,0.085;QLDEGLFGR,0.450 |
F1LWD0 | 0.867 | ANSYTTEYNPSVK,0.033 |
F1LWS4 | 1.292 | NGYLYHENIRR,0.227;SYFPVPIGK,0.333;QCVFHYVENGESSYWQR,0.375 |
F1LWW1 | 0.902 | VTISCR,1.485 |
F1LXY6 | 0.040 | APEWLGFIR,0.037;ANGYTTEYNPSVK,0.040;AEDTATYYCAR,0.062 |
F1LYU4 | 1.732 | ASNLASGIPAR,0.020 |
G3V7L3 | 0.193 | TNVIQLR,0.019;CGTYGIYTK,0.066;LPITSLEK,0.080 |
G3V7N9 | 0.055 | VITNVNDNYEPR,0.022;TVNSALRPNQAIR,0.057;TVNSALRPNQAIRFEK,0.146 |
G3V7P2 | 0.250 | TLQEAVDSLKK,0.296 |
G3V7P5 | 1.076 | WQSLPR,0.011;SCDVPVFENAK,0.022;IDHGSIKLPR,0.026 |
Fig.5 Qualitative and quantitative results of blood sample proteome based on optimized workflow A:Venn diagram of DDA qualitative results. B:CV distribution diagram of DDA protein quantitative results
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