研究領域與專長

Experience in qualitative and quantitative proteomics (iTRAQ, SILAC, label-free) workflows by NanoLC-MS/MS analyses, in conjunction with utilizing a variety of database search engine and data handling programs for high-throughput expression profiling and quantification.

Comprehensive proteome-wide analysis of post-translational modifications, such as phosphorylation, and targeted analysis of protein sumoylation, neddylation and cysteine modifications etc.

Targeted analysis or manual examination of MS and MS/MS data to determine a true protein ID hit from false positive, to rescue false negative from the data, to confirm predicted sequence or modifications, and to determine site-specific PTM.

學經歷
經歷
  • 2014 – 迄今   研究副技師, 中央研究院生物化學所 / 儀器中心
  • 2009 – 2014   研究助技師 , 中央研究院生物化學所 / 儀器中心
  • 2003 – 2009   博士後研究員, 基因體醫學國家型科技計畫 蛋白體暨醣質體分析核心設施
學歷
  • 1997 – 2002   博士, 化學, 臺灣大學
主要著作
Ko YC, Tsai WH, Wang PW, Wu IL, Lin SY, Chen YL, Chen JY, Lin SF
Journal of biomedical science (2012)
Tsai WH, Wang PW, Lin SY, Wu IL, Ko YC, Chen YL, Li M, Lin SF
Frontiers in microbiology (2012)
Chang CC, Naik MT, Huang YS, Jeng JC, Liao PH, Kuo HY, Ho CC, Hsieh YL, Lin CH, Huang NJ, Naik NM, Kung CC, Lin SY, Chen RH, Chang KS, Huang TH, Shih HM
Molecular cell (2011)
Huang KY, Chen GD, Cheng CH, Liao KY, Hung CC, Chang GD, Hwang PP, Lin SY, Tsai MC, Khoo KH, Lee MT, Huang CJ
PloS one (2011)
Tang HW, Wang YB, Wang SL, Wu MH, Lin SY, Chen GC
EMBO JOURNAL (2011)
Chou YT, Lin HH, Lien YC, Wang YH, Hong CF, Kao YR, Lin SC, Chang YC, Lin SY, Chen SJ, Chen HC, Yeh SD, Wu CW
Cancer research (2010)
Lin MH, Hsu TL, Lin SY, Pan YJ, Jan JT, Wang JT, Khoo KH, Wu SH
MOLECULAR & CELLULAR PROTEOMICS (2009)
Chang YC, Lin SY, Liang SY, Pan KT, Chou CC, Chen CH, Liao CL, Khoo KH, Meng TC
Journal of proteome research (2008)
Lin SY, Chen YY, Fan YY, Lin CW, Chen ST, Wang AH, Khoo KH
Journal of proteome research (2008)
Hsiao HH, Hsieh HY, Chou CC, Lin SY, Wang AH, Khoo KH
Journal of proteome research (2007)
著作列表
  1. Chen YS, Ho TD, Liu L, Lee DH, Lee CH, Chen YR, (Lin SY), Lu CA, Yu SM  (2019-10)  Proceedings of the National Academy of Sciences of the United States of America  116(43), 21925-21935  "Sugar starvation-regulated MYBS2 and 14-3-3 protein interactions enhance plant growth, stress tolerance, and grain weight in rice."
  2. Chen FY, Huang MY, Lin YM, Ho CH, (Lin SY), Chen HY, Hung MC, Chen RH  (2019-09)  Journal of cell biology  218(9), 3002-3018  "BIK ubiquitination by the E3 ligase Cul5-ASB11 determines cell fate during cellular stress."
  3. Lee YR, Chen M, Lee JD, Zhang J, (Lin SY), Fu TM, Chen H, Ishikawa T, Chiang SY, Katon J, Zhang Y, Shulga YV, Bester AC, Fung J, Monteleone E, Wan L, Shen C, Hsu CH, Papa A, Clohessy JG, Teruya-Feldstein J, Jain S, Wu H, Matesic L, Chen RH, Wei W, Pandolfi PP  (2019-05)  Science  364(6441), eaau0159  "Reactivation of PTEN tumor suppressor for cancer treatment through inhibition of a MYC-WWP1 inhibitory pathway."
  4. Wu JS, Chen TY, Lin SS, (Lin SY), Hung CY, Tu IP, Chen HT, Chang WH  (2019-04)  Methods  159-160, 59-69  "Deriving a sub-nanomolar affinity peptide from TAP to enable smFRET analysis of RNA polymerase II complexes."
  5. Cheng AN, Fan CC, Lo YK, Kuo CL, Wang HC, Lien IH, (Lin SY), Chen CH, Jiang SS, Chang IS, Juan HF, Lyu PC, Lee AY  (2017-12)  Scientific reports  7(1), 17024  "Cdc7-Dbf4-mediated phosphorylation of HSP90-S164 stabilizes HSP90-HCLK2-MRN complex to enhance ATR/ATM signaling that overcomes replication stress in cancer."
  6. Liang SY, (Lin SY), Chiang IC, Shih YL  (2016-05)  Data in brief  8, 304-307  "Quantitative inner membrane proteome datasets of the wild-type and the Deltamin mutant of Escherichia coli."
  7. Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, Wang KY, (Lin SY), Shih YL  (2016-02)  Molecular & cellular proteomics : MCP  15(5), 1572-1583  "Quantitative proteomics analysis reveals the Min system of Escherichia coli modulates reversible protein association with the inner membrane."
  8. Hong CF, (Lin SY), Chou YT, Wu CW  (2016-01)  The Journal of biological chemistry  291(4), 1877-1889  "MicroRNA-7 Compromises p53-dependent Apoptosis by Controlling the Expression of the Chromatin Remodeling Factor SMARCD1."
  9. Hsieh YC, Chen YM, Li CY, Chang YH, Liang SY, (Lin SY), Lin CY, Chang SH, Wang YJ, Khoo KH, Aoki T, Wang HC  (2015-11)  Developmental and comparative immunology  53(1), 85-95  "To complete its replication cycle, a shrimp virus changes the population of long chain fatty acids during infection via the PI3K-Akt-mTOR-HIF1alpha pathway."
  10. Lin CH, (Lin SY), Chang HW, Ko LJ, Tseng YS, Chang VH, Yu WC  (2015-05)  Biochimica et Biophysica Acta-Molecular Cell Research  1853(5), 1174-1181  "CDK2 phosphorylation regulates the protein stability of KLF10 by interfering with binding of the E3 ligase SIAH1."
  11. Wang CY, Lin HC, Song YP, Hsu YT, (Lin SY), Hsu PC, Lin CH, Hung CC, Hsu MC, Kuo YM, Lee YJ, Hsu CY, Lee YH  (2015-05)  Molecular and cellular biology  35(10), 1712-1726  "Protein kinase C-dependent growth-associated protein 43 phosphorylation regulates gephyrin aggregation at developing GABAergic synapses."
  12. Chen KE, (Lin SY), Wu MJ, Ho MR, Santhanam A, Chou CC, Meng TC, Wang AH  (2014-10)  Science signaling  7(347), ra98  "Reciprocal allosteric regulation of p38gamma and PTPN3 involves a PDZ domain-modulated complex formation."
  13. Su MA, Huang YT, Chen IT, Lee DY, Hsieh YC, Li CY, Ng TH, Liang SY, (Lin SY), Huang SW, Chiang YA, Yu HT, Khoo KH, Chang GD, Lo CF, Wang HC  (2014-06)  PLoS pathogens  10(6), e1004196  "An invertebrate Warburg effect: a shrimp virus achieves successful replication by altering the host metabolome via the PI3K-Akt-mTOR pathway."
  14. Yuan WC, Lee YR, (Lin SY), Chang LY, Tan YP, Hung CC, Kuo JC, Liu CH, Lin MY, Xu M, Chen ZJ, Chen RH  (2014-05)  Molecular cell  54(4), 586-600  "K33-Linked Polyubiquitination of Coronin 7 by Cul3-KLHL20 Ubiquitin E3 Ligase Regulates Protein Trafficking."
  15. Loo CS, Chen CW, Wang PJ, Chen PY, (Lin SY), Khoo KH, Fenton RA, Knepper MA, Yu MJ  (2013-10)  Proceedings of the National Academy of Sciences of the United States of America  110(42), 17119-17124  "Quantitative apical membrane proteomics reveals vasopressin-induced actin dynamics in collecting duct cells."
  16. Wang CC, Lo HF, (Lin SY), Chen H  (2013-07)  The Biochemical journal  453(2), 201-208  "RACK1 (receptor for activated C-kinase 1) interacts with FBW2 (F-box and WD-repeat domain-containing 2) to up-regulate GCM1 (glial cell missing 1) stability and placental cell migration and invasion."
  17. Tsai WH, Wang PW, (Lin SY), Wu IL, Ko YC, Chen YL, Li M, Lin SF  (2012)  Frontiers in Microbiology  3, 60  "Ser-634 and Ser-636 of Kaposi's Sarcoma-Associated Herpesvirus RTA are Involved in Transactivation and are Potential Cdk9 Phosphorylation Sites."
  18. Ko YC, Tsai WH, Wang PW, Wu IL, (Lin SY), Chen YL, Chen JY, Lin SF  (2012)  Journal of biomedical science  19, 12  "Suppressive regulation of KSHV RTA with O-GlcNAcylation."
  19. Tang HW, Wang YB, Wang SL, Wu MH, (Lin SY), Chen GC  (2011-02)  EMBO JOURNAL  30(4), 636-651  "Atg1-mediated myosin II activation regulates autophagosome formation during starvation-induced autophagy."
  20. Huang KY, Chen GD, Cheng CH, Liao KY, Hung CC, Chang GD, Hwang PP, (Lin SY), Tsai MC, Khoo KH, Lee MT, Huang CJ  (2011)  PloS one  6(10), e26461  "Phosphorylation of the zebrafish M6Ab at serine 263 contributes to filopodium formation in PC12 cells and neurite outgrowth in zebrafish embryos."
  21. Chang CC, Naik MT, Huang YS, Jeng JC, Liao PH, Kuo HY, Ho CC, Hsieh YL, Lin CH, Huang NJ, Naik NM, Kung CC, (Lin SY), Chen RH, Chang KS, Huang TH, Shih HM  (2011)  Molecular cell  42(1), 62-74  "Structural and functional roles of Daxx SIM phosphorylation in SUMO paralog-selective binding and apoptosis modulation."
  22. Chou YT, Lin HH, Lien YC, Wang YH, Hong CF, Kao YR, Lin SC, Chang YC, (Lin SY), Chen SJ, Chen HC, Yeh SD, Wu CW  (2010-11)  Cancer research  70(21), 8822-8831  "EGFR promotes lung tumorigenesis by activating miR-7 through a Ras/ERK/Myc pathway that targets the Ets2 transcriptional repressor ERF."
  23. Lin MH, Hsu TL, Lin SY, Pan YJ, Jan JT, Wang JT, Khoo KH, Wu SH  (2009-12)  MOLECULAR & CELLULAR PROTEOMICS  8(12), 2613-2623  "Phosphoproteomics of Klebsiella pneumoniae NTUH-K2044 reveals a tight link between tyrosine phosphorylation and virulence."
  24. Lin SY, Chen YY, Fan YY, Lin CW, Chen ST, Wang AH, Khoo KH  (2008)  Journal of proteome research  7(8), 3293-3303  "Precise mapping of increased sialylation pattern and the expression of acute phase proteins accompanying murine tumor progression in BALB/c mouse by integrated sera proteomics and glycomics."
  25. Chang YC, Lin SY, Liang SY, Pan KT, Chou CC, Chen CH, Liao CL, Khoo KH, Meng TC  (2008)  Journal of proteome research  7(3), 1055-1066  "Tyrosine phosphoproteomics and identification of substrates of protein tyrosine phosphatase dPTP61F in Drosophila S2 cells by mass spectrometry-based substrate trapping strategy."
  26. Hsiao HH, Hsieh HY, Chou CC, Lin SY, Wang AH, Khoo KH  (2007)  Journal of proteome research  6(4), 1313-1324  "Concerted experimental approach for sequential mapping of peptides and phosphopeptides using C18-functionalized magnetic nanoparticles."
  27. Chen YY, Lin SY, Yeh YY, Hsiao HH, Wu CY, Chen ST, Wang AH  (2005)  Electrophoresis  26(11), 2117-2127  "A modified protein precipitation procedure for efficient removal of albumin from serum."

Experience in qualitative and quantitative proteomics (iTRAQ, SILAC, label-free) workflows by NanoLC-MS/MS analyses, in conjunction with utilizing a variety of database search engine and data handling programs for high-throughput expression profiling and quantification.

Comprehensive proteome-wide analysis of post-translational modifications, such as phosphorylation, and targeted analysis of protein sumoylation, neddylation and cysteine modifications etc.

Targeted analysis or manual examination of MS and MS/MS data to determine a true protein ID hit from false positive, to rescue false negative from the data, to confirm predicted sequence or modifications, and to determine site-specific PTM.

經歷
  • 2014 – 迄今   研究副技師, 中央研究院生物化學所 / 儀器中心
  • 2009 – 2014   研究助技師 , 中央研究院生物化學所 / 儀器中心
  • 2003 – 2009   博士後研究員, 基因體醫學國家型科技計畫 蛋白體暨醣質體分析核心設施
學歷
  • 1997 – 2002   博士, 化學, 臺灣大學
Ko YC, Tsai WH, Wang PW, Wu IL, Lin SY, Chen YL, Chen JY, Lin SF
Journal of biomedical science (2012)
Tsai WH, Wang PW, Lin SY, Wu IL, Ko YC, Chen YL, Li M, Lin SF
Frontiers in microbiology (2012)
Chang CC, Naik MT, Huang YS, Jeng JC, Liao PH, Kuo HY, Ho CC, Hsieh YL, Lin CH, Huang NJ, Naik NM, Kung CC, Lin SY, Chen RH, Chang KS, Huang TH, Shih HM
Molecular cell (2011)
Huang KY, Chen GD, Cheng CH, Liao KY, Hung CC, Chang GD, Hwang PP, Lin SY, Tsai MC, Khoo KH, Lee MT, Huang CJ
PloS one (2011)
Tang HW, Wang YB, Wang SL, Wu MH, Lin SY, Chen GC
EMBO JOURNAL (2011)
Chou YT, Lin HH, Lien YC, Wang YH, Hong CF, Kao YR, Lin SC, Chang YC, Lin SY, Chen SJ, Chen HC, Yeh SD, Wu CW
Cancer research (2010)
Lin MH, Hsu TL, Lin SY, Pan YJ, Jan JT, Wang JT, Khoo KH, Wu SH
MOLECULAR & CELLULAR PROTEOMICS (2009)
Chang YC, Lin SY, Liang SY, Pan KT, Chou CC, Chen CH, Liao CL, Khoo KH, Meng TC
Journal of proteome research (2008)
Lin SY, Chen YY, Fan YY, Lin CW, Chen ST, Wang AH, Khoo KH
Journal of proteome research (2008)
Hsiao HH, Hsieh HY, Chou CC, Lin SY, Wang AH, Khoo KH
Journal of proteome research (2007)
  1. Chen YS, Ho TD, Liu L, Lee DH, Lee CH, Chen YR, (Lin SY), Lu CA, Yu SM  (2019-10)  Proceedings of the National Academy of Sciences of the United States of America  116(43), 21925-21935  "Sugar starvation-regulated MYBS2 and 14-3-3 protein interactions enhance plant growth, stress tolerance, and grain weight in rice."
  2. Chen FY, Huang MY, Lin YM, Ho CH, (Lin SY), Chen HY, Hung MC, Chen RH  (2019-09)  Journal of cell biology  218(9), 3002-3018  "BIK ubiquitination by the E3 ligase Cul5-ASB11 determines cell fate during cellular stress."
  3. Lee YR, Chen M, Lee JD, Zhang J, (Lin SY), Fu TM, Chen H, Ishikawa T, Chiang SY, Katon J, Zhang Y, Shulga YV, Bester AC, Fung J, Monteleone E, Wan L, Shen C, Hsu CH, Papa A, Clohessy JG, Teruya-Feldstein J, Jain S, Wu H, Matesic L, Chen RH, Wei W, Pandolfi PP  (2019-05)  Science  364(6441), eaau0159  "Reactivation of PTEN tumor suppressor for cancer treatment through inhibition of a MYC-WWP1 inhibitory pathway."
  4. Wu JS, Chen TY, Lin SS, (Lin SY), Hung CY, Tu IP, Chen HT, Chang WH  (2019-04)  Methods  159-160, 59-69  "Deriving a sub-nanomolar affinity peptide from TAP to enable smFRET analysis of RNA polymerase II complexes."
  5. Cheng AN, Fan CC, Lo YK, Kuo CL, Wang HC, Lien IH, (Lin SY), Chen CH, Jiang SS, Chang IS, Juan HF, Lyu PC, Lee AY  (2017-12)  Scientific reports  7(1), 17024  "Cdc7-Dbf4-mediated phosphorylation of HSP90-S164 stabilizes HSP90-HCLK2-MRN complex to enhance ATR/ATM signaling that overcomes replication stress in cancer."
  6. Liang SY, (Lin SY), Chiang IC, Shih YL  (2016-05)  Data in brief  8, 304-307  "Quantitative inner membrane proteome datasets of the wild-type and the Deltamin mutant of Escherichia coli."
  7. Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, Wang KY, (Lin SY), Shih YL  (2016-02)  Molecular & cellular proteomics : MCP  15(5), 1572-1583  "Quantitative proteomics analysis reveals the Min system of Escherichia coli modulates reversible protein association with the inner membrane."
  8. Hong CF, (Lin SY), Chou YT, Wu CW  (2016-01)  The Journal of biological chemistry  291(4), 1877-1889  "MicroRNA-7 Compromises p53-dependent Apoptosis by Controlling the Expression of the Chromatin Remodeling Factor SMARCD1."
  9. Hsieh YC, Chen YM, Li CY, Chang YH, Liang SY, (Lin SY), Lin CY, Chang SH, Wang YJ, Khoo KH, Aoki T, Wang HC  (2015-11)  Developmental and comparative immunology  53(1), 85-95  "To complete its replication cycle, a shrimp virus changes the population of long chain fatty acids during infection via the PI3K-Akt-mTOR-HIF1alpha pathway."
  10. Lin CH, (Lin SY), Chang HW, Ko LJ, Tseng YS, Chang VH, Yu WC  (2015-05)  Biochimica et Biophysica Acta-Molecular Cell Research  1853(5), 1174-1181  "CDK2 phosphorylation regulates the protein stability of KLF10 by interfering with binding of the E3 ligase SIAH1."
  11. Wang CY, Lin HC, Song YP, Hsu YT, (Lin SY), Hsu PC, Lin CH, Hung CC, Hsu MC, Kuo YM, Lee YJ, Hsu CY, Lee YH  (2015-05)  Molecular and cellular biology  35(10), 1712-1726  "Protein kinase C-dependent growth-associated protein 43 phosphorylation regulates gephyrin aggregation at developing GABAergic synapses."
  12. Chen KE, (Lin SY), Wu MJ, Ho MR, Santhanam A, Chou CC, Meng TC, Wang AH  (2014-10)  Science signaling  7(347), ra98  "Reciprocal allosteric regulation of p38gamma and PTPN3 involves a PDZ domain-modulated complex formation."
  13. Su MA, Huang YT, Chen IT, Lee DY, Hsieh YC, Li CY, Ng TH, Liang SY, (Lin SY), Huang SW, Chiang YA, Yu HT, Khoo KH, Chang GD, Lo CF, Wang HC  (2014-06)  PLoS pathogens  10(6), e1004196  "An invertebrate Warburg effect: a shrimp virus achieves successful replication by altering the host metabolome via the PI3K-Akt-mTOR pathway."
  14. Yuan WC, Lee YR, (Lin SY), Chang LY, Tan YP, Hung CC, Kuo JC, Liu CH, Lin MY, Xu M, Chen ZJ, Chen RH  (2014-05)  Molecular cell  54(4), 586-600  "K33-Linked Polyubiquitination of Coronin 7 by Cul3-KLHL20 Ubiquitin E3 Ligase Regulates Protein Trafficking."
  15. Loo CS, Chen CW, Wang PJ, Chen PY, (Lin SY), Khoo KH, Fenton RA, Knepper MA, Yu MJ  (2013-10)  Proceedings of the National Academy of Sciences of the United States of America  110(42), 17119-17124  "Quantitative apical membrane proteomics reveals vasopressin-induced actin dynamics in collecting duct cells."
  16. Wang CC, Lo HF, (Lin SY), Chen H  (2013-07)  The Biochemical journal  453(2), 201-208  "RACK1 (receptor for activated C-kinase 1) interacts with FBW2 (F-box and WD-repeat domain-containing 2) to up-regulate GCM1 (glial cell missing 1) stability and placental cell migration and invasion."
  17. Tsai WH, Wang PW, (Lin SY), Wu IL, Ko YC, Chen YL, Li M, Lin SF  (2012)  Frontiers in Microbiology  3, 60  "Ser-634 and Ser-636 of Kaposi's Sarcoma-Associated Herpesvirus RTA are Involved in Transactivation and are Potential Cdk9 Phosphorylation Sites."
  18. Ko YC, Tsai WH, Wang PW, Wu IL, (Lin SY), Chen YL, Chen JY, Lin SF  (2012)  Journal of biomedical science  19, 12  "Suppressive regulation of KSHV RTA with O-GlcNAcylation."
  19. Tang HW, Wang YB, Wang SL, Wu MH, (Lin SY), Chen GC  (2011-02)  EMBO JOURNAL  30(4), 636-651  "Atg1-mediated myosin II activation regulates autophagosome formation during starvation-induced autophagy."
  20. Huang KY, Chen GD, Cheng CH, Liao KY, Hung CC, Chang GD, Hwang PP, (Lin SY), Tsai MC, Khoo KH, Lee MT, Huang CJ  (2011)  PloS one  6(10), e26461  "Phosphorylation of the zebrafish M6Ab at serine 263 contributes to filopodium formation in PC12 cells and neurite outgrowth in zebrafish embryos."
  21. Chang CC, Naik MT, Huang YS, Jeng JC, Liao PH, Kuo HY, Ho CC, Hsieh YL, Lin CH, Huang NJ, Naik NM, Kung CC, (Lin SY), Chen RH, Chang KS, Huang TH, Shih HM  (2011)  Molecular cell  42(1), 62-74  "Structural and functional roles of Daxx SIM phosphorylation in SUMO paralog-selective binding and apoptosis modulation."
  22. Chou YT, Lin HH, Lien YC, Wang YH, Hong CF, Kao YR, Lin SC, Chang YC, (Lin SY), Chen SJ, Chen HC, Yeh SD, Wu CW  (2010-11)  Cancer research  70(21), 8822-8831  "EGFR promotes lung tumorigenesis by activating miR-7 through a Ras/ERK/Myc pathway that targets the Ets2 transcriptional repressor ERF."
  23. Lin MH, Hsu TL, Lin SY, Pan YJ, Jan JT, Wang JT, Khoo KH, Wu SH  (2009-12)  MOLECULAR & CELLULAR PROTEOMICS  8(12), 2613-2623  "Phosphoproteomics of Klebsiella pneumoniae NTUH-K2044 reveals a tight link between tyrosine phosphorylation and virulence."
  24. Lin SY, Chen YY, Fan YY, Lin CW, Chen ST, Wang AH, Khoo KH  (2008)  Journal of proteome research  7(8), 3293-3303  "Precise mapping of increased sialylation pattern and the expression of acute phase proteins accompanying murine tumor progression in BALB/c mouse by integrated sera proteomics and glycomics."
  25. Chang YC, Lin SY, Liang SY, Pan KT, Chou CC, Chen CH, Liao CL, Khoo KH, Meng TC  (2008)  Journal of proteome research  7(3), 1055-1066  "Tyrosine phosphoproteomics and identification of substrates of protein tyrosine phosphatase dPTP61F in Drosophila S2 cells by mass spectrometry-based substrate trapping strategy."
  26. Hsiao HH, Hsieh HY, Chou CC, Lin SY, Wang AH, Khoo KH  (2007)  Journal of proteome research  6(4), 1313-1324  "Concerted experimental approach for sequential mapping of peptides and phosphopeptides using C18-functionalized magnetic nanoparticles."
  27. Chen YY, Lin SY, Yeh YY, Hsiao HH, Wu CY, Chen ST, Wang AH  (2005)  Electrophoresis  26(11), 2117-2127  "A modified protein precipitation procedure for efficient removal of albumin from serum."