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Antibody Sequencing by LC-MS/MS. Paul Shan Bioinformatics Solutions Inc. Antibody. Protein sequence variation Sequencing by LC-MS/MS Full coverage High confidence Workflow of sequencing Multiple enzyme digestion High resolution MS/MS Data analysis - PowerPoint PPT Presentation
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Antibody Sequencing by LC-MS/MS
Paul ShanBioinformatics Solutions Inc.
Antibody
• Protein sequence variation• Sequencing by LC-MS/MS– Full coverage– High confidence
• Workflow of sequencing– Multiple enzyme digestion– High resolution MS/MS– Data analysis
Interactive de novo-based sequence reconstruction
Experimental
• MaterialsI 5154 IgG1 Kappa and SAB4700580 IgG2
• Enzymes AspN, Chymotrypsin, GluC, LysC, Proteinase K, and Trypsin
• Sample preparation Reduction / alkylation -> de-glycosylation -> separation ->
digestion
• LC-MS/MSOrbitrap with HCD
Database searching
Homolog protein sequence
GapLow confidence
Peptide De Novo Sequencing
• Local confidence score
• De novo sequence tag
Assembly of De Novo Tags
EPEDFALYYCQQRSNWPPSFTFGPTGRVDLKR Contig
De Novo tags
[200.12]EPEDFALYYCQQR
[204.09]PGTRVDLKR[200.12]
CQQRSNWPPSFTF[201.08]WPPSFTFGPGTR
...
[200.12]EPEDFALYYCQQR
[204.09]PGTRVDLKR[200.12]
CQQRSNWPPSFTF
[201.08]WPPSFTFGPGTR
MEIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPWTFGQGTKVEIKRT
Sequence Reconstruction
Problem: de novo errors、 database mutations
(denovo) X: [LS]CAFK(real) Y: [SI]CAFK || +|||(homolog) Z: [SI]AAFK
de novo error
mutation
(denovo) X: LSCAFK |||(homolog) Z: SIAAFK
Solution: minimize de novo errors and mutations
SPIDER
(de novo) : LLLYDASTR(real) : LLIYDASTR |||||||+|(homolog) : LLIYDASNR
MEIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPWTFGQGTKVEIKRT
(de novo): EPEDFALYYCQQRSNWPPSFTFGPTGRVDLKR(real) : EPEDFALYYCQQRSNWPPSFTFGPGTRVDIKR ||||||+|||||||||||+ ||||||||||||(homolog) : EPEDFAVYYCQQRSNWPPW TFGPGTRVEIKR
de novo error
mutation
GapLow confidence
EPEDFALYYCQQRSNWPPSFTFGPTGRVDLKR
Contigs
LLLYDASTRVLTQSPASLSLSPER
...
Sequence Validation
• Coverage – Peptide map at 0.1 % FDR
• Confidence– De Novo sequence tag map
EIVLTQSPASLSLSPGERATLSCRASQSVSSYLAWYQHKPGQAPRLLIYDASTRATGIPARFSGSGSGTDFTLTISSLEPEDFALYYCQQRSNWPPSFTFGPGTRVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
VLTQSPASLSLSPERATLSCR
EIVLTQSPASLSLSPGERATLSCRASQSVSSYLAWYQHKPGQAPRLLIYDASTRATGIPARFSGSGSGTDFTLTISSLEPEDFALYYCQQRSNWPPSFTFGPGTRVDIKRT
Report
CHAMPS - Antibody Sequencing Service
• Data analysis• Sample analysis
http://www.bioinfor.com/peaks/products/champs.html