N-terminal Edman Sequencing Sample Preparation ABRF 2002, Austin, Texas, March 9-12 John Neveu, Harvard University, Cambridge, MA Bill Henzel, Genentech Inc., South San Francisco, CA http://www.arbf.org ABRF 2002, March 8 - 12, Austin, Texas Objective: Get sample onto the instrument in sufficient purity, quantity and cleanliness to allow successful sequence analysis. • Sample is the intact protein(s) or peptide(s) for analysis. • Instrument defines the types of supports used for analysis. • Purity describes the number of proteins or peptides in a sample; assess by various methods including SDS-PAGE gel, HPLC. • Quantity can be determined by AAA, Bradford/Lowry/BCA assay, gel stain intensity, semi-quantitative HPLC. • Cleanliness is a lack of common interfering compounds that could impede the analysis. These five factors will define what types of sample preparation we must do for a successful analysis. Supports for analysis • Glass fiber filter, w/polybrene (quaternary polyamine) (ABI) • PVDF membrane by electroblotting, filtration, adsorption, and covalent linkage. • Bimodal reaction columns (RP/SAX) (HP) Biobrene / Polybrene Common Interferences • TRIS and other amines cause large chemical artifacts. • Buffering salts can interfere with the chemistry of the analysis. • Detergents can affect sample washout from reaction cartridge and conversion flask dynamics. SDS can also precipitate in the instrument. • Free amino acids contribute to high background in early cycles. Quantitation basics • Limited by the absolute instrument sensitivity, about 1pmol loaded at ~50% IY for an average lab. • Important to establish a reasonable level of quantitation for the researcher and the lab. • Rule: 1ug of 1kDa protein = 1 nmol • • • • 100ug of 100kDa protein = 1,000 pmol 10ug of 100kDa protein = 100 pmol 1.0ug of 100kDa protein = 10 pmol 0.5ug of 250kDa protein = 2 pmol PVDF Stain Intensity by Amido Black Common Sample Preparation Techniques for Soluble Samples • • • • • • • • • • • Direct Adsorption to PVDF Prosorb PVDF cartridge Reversed-phase (other media) packed micro pipettor tip devices Ultrafiltration membrane cartridge Precipitation methods 1D / 2D gel electrophoresis to PVDF by electroblotting HPLC separation and collection Micro-spin type cartridges Bimodal reaction cartridges On-bead synthetic peptides Covalent bonding to PVDF membrane Direct absorption to PVDF (and Zitex) membrane • Use for samples with high purity. • Suitable for samples of reasonably high concentration. • Allows removal of salts, buffers, free amino acids and some detergents. • Sample remains bound to membrane for analysis (addition of polybrene is recommended). Prosorb PVDF membrane • Use for samples with high purity. • Can be used with dilute samples. • Allows extensive washing to remove most contaminants. • Sample remains bound to membrane for analysis (addition of polybrene recommended). Reverse phase (or other media) packed micropipettor-tip devices • Suitable for samples of medium to high purity. • Can be used with dilute samples, binding to media can be a concern. • Extensive desalting, detergent removal possible. • Enrichment of specific species (i.e.. PO4), possible. • Sample is eluted in high concentration in solution for analysis or purification. Ultrafiltration membrane cartridge • Can be used to remove unwanted low MW components, peptides and proteins from complex mixtures by MW cutoff selection. • Can be used with dilute samples. • Allows extensive washing, buffer exchange, removal of detergents. • Sample is eluted in high concentration in solution for analysis or other chemistries. Precipitation methods • Acetone, chloroform/methanol, TCA • Low to high purity samples. • Used to concentrate dilute samples from solution, as little as 50ng total protein. • Complete buffer exchange possible. • Sample resolubilized in high concentration solution, ideal for loading onto SDS-PAGE gel. 1D or 2D Gel Electrophoresis Electroblotted to PVDF • Used for low (1D) to very complex mixtures (2D) of proteins or peptides. • High sample concentration needed due to limiting gel load volumes. Sample solubility issues may arise. • Sample is strongly bound to PVDF membrane in a highly concentration for analysis. HPLC separation and collection • Suitable for complex mixtures of proteins and peptides. • High sample concentration needed, injection volumes can be limited by column and flow. • Potential separation and concentration of individual protein and peptide species. • Sample is collected in high concentration solution. Capillary RP HPLC Separation of Peptides Micro-spin cartridges for protein and peptide preparation • Many new vendors, many chemistries and formats. • Uses range from crude preparation of mixtures to final clean up of single analyte for analysis. • Match sample with media for optimal results. • Multistage processes in convenient formats. Hewlett Packard Bimodal reaction columns • Very convenient reverse phase sample loading, concentration and washing. • On-column chemistries possible, easy clean up. On-bead synthetic peptides • • • • Used to confirm synthesis efficiency and correctness. Single beads can contain nanomoles of peptide. In practice, cleavage from the resin is best. Handling of single beads is a difficult task to do reproducibly. Covalent binding to Sequelon membrane • Chemically bind a single protein or peptide to hydrophobic membrane for analysis. • Allows efficient extraction of P32 labeled residues, extended sequencing of immobilized proteins, and other special chemistries to be applied. • Detergents can inhibit efficient binding. Sequelon DITC & Aryl Amine Chemistries Solid Phase Sequencing of DITC Coupled B e t a l a c t o g o l u b l i n 100 pmol value 10 1 0.1 0.01 0.001 0 20 40 60 Cycle 80 100 Peptide Standard: 10pmol (Tyr, Ala, Glu) 0226B PSS 10pmol Standard 1 0226B PSS 10pmol Residue 1 DPTU Y 6.00 6.00 D K 3.00 N 3.00 E Q T H G S 0.00 D A R W MV Y P F L I T G 0.00 DPTU dpu S dpu A -3.00 -3.00 E Q N R P 6.0 8.0 10.0 12.0 14.0 0226B PSS 10pmol 6.0 4.0 16.0 Residue 2 8.0 10.0 12.0 14.0 6.00 3.00 3.00 KL 16.0 Residue 3 E 6.00 I W 0226B PSS 10pmol DPTU A F M H 4.0 V DPTU K 0.00 0.00 G S V D -3.00 T N Q 4.0 R E P I L -3.00 N 8.0 10.0 12.0 S H T 14.0 16.0 4.0 P R V dpu Y Q M H 6.0 F A D K dpu Y G 6.0 8.0 10.0 L F 12.0 14.0 16.0 I Dirty Peptide Run: No Sequence Data 0227A 10pmol PSS Dirty Boy Standard 1 0227A 10pmol PSS Dirty Boy D 4.00 N S TG E Residue 1 H A R DPTU Y dpu 4.00 D K 2.00 2.00 E N M Q M T S 0.00 H G A V L I 0.00 DPTU P Q F Y R K V W L P dpu F I -2.00 -2.00 -4.00 -4.00 W 6.0 4.0 8.0 10.0 12.0 14.0 0227A 10pmol PSS Dirty Boy D S G E 4.0 16.0 Residue 2 H A R 6.0 8.0 10.0 12.0 14.0 16.0 0227A 10pmol PSS Dirty Boy DPTU D S G E Residue 3 H A DPTU T 4.00 4.00 R Y N 2.00 2.00 dpu N M 0.00 Q K K dpu 0.00 V P T M P L -2.00 Q Y L V -2.00 F I F W -4.00 -4.00 4.0 6.0 8.0 10.0 12.0 14.0 16.0 4.0 6.0 8.0 10.0 12.0 14.0 16.0 I Direct Adsorption to PVDF Membrane 0301C PSS via PVDF Direct Standard 1 0301C PSS via PVDF Direct G 4.00 Residue 1 H DPTU Y 4.00 S D K 2.00 2.00 dpu D E N K W Q 0.00 MV T S H G A F Y P R T L I 0.00 DPTU A N dpu L F V -2.00 I -2.00 E R P -4.00 M -4.00 6.0 4.0 8.0 10.0 12.0 14.0 16.0 0301C PSS via PVDF Direct G A 6.0 4.0 Residue 2 10.0 12.0 14.0 16.0 Residue 3 G DPTU 4.00 8.0 PSS via PVDF Cycle 2 E DPTU 4.00 2.00 2.00 H K K N 0.00 D N 0.00 S D dpu V Y dpu S F T -2.00 I L P H -2.00 I P E A R Q V R M Y M Q -4.00 -4.00 4.0 6.0 8.0 10.0 12.0 14.0 16.0 4.0 L F T 6.0 8.0 10.0 12.0 14.0 16.0 Prosorb PVDF Filter Cartridge 0301B PSS Prosorb Standard 1 0301B PSS Prosorb Residue 1 Y 4.00 DPTU 4.00 D K D 2.00 2.00 E N W Q 0.00 T S A H G F MV Y R L I T 0.00 DPTU P G dpu dpu K S -2.00 -2.00 A Q N E -4.00 6.0 8.0 10.0 12.0 14.0 16.0 0301B PSS Prosorb 6.0 4.0 Residue 2 A R P 8.0 10.0 12.0 14.0 16.0 0301B PSS Prosorb Residue 3 DPTU DPTU E 4.00 4.00 2.00 2.00 L I H -4.00 4.0 F V K D 0.00 0.00 K S G L I F P N Q R E 4.0 6.0 -2.00 I T N Q 10.0 12.0 14.0 16.0 4.0 R H -4.00 6.0 8.0 F V A S M 8.0 L P Y H -4.00 dpu G dpu V T -2.00 D Y 10.0 12.0 14.0 16.0 C18 Zip Tip Clean Up 0228C PSS by ZIP tip Standard 1 0228C PSS by ZIP tip Residue 1 Y 4.00 DPTU 4.00 D K 2.00 N Q 0.00 2.00 E G D W T S H G MV A R P L I F Y 0.00 N DPTU S dpu dpu -2.00 -2.00 T V A E L R P Q -4.00 6.0 8.0 10.0 12.0 14.0 4.0 16.0 PSS by ZIP tip Cycle 1 Residue 2 6.0 8.0 10.0 12.0 14.0 Residue 3 DPTU E 4.00 4.00 2.00 2.00 K 16.0 PSS by ZIP tip Cycle 1 DPTU A I M H -4.00 4.0 F G G D 0.00 0.00 D A P V -2.00 -2.00 S E N R P Y QT F H -4.00 4.0 K dpu 6.0 10.0 12.0 14.0 16.0 K S N I Q R H T dpu F Y M -4.00 M 8.0 V L 4.0 6.0 8.0 10.0 12.0 14.0 16.0 I L OK, so what if we get no data? • Insufficient quantities. • Highly heterogeneous sample leading to uninterpretable results. • A blocked n-terminus, leading into Bill Henzel’s part of this presentation.
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