Biopolymers & Proteomics Laboratory

The David H.Koch Institute for Integrative Cancer Research at MIT

Bldg 76 Room 181

Telephone: 617-253-7038

Peptide Array Examples

Some Sample Array Sequences

Frame shift peptides from protein - The arrayer can be used to generate comprehensive sets of peptides from imported protein sequences. The seq.12.2 command tells the instrument to make 12mer peptides from the protein sequence pasted in below, with a frame shift of two residues. The C-terminal peptide is generated regardless of frame shift

.seq,12,2

P I S P I E T V P V K L K P G M D G P K V K Q W P L T E E K I K A L V E I C T E M E K E G K I S K I G P E N P Y N T P V F A I K K K D S T K W R K L V D F R E L N K R T Q D F W E V Q L G I P H P A G L K K K K S V T V L D V G D A Y F S V P L D E D F R K Y T A F T I P S I N N E T P G I R Y Q Y N V L P Q G W K G S P A I F Q S S M T K I L E P F R K Q N P D I V I Y Q Y M D D L Y V G S D L E I G Q H R T A D Q

.end

Below are listed the first few peptides from this run.

97 P I S P I E T V P V K L 1293.9
98 S P I E T V P V K L K P 1308.9
99 I E T V P V K L K P G M 1312.2
100 T V P V K L K P G M D G 1242.1
101 P V K L K P G M D G P K 1267.2
102 K L K P G M D G P K V K 1298.2
103 K P G M D G P K V K Q W 1371.3
104 G M D G P K V K Q W P L 1356.3

Generation of different sized peptides

The command below instructs the instrument to make all 8mers through 4mers from the entered peptide sequence with a frame shift of one residue.

".seq,n1,n2,n3" and ".end", where n1 defines the longest peptide

seq,8,1,4H I D D E N E P I T O P E S E Q E N C E.end

231 O P E S E Q 692.5

Replacement set or Analog Peptides

The command below instructs the arrayer to substitute any desired set of amino acids positioned between the asterisks in "analog,* *" at the position designated by the asterisk in the peptide sequence.

.analog,*= replace star with each of the residues defined in the list.

.analog,*=*

E * A M P L E

275 E A A M P L E 760.1
276 E R A M P L E 845.2
277 E N A M P L E 803.2
278 E D A M P L E 804.1
279 E C A M P L E 792.2
280 E Q A M P L E 817.2
281 E E A M P L E 818.1
282 E G A M P L E 746.1
283 E H A M P L E 826.2
284 E I A M P L E 802.2
285 E L A M P L E 802.2
286 E K A M P L E 817.2
287 E M A M P L E 820.3
288 E F A M P L E 836.2
289 E P A M P L E 786.2
290 E S A M P L E 776.9
291 E T A M P L E 790.1
292 E W A M P L E 875.3
293 E Y A M P L E 852.2
294 E V A M P L E 788.2

Library Peptides

.analog,*=A,B,C

L I B R A R Y * *

295 L I B R A R Y A A 976.3
296 L I B R A R Y B B 920.1
297 L I B R A R Y C C 1040.5

Individual Peptides

.pep

T E S T P E P T I D E

E X A M P L E P E P T I D E

298 T E S T P E P T I D E 1219.2
299 E X A M P L E P E P T I D E 1584.2

You can browse the ABIMED manual in our lab for a complete list of options.

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