MS Interpreter is a software tool for automated interpretation of mass spectral data. The current version uses a brute-force algorithm to determine all amino acid sequences from MS2 spectra of underivatized peptides.

Technical specifications and costs
  1. MS Interpreter considers the following fragment ion types: A, B, C, X, Y, Z, internal A- and B-ions, A-, B- and Y- ion types -H2O (the ion -H2O must contain at least one of the amino acid residues D, E, S or T), and A-, B-, C- and Y- ion types -NH3 (the ion -NH3 must contain at least one of the amino acid residues K, N, Q or R). MS Interpreter uses a brute force algorithm, thus ensuring that all amino acid sequences that fit the mass spectral data will be found. Figure 1 shows an example of the output. 

    Results from MS-Interpreter:
<?xml version=1.0 encoding=utf-8?>
<!DOCTYPE plist PUBLIC -//Apple Computer//DTD PLIST 1.0//EN http://www.apple.com/DTDs/PropertyList-1.0.dtd>
<plist version=1.0>
	<dict>
		<key>C-terminus</key>
		<string>OH</string>
		<key>spectrum</key>
		<string>
BEGIN IONS
TITLE= Cmpd 44, +MSn(615.9), 54.6 min
PEPMASS=614.350834        1501
CHARGE=2+
213.159766        329
230.113536        1336        1+
248.124101        997
282.144852        304
299.135002        5823        1+
317.181966        1552        1+
335.156131        1819
398.203422        531
416.213986        372
434.224551        815
438.307506        149
482.297332        291
483.292592        244
511.287506        565        1+
516.266422        574
566.402482        169
583.345013        149
594.397396        1172        1+
624.371576        799        1+
695.408696        736        1+
705.429432        995        1+
723.439996        2865        1+
794.477116        3249        1+
811.503666        191
871.524781        584        1+
875.534972        211
893.545536        14591        1+
911.519706        444
928.546251        1146        1+
962.567002        157
964.582647        473        1+
980.577566        4226        1+
1063.614682        434
1064.598697        267
1081.625246        7613        1+

END IONS


</string>
		<key>Monomers</key>
		<string>Amino acids</string>
		<key>N-terminus</key>
		<string>H</string>
		<key>Tolerance</key>
		<integer>1</integer>
		<key>Tolerance unit</key>
		<string>ppm</string>
		<key>Use restrictions</key>
		<false />
		<key>Email</key>
		<string>UserMSinterpreter@mail.address </string>
		<key>Feedback</key>
		<string />
	</dict>
</plist>
amino acid composition 1: [X2V2TSQPKGDA] (1 sequences):
Sequence	#Permutations
A[DX]G[KP]XVVSTQ	4

amino acid composition 2: [XV3TSQPKGEA] (1 sequences):
Sequence	#Permutations
A[EV]G[KP]XVVSTQ	4

2 solutions

Thank you for using MS-Interpreter.
    Figure 1. Example of an Interpretation report from MS Interpreter
  2. MS2 parent: [M + H]+ up to [M + 5H]5+; see Table 1 for costs, mass- and tolerance limits.
  3. For now, AIMS can handle up to five unexplained MS2 fragments (a deisotope algorithm is under construction).
  4. Possibility to specify minimum and maximum numbers for individual amino acids.
  5. Either manual input or copy-paste data from deisotisotoped Mascot-file with possibility to specify a minimum intensity level. Peaks below this level are not considered. A high minimum increases the number of solutions, whereas too low a minimum results in zero solutions (only solutions with more than five unexplained peaks).

Table 1 MS-Interpreter: mass- and tolerance limits and costs.
Monoisotopic mass (amu) Tolerance parent ion (ppm) Tolerance ms2 ions (ppm) Price (€)
< 1000 <= 10 <= 25 Free
1000 - 1100 <= 10 <= 25 1
1100 - 1200 <= 10 <= 25 2
1200 - 1300 <= 10 <= 25 3
1300 - 1400 <= 10 <= 25 4
1400 - 1500 <= 10 <= 25 5
1500 - 1600 <= 5 <= 25 10
1600 - 1700 <= 2 <= 25 20
1700 – 1800 <= 1 <= 25 40
How to use?

1. Enter your email address and login key
2. Click OK
3. Complete the form
(see Fig. 1 for an example).

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FOR FREE!
MS-INTERPRETER is temporary for free!

In case of sufficient interest, features will be expanded for future commercial versions.
 
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