A quick search pulled up this paper;

https://www.biomedcentral.com/1471-2105/12/432

The software doesn't look complete, but it seems to do what you want.

Perhaps a search on Pubmed search would reveal more?

Good luck,

Peter

The ProtParam tool available at ExPASy server (http://web.expasy.org/protparam/) provides the general physical and chemical information regarding an amino acid sequence/peptide which includes AA composition, atomic composition, no of charged residues and much more.

Apart protparam try this

http://pipe.ibibiosolutions.com

To obtain the mass from a sequence use PAWS free software (http://www.softpedia.com/get/Science-CAD/Genomic-PAWS.shtml)

If You know precursor of peptides You may try with programs at the following website:

http://prowl.rockefeller.edu/prowl/prowl.html

I am looking for such a tool for a while now.

As far as I now there is no small tool to do it.

If what you want to do is submit a mass and get all possible sequences for this mass.

Peter Hains' answer was quite good but note that this software would give you all possible amino acid composition for a peptide of a determined length (in amino acid). To be clearer, you can ask for all possibilities of peptides containing 10 amino acid. Beware that it will not give you the sequences but only the composition (how many amino acid of each kind). It could be practical, but I don't think it match your need.

Good luck.

I can add comment. Usually we know something more about peptide, not only mass. For instance sequence of its protein precursor, specificity of proteolytic enzyme releasing this peptide or MS/MS data. This knowledge enables narrowing spece of potential candidates.

Well, thanks for all the answers. It seems that my question was not clear to everybody. In fact I am working in the field of proteomics for many years and I know how to derive sequences of peptides pretty well. However, there is a reason why I am looking for such a program, but there are probably not enough lines here to explain the entire story and also I do not think that it would be useful. The program I am looking for works like an elemental composition determination based on accurate masses (less than 1 ppm for instance) but does not provide the elemental compositions, but candidates for amino acid compositions.

Here is an example:

the monoisotopic neutral mass derived is 491.2744

the software calculates the following AA compositions + termini:

1) 3xA, 1xL, 1xF

2) 3xA, 1xI, 1xF

3) 1xK, 1xF, 1xP, 1xT

4) 1xG, 1xL, 1xF, 1xV

5) 1xQ, 1xF, 2xV

6) a.s.o.

It would be great if such a small tool exists. If not we will write one.

Best regards,

Christian

At that time I do not remember such tool. If I'll find it I will let You know. Good luck.

Hi Christian,

I think for (very) small peptides it might be possible to write such a programm - but for larger peptides it seems to be impossible due to the almost unlimited number possibilities. I know this problem from the determination of elemental composition, you mentioned...

How large are your peptides?

Best regards from Halle,

Simon

Hi Simon,

the number of possible compositions indeed depends on the achievable mass accuracy and other parameters that could be used as constraints. I need the tool for MS2 data of peptides with native cross-links and the masses I am looking at are less than 1000 Da.

Best regards,

Christian

Hi, Kindly go through the attached article. The program, 'Peptide Fragment Ion Analyzer (PFIA)' can provide amino acid compositions up to 3 or 4 amino acids for a queried m/z value. If you want this program, let me know. I can send to you through this discussion itself. PFIA is a standalone program.

Hi,

Thank you for the interesting article. Yes, would like to try your program.

Best regards,

Christian

Hi, Check the attachment and let me know, whether you are able to install the program and use.

Thank you. I just tried it with the mass of the tripeptide VAG, which would be 246.1448 for [M+H]+. However, I got the following output:

Type of ion m/z value Amino acids

Queried m/z value : 246.1448

Window Range : 0.01

Mode of Mass Calculation : Monoisotopic

N-terminus modification : None (H)

C-terminus modification : None (OH)

C-terminus modification : None (OH)

Cysteine modification (C*) : None

Sum : 246.13682 F,V

Sum : 246.13682 F,J

Sum : 246.13682 F,n

Well, res(F) is 147.07 and res(V) is 99.07, but together it would be H-Phe-Val-OH and the sum is 1+147.07+99.07+17.01=264.15+H+=265.15.

It seems that the termini were not taken into account. Any idea why it is like this?

Regards,

Christian

This program is meant for analyzing peptide fragment ion masses. So, for a queried m/z value and for one or more chosen fragment ion(s), the output will be obtained. I think, you would have chosen "b- ion" for queried m/z 246.1448. The amino acid compositions obtained in this case correspond to b- type ion. Since, your requirement is for molecular masses, the output obtained through PFIA will be different. However, from the output of PFIA, you can get some idea about the possible amino acid compositions. I think, the source code of PFIA is available. You may modify it as per your requirement. You may also try in http://prospector.ucsf.edu.

Thank you for all the answers. Especially, PFIA and MS-comp are pretty useful for the problem were are working on.

Regards,

Christian