All the tools below can be used, but this one looks like a probable solution to your problem:

NeuroPedia: neuropeptide database and spectral library

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179654/

"NeuroPedia is a convenient and accessible repository of neuropeptide sequences and MS/MS spectral libraries. It offers advantages in terms of faster and more precise identification of small sized or nontryptic neuropeptides. We anticipate that NeuroPedia will continue to grow as data from more laboratories and experiments are contributed directly to NeuroPedia or otherwise become publicly available in mass spectrometry data repositories. In particular, it is expected that NeuroPedia will expand to include neuropeptide information for more species and mass spectrometry data of post-translationally modified neuropeptides. NeuroPedia can be accessed at http://proteomics.ucsd.edu/Software/NeuroPedia.html."

Also pay attetion to the right panel being inside the article - there are a lot of other paper links etc.

Most tools require MS.

Like this one: http://www.ch.embnet.org/CoursEMBnet/Basel08/MS-practical.html

or this one:http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-288

What do you mean with a proteome file? Amino acid sequences? Mass spectrometry data?

Please use accurate tags with your question. Either your question is incomplete, or the tags are inappropriately chosen. In addition, providing more information will get you a quicker and more accurate response.

There is one more useful tool.

http://papers.genomics.lbl.gov/cgi-bin/litSearch.cgi

You will insert your protein sequence and receive a list of papers about its homologs,

it is called PaperBlast