I think these tools are among the most important for studying protein annotations

InterProScan

Protein Functional Analysis using the InterProScan program.

PfamScan

PfamScan is used to search a FASTA sequence against a library of Pfam HMM.

Phobius

Prediction of transmembrane topology and signal peptides using the Phobius program.

Pratt

Search patterns conserved in sets of unaligned protein sequences.

RADAR

Detection and alignment of repeats in protein sequences.

Hi,

For prediction of internal features of protein such as motif and domains MEME server is suitable and for prediction of protein-protein interaction HEX software is good as well as for prediction of protein pathway and interaction network NatalieQ server is useful.

Protein identification from MS/MS data can be performed using the Andromeda search engine in MaxQuant (version 1.6.0.1; http://maxquant.org/).

Processing of results, statistical analyses, and graphics generation may be conducted using Perseus V. 1.5.8.5.

Lists of proteins exclusively identified may be submitted to STRING for functional gene ontology enrichment analyses.

You can deposit proteomic data to the ProteomeXchange Consortium via PRoteomics IDEntifications (PRIDE).