UniMaP: finding unique mass and peptide signatures in the human proteome

Abstract

Summary: The uniqueness of a measured molecular mass or peptide sequence plays a very important role in the fields of protein identification and peptide/protein-biomarker investigation. We present a publicly available web application that offers information concerning the uniqueness of one or more molecular masses and one or more peptide sequences in the human proteome. When a sequence is found to be unique in humans, the application is able to search across all species querying whether this sequence is unique, not only in humans but also in other species found in the Swiss-Prot Database. The application is also able to search for unique protein fragments derived computationally from enzymatic digestion driven by certain enzymes. Furthermore, the application can list all the unique masses and peptides of a given protein. Through this application, researchers are able to find unique tags, either on a molecular mass level or on a sequence level. These unique tags are remarkably important in research related to protein identification or biomarker discovery and measurements. Availability: UniMaP web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/UniMaP/ Contact: gspyrou@bioacademy.gr Supplementary information: Supplementary data are available at Bioinformatics online.

PepServe: a web server for peptide analysis, clustering and visualization

“…The system uses the file repositories from our previous works (4,9) which contain peptide fragments classified according to their molecular mass, derived from extensive digestion of human proteins in the UniProt Database. The current repositories contain UniProt’s release 6/2010 and it has been scheduled for an update once a year.…”

“…There are three major classes where the tools for peptide analysis can be classified: (i) the peptide/protein identification tools like RAId_DbS (1), Peptizer (2), DeNovoID (3) and PeptideFinder (4); (ii) tools for the mapping of post-translational peptide modifications like MODi (5), for peptide phosphorylation like PhosCalc (6) and proteolysis (7); (iii) tools for the investigation of specific characteristics of the peptide fragments like Remus (8) and UniMaP (9) for the property of uniqueness, like SignalP (10) for the signaling property, of the peptide–MHC binding affinity like BiodMHC (11) and MHCPred (12). However, to our knowledge, there is not any web server dedicated to the broad analysis of peptide characteristics performing peptide clustering and visualization in the peptide feature space.…”

Bioinformatics approaches in the discovery and understanding of reproduction-related biomarkers

“…Software such as SEQUEST ® (Eng), Mascot™ [41], X!Tandem [42], PrepMS™ [43] and the msProcess R package [101] perform protein identification, quantification and characterization. Complementary software such as PeptideFinder and UniMaP facilitate the high-resolution mapping of the measured molecular masses to peptides and proteins, irrespective of the enzyme/digestion method used, as well as the discovery of unique tags, either at a molecular mass level or a sequence level, respectively [44,45].…”

Cysteine-Selective Peptide Identification: Selenium-Based Chromophore for Selective S–Se Bond Cleavage with 266 nm Ultraviolet Photodissociation

“…19 Strategies to resolve these issues have employed database filtering prior to the search to incorporate only unique peptides. [20][21][22] This workaround has shown to lower statistical q-values (not to be confused with ion trap Mathieu stability) by reducing the search space, thus increasing peptide confidence. [22][23][24][25] Building selectivity into a proteomic work-flow to allow meaningful database filtering to include only those peptides that contain a more specific type of amino acid composition have shown similar types of improvement.…”