Manual checking is commonly employed to validate the phosphopeptide identifications from database searching of tandem mass spectra. However it is very time consuming and labor intensive as the number of phosphopeptide identifications increase greatly. APIVASE (Automatic Phosphopeptide Identification Validation for SEQUEST) was developed for phosphopeptide validation by combining the information obtained from MS2 spectra and its corresponding neutral loss MS3 spectra. The valid MS2 and MS3 pairs were extracted for database searching using target-decoy database. And the resulting MS2 and MS3 search results were combined. Three new defined scores were used to filter phosphopeptide identifications with specific false-discovery rate (FDR). Compared with the approach based on either MS2 or MS3, this combined MS2/MS3 approach allowed the identification of phosphopeptides with relative low quality spectra, which significantly improve the sensitivity for phosphopeptide identification.


1. Software usage;

2. Decoy database format;

Cition: Jiang, X. N.; Han, G. H.; Feng, S.; Jiang, X. G.; Ye, M. L.; Yao, X. B.; Zou, H. F., Automatic Validation of Phosphopeptide Identifications by the MS2/MS3 Target-Decoy Search Strategy. J. Proteome Res. 2008, 7, (4), 1640-1649. [Go to this artical]

APIVASE algorithm has been integreated into ArMone proteome data set process platform. Details of the usage can be found at ArMone homepage. The following stand alone verion can still be used.

APIVASE v2.5.4 is released. Fix some bugs.


APIVASE v2.5.3.2 is released. Add the support for SEQUEST v.28 (Bioworks 3.3).

APIVASE v2.5 is released.
Changes and improvements:
1. Add some identification informations for final phosphopeptide.
2. Fix the issue of exceptions when processing ".out" files generated by some version of SEQUEST.

APIVASE v2.3 is release. Unzip the package and the ".jar" will be excuable after the installation of JRE 6.0.
Changes and improvements:
1. The m/z values of precursor ions for ms2 and ms3 are added in the final outputted results.
2. The protein full name is given in this version.

As the generation of protein full name needs the accession of protein fasta database, please make sure the database name in the sequest database search directory is valid. If the database search was performed on an indexed database, check the original database path for the creation of this indexed database in the ".hdr" file.

APIVASE v2.2 is release. Unzip the package and the ".jar" will be excuable after the installation of JRE. Changes:
1. Some Gui improvements.
2. Some small changes.

APIVASE v2.1 is distributed.

1. Using Tscore to determine the most probable phosphorylation site localization.
2. Few modifications of the output format.