We have developed Integrated GlycoProteomeAnalyzer (GPA) for high throughput analysis of N-and O-glycoproteome, which combines methods for tandem mass spectrometry with a database search and algorithmic suite. For precise identification, we created novel scoring algorithms such as M-score for glycopeptide selection from oxonium-ions, S-score for theoretical isotope pattern match of molecular ion, and Y-score for glycopeptide identification from MS/MS fragmentation with calculation of estimated false discovery rate (FDR). All glycoprotein samples were digested with trypsin. Then, those site-specific glycopeptides were enriched by hydrophobic interaction liquid chromatography and analyzed by nano-reversed-phase liquid chromatography coupled to tandem mass spectrometry with both HCD and CID-MS/MS fragmentation. The resultant LC/MS/MS data were then automatically analyzed using GPA: tryptic glycopeptides were identified against the database from Uniprot database. In GPA, all amino acid sequence and N-and O-glycosylation site information were obtained from the Uniprot database. From the Swiss-Prot accession number of human protein, GPA program automatically construct glycopeptide database for human sample. GPA has been designed to easily handle high-throughput glycoproteomic data with a graphical user interface. GPA software is demonstrated on website (https://www.igpa.kr/). Additionally, O-GPA, newly developed search engine, allows direct analysis of site-specific O-glycopeptides from glycoprotein mixtures using the O-GPA-DB from Uniprot with estimated FDR ≤ 1%. O-GPA is capable of automatic identification and quantification of O-glycopeptides using HCD and ETD-MS/MS spectra.