Xu H, Freitas MA. A dynamic noise level algorithm for spectral screening of peptide MS/MS spectra. BMC Bioinformatics. 2010 Aug 23;11:436. doi: 10.1186/1471-2105-11-436. PubMed PMID: 20731867PubMed Central PMCID: PMC2939612.

Xu H, Hsu PH, Zhang L, Tsai MD, Freitas MA. Database search algorithm for identification of intact cross-links in proteins and peptides using tandem mass spectrometry. J Proteome Res. 2010 Jul 2;9(7):3384-93. doi: 10.1021/pr100369y. PubMed PMID: 20469931PubMed Central PMCID: PMC4141472.

Xu H, Freitas MA. Automated diagnosis of LC-MS/MS performance. Bioinformatics. 2009 May 15;25(10):1341-3. doi: 10.1093/bioinformatics/btp155. PubMed PMID: 19304874PubMed Central PMCID: PMC2677746.

Xu H, Wang L, Sallans L, Freitas MA. A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra. Proteomics. 2009 Apr;9(7):1763-70. doi: 10.1002/pmic.200800282. PubMed PMID: 19288523PubMed Central PMCID: PMC2775432.

Xu H, Freitas MA. MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data. Proteomics. 2009 Mar;9(6):1548-55. doi: 10.1002/pmic.200700322. PubMed PMID: 19235167PubMed Central PMCID: PMC2759086.

Zhang L, Xu H, Chen CL, Green-Church KB, Freitas MA, Chen YR. Mass spectrometry profiles superoxide-induced intramolecular disulfide in the FMN-binding subunit of mitochondrial Complex I. J Am Soc Mass Spectrom. 2008 Dec;19(12):1875-86. doi: 10.1016/j.jasms.2008.08.004. PubMed PMID: 18789718PubMed Central PMCID: PMC2614441.

Xu H, Yang L, Freitas MA. A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time. BMC Bioinformatics. 2008 Aug 19;9:347. doi: 10.1186/1471-2105-9-347. PubMed PMID: 18713471PubMed Central PMCID: PMC2553802.

Xu H, Freitas MA. Monte carlo simulation-based algorithms for analysis of shotgun proteomic data. J Proteome Res. 2008 Jul;7(7):2605-15. doi: 10.1021/pr800002u. PubMed PMID: 18543962PubMed Central PMCID: PMC2749500.

Xu H, Zhang L, Freitas MA. Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine. J Proteome Res. 2008 Jan;7(1):138-44. PubMed PMID: 18072732PubMed Central PMCID: PMC2749473.

Xu H, Freitas MA. A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data. BMC Bioinformatics. 2007 Apr 20;8:133. PubMed PMID: 17448237PubMed Central PMCID: PMC1876247.