Robust Accurate Identification (RAId)

RAId is a suite of proteomics tools for analyzing tandem mass spectrometry data. In addition to providing accurate statistical significance assignment, RAId offers users with different modes of data analysis: database search, generation of score distribution of all possible peptides using different scoring functions (RAId, XCorr, Hyperscore, Kscore), and statistical confidence reassignment. In particular, RAId's integrated knowledge databases incorporate known single amino polymorphisms, post-translational modifications and disease information, providing dynamic information retrieval for biomedical applications.

Web interface: RAId

Standalone versions: Linux 64bits (including GUI)

Organismal databases: RAId databases

References:
1. Ogurtsov AY, Alves G, Yu YK (2019) RAId: Knowledge-Integrated Proteomics Web Service with Accurate Statistical Significance Assignment. Proteomics, 19: 19.
PMID: 30908818

2. Joyce B, Lee D, Rubio A, Ogurtsov A, Alves G, Yu YK (2018) A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics. BMC Res Notes, 11: 11.
PMID: 29544540

3. Alves G, Yu YK (2016) Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution. Bioinformatics, 32: 32.
PMID: 27153659

4. Alves G, Yu YK (2015) Mass spectrometry-based protein identification with accurate statistical significance assignment. Bioinformatics, 31: 31.
PMID: 25362092

5. Alves G, Yu YK (2014) Accuracy evaluation of the unified P-value from combining correlated P-values. PLoS One, 9: 9.
PMID: 24663491

6. Alves G, Yu YK (2011) Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy. PLoS One, 6: 6.
PMID: 21912585

7. Alves G, Ogurtsov AY, Yu YK (2010) RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics. PLoS One, 5: 5.
PMID: 21103371

8. Alves G, Ogurtsov AY, Yu YK (2011) Assigning statistical significance to proteotypic peptides via database searches. J Proteomics, 74: 74.
PMID: 21055489

9. Alves G, Yu YK (2008) Statistical Characterization of a 1D Random Potential Problem - with applications in score statistics of MS-based peptide sequencing. Physica A, 387: 387.
PMID: 19918268

10. Alves G, Ogurtsov AY, Yu YK (2008) RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration. BMC Genomics, 9: 9.
PMID: 18954448

11. Alves G, Ogurtsov AY, Kwok S, Wu WW, Wang G, Shen RF, Yu YK (2008) Detection of co-eluted peptides using database search methods. Biol Direct, 3: 3.
PMID: 18597684

12. Alves G, Wu WW, Wang G, Shen RF, Yu YK (2008) Enhancing peptide identification confidence by combining search methods. J Proteome Res, 7: 7.
PMID: 18558733

13. Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK (2007) Calibrating E-values for MS2 database search methods. Biol Direct, 2: 2.
PMID: 17983478

14. Alves G, Ogurtsov AY, Yu YK (2007) RAId_DbS: peptide identification using database searches with realistic statistics. Biol Direct, 2: 2.
PMID: 17961253

15. Doerr TP, Alves G, Yu YK (2005) Ranked solutions to a class of combinatorial optimizations - with applications in mass spectrometry based peptide sequencing and a variant of directed paths in random media. Physica A, 354: 558-70.
DOI: 10.1016/j.physa.2005.03.004

16. Sardiu ME, Alves G, Yu YK (2005) Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem. Phys Rev E Stat Nonlin Soft Matter Phys, 72: 72.
PMID: 16485984

17. Alves G, Yu YK (2005) Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics. Bioinformatics, 21: 21.
PMID: 16105903