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.
1. Alves G, Yu YK (2016) Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution.
Bioinformatics,
32: 32.
PMID: 27153659
2. Alves G, Yu YK (2015) Mass spectrometry-based protein identification with accurate statistical significance assignment.
Bioinformatics,
31: 31.
PMID: 25362092
3. Alves G, Yu YK (2014) Accuracy evaluation of the unified P-value from combining correlated P-values.
PLoS One,
9: 9.
PMID: 24663491
4. 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
5. 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
6. Alves G, Ogurtsov AY, Yu YK (2011) Assigning statistical significance to proteotypic peptides via database searches.
J Proteomics,
74: 74.
PMID: 21055489
7. 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
8. 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
9. 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
10. 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
11. 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
12. Alves G, Ogurtsov AY, Yu YK (2007) RAId_DbS: peptide identification using database searches with realistic statistics.
Biol Direct,
2: 2.
PMID: 17961253
13. 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
14. 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
15. 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