Cited by 513Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsGenomics and Phylogenetic Studies

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ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

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Xu, T., Park, S.K., Venable, J.D., Wohlschlegel, J.A., Diedrich, J.K., Cociorva, D., Lu, B., Liao, L., Hewel, J., Han, X., Wong, C.C.L., Fonslow, B., Delahunty, C., Gao, Y., Shah, H., Yates, J.R.·2015·Journal of Proteomics

DOI 10.1016/j.jprot.2015.07.001PMC PMC4630125

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Abstract

ProLuCID, a new algorithm for peptide identification using tandem mass spectrometry and protein sequence databases has been developed. This algorithm uses a three tier scoring scheme. First, a binomial probability is used as a preliminary scoring scheme to select candidate peptides. The binomial probability scores generated by ProLuCID minimize molecular weight bias and are independent of database size. A modified cross-correlation score is calculated for each candidate peptide identified by the binomial probability. This cross-correlation scoring function models the isotopic distributions of fragment ions of candidate peptides which ultimately results in higher sensitivity and specificity than that obtained with the SEQUEST XCorr. Finally, ProLuCID uses the distribution of XCorr values for all of the selected candidate peptides to compute a Z score for the peptide hit with the highest XCorr. The ProLuCID Z score combines the discriminative power of XCorr and DeltaCN, the standard parameters for assessing the quality of the peptide identification using SEQUEST, and displays significant improvement in specificity over ProLuCID XCorr alone. ProLuCID is also able to take advantage of high resolution MS/MS spectra leading to further improvements in specificity when compared to low resolution tandem MS data. A comparison of filtered data searched with SEQUEST and ProLuCID using the same false discovery rate as estimated by a target-decoy database strategy, shows that ProLuCID was able to identify as many as 25% more proteins than SEQUEST. ProLuCID is implemented in Java and can be easily installed on a single computer or a computer cluster. This article is part of a Special Issue entitled: Computational Proteomics.

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Additional file 6 of Changes in saliva protein profile throughout Rhipicephalus microplus blood feeding
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Additional file 10 of Changes in saliva protein profile throughout Rhipicephalus microplus blood feeding
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Additional file 11 of Changes in saliva protein profile throughout Rhipicephalus microplus blood feeding
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Additional file 7 of Changes in saliva protein profile throughout Rhipicephalus microplus blood feeding
da Silva Vaz Junior, I., Lu, S., Pinto, A. F. M., Diedrich, J. K., Yates, J. R., Mulenga, A., Termignoni, C., Ribeiro, J. M., & Tirloni, L. (2024) · Figshare · doi:10.6084/m9.figshare.26673597
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Additional file 9 of Changes in saliva protein profile throughout Rhipicephalus microplus blood feeding
da Silva Vaz Junior, I., Lu, S., Pinto, A. F. M., Diedrich, J. K., Yates, J. R., Mulenga, A., Termignoni, C., Ribeiro, J. M., & Tirloni, L. (2024) · Figshare · doi:10.6084/m9.figshare.26673603
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Additional file 2 of Changes in saliva protein profile throughout Rhipicephalus microplus blood feeding
da Silva Vaz Junior, I., Lu, S., Pinto, A. F. M., Diedrich, J. K., Yates, J. R., Mulenga, A., Termignoni, C., Ribeiro, J. M., & Tirloni, L. (2024) · Figshare · doi:10.6084/m9.figshare.26673582
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Additional file 12 of Changes in saliva protein profile throughout Rhipicephalus microplus blood feeding
da Silva Vaz Junior, I., Lu, S., Pinto, A. F. M., Diedrich, J. K., Yates, J. R., Mulenga, A., Termignoni, C., Ribeiro, J. M., & Tirloni, L. (2024) · Figshare · doi:10.6084/m9.figshare.26673612
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Additional file 1 of Changes in saliva protein profile throughout Rhipicephalus microplus blood feeding
da Silva Vaz Junior, I., Lu, S., Pinto, A. F. M., Diedrich, J. K., Yates, J. R., Mulenga, A., Termignoni, C., Ribeiro, J. M., & Tirloni, L. (2024) · Figshare · doi:10.6084/m9.figshare.26673579
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Authors: Xu, T., Park, S. K., Venable, J. D., Wohlschlegel, J. A., Diedrich, J. K., Cociorva, D., Lu, B., Liao, L., Hewel, J., Han, X., Wong, C. C. L., Fonslow, B., Delahunty, C., Gao, Y., Shah, H., & Yates, J. R.
Affiliations: Scripps Research Institute (US)
Corresponding author: Yates, J.R.
ORCID: Xu, T.
Venable, J.D.
Wohlschlegel, J.A.
Diedrich, J.K.
Lu, B.
Liao, L.
Han, X.
Wong, C.C.L.
Delahunty, C.
Gao, Y.
Yates, J.R.
Venue: Journal of Proteomics
Publisher: Elsevier BV
Published: 2015-11
Volume: 129
Pages: 16-24
ISSN: 1874-3919 (ISSN-L)
DOI: 10.1016/j.jprot.2015.07.001
PMC: PMC4630125
OpenAlex: W2182963873
Cited by: 511
References: 51
Citations by year: 2026: 23 · 2025: 41 · 2024: 65 · 2023: 45 · 2022: 51 · 2021: 56 · 2020: 56 · 2019: 60 · 2018: 43 · 2017: 46 · 2016: 22 · 2015: 3
FWCI: 16.92
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
creativecommons.org/licenses/by/4.0/ (vor)
Locations: Journal of Proteomics (publishedVersion, cc-by)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion, cc-by)
Funders: NIH (5U01 DE016267-04, 5R01 HL079442-04, R01 MH067880, P41 GM103533)
NHLBI (HHSN268201000035C)
Topics: Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: peptide identification, tandem mass spectrometry, SEQUEST, Z-score
MeSH terms: Algorithms, Amino Acid Sequence, Molecular Sequence Data, Pattern Recognition, Automated, Peptide Mapping, Proteins, Sensitivity and Specificity, Software, Reproducibility of Results, Sequence Analysis, Protein, Databases, Protein, Tandem Mass Spectrometry, Data Mining

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ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

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