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ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity
Open accessAbstract
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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“Under serum-free survival conditions, we have previously observed that the cells do not proliferate, and thus we are measuring loss of viability in these cells under serum-free conditions with pharmacological treatment 49.”
From Manumycin polyketides act as molecular glues between UBR7 and P53 (2020) · cites this paper as [49]
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Li, X., Xiong, X., Zhang, M., Wang, K., Chen, Y., Zhou, J. L., Mao, Y., Lv, J., Yi, D., Chen, X., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.019 · Cited by 482
Harnessing the anti-cancer natural product nimbolide for targeted protein degradation
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“…°C and the nanospray voltage was set to 2.75 kV. Data was extracted in the form of MS1 and MS2 files using Raw Extractor 1.9.9.2 (Scripps Research Institute) and searched against the Uniprot human database using ProLuCID search methodology in IP2 v.3 (Integrated Proteomics Applications, Inc) 36 .”
InfluentialHe, M., Chiang, H.-H., Luo, H., Zheng, Z., Qiao, Q., Wang, L., Tan, M., Ohkubo, R., Mu, W.-C., Zhao, S., et al. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2020.01.009 · Cited by 425
“San Diego, CA) using ProLuCID/Sequest, DTASelect2 and Census (Cociorva et al., 2007; Park et al., 2008; Tabb et al., 2002; Xu et al., 2015).”
MethodDeubiquitinase-targeting chimeras for targeted protein stabilization
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Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping
Sas‐Chen, A., Thomas, J. M., Matzov, D., Taoka, M., Nance, K. D., Nir, R., Bryson, K. M., Shachar, R., Liman, G. L. S., Burkhart, B. W., et al. (2020) · Nature · doi:10.1038/s41586-020-2418-2 · Cited by 336
Metadata
- 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
- Venue
- Journal of Proteomics
- Publisher
- Elsevier BV
- Published
- 2015-11
- Volume
- 129
- Pages
- 16-24
- ISSN
- 1874-3919 (ISSN-L)
- 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
- 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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