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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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Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota
Wang, Y., Zhou, Y., Xiao, X., Zheng, J., & Zhou, H. (2020) · Journal of Proteomics · doi:10.1016/j.jprot.2020.103737 · Cited by 97
Mitohormesis reprogrammes macrophage metabolism to enforce tolerance
Timblin, G. A., Tharp, K. M., Ford, B., Winchester, J., Wang, J., Zhu, S., Khan, R. I., Louie, S. K., Iavarone, A. T., ten Hoeve, J., et al. (2021) · Nature Metabolism · doi:10.1038/s42255-021-00392-w · Cited by 91
A large dataset of protein dynamics in the mammalian heart proteome
Lau, E., Cao, Q., Ng, D. C. M., Bleakley, B. J., Dincer, T. U., Bot, B. M., Wang, D., Liem, D. A., Lam, M. P. Y., Ge, J., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.15 · Cited by 87
Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans
Li, W.-J., Wang, C., Li, T., Yan, Y.-H., Zhang, M.-J., Liu, Z., Li, Y.-X., Zhao, H., Li, X.-M., He, X.-D., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24816-z · Cited by 86
Tirloni, L., Kim, T. K., Pinto, A. F. M., Yates, J. R., Vaz, I. D. S., & Mulenga, A. (2017) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2017.00517 · Cited by 86
“Tandem mass spectra were extracted from Thermo RAW files using RawExtract 1.9.9.2 (McDonald et al., 2004) and searched with ProLuCID (Xu et al., 2015) against a non-redundant tick databases.”
MethodInfluentialSelf-citationCaldwell, A. L. M., Sancho, L., Deng, J., Bosworth, A., Miglietta, A., Diedrich, J. K., Shokhirev, M. N., & Allen, N. J. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01150-1 · Cited by 86
Self-citationProtein signatures of seminal plasma from bulls with contrasting frozen-thawed sperm viability
Gomes, F. P., Park, S. K. R., Viana, A. G. D. A., Fernández-Costa, C., Topper, E., Kaya, A., Memili, E., Yates, J. R., & Moura, A. A. (2020) · Scientific Reports · doi:10.1038/s41598-020-71015-9 · Cited by 85
Self-citationOrphan receptor GPR158 controls stress-induced depression
Sutton, L. P., Orlandi, C., Song, C., Oh, W. C., Muntean, B. S., Xie, K., Filippini, A., Xie, X., Satterfield, R., Yaeger, J. D. W., et al. (2018) · eLife · doi:10.7554/elife.33273 · Cited by 88
Ortega, J. A., Daley, E. L., Kour, S., Samani, M., Tellez, L., Smith, H. S., Hall, E., Esengul, Y. T., Tsai, Y., Gendron, T. F., et al. (2020) · Neuron · doi:10.1016/j.neuron.2020.01.020 · Cited by 81
Willis, J. R., Berndsen, Z. T., Krystal, M., Steichen, J. M., Schiffner, T., Landais, E., Liguori, A., Kalyuzhniy, O., Allen, J. D., Baboo, S., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.09.001 · Cited by 76
“, 2015) and searched with ProLuCID (Xu et al., 2015) against a database comprising UniProt reviewed (Swiss-Prot) proteome for Homo sapiens (UP000005640), UniProt amino acid sequences for Endo H (P04067), PNGase F (Q9XBM8), and PK (P06873), amino acid sequences for the examined proteins, and a list of general protein c…”
MethodSelf-citationSharma, S., Chung, C., Uryu, S. A., Petrovic, J., Cao, J. Q., Rickard, A. J., Nady, N., Greasley, S. E., Johnson, E., Brodsky, O., et al. (2023) · Cell chemical biology · doi:10.1016/j.chembiol.2023.07.005 · Cited by 82
Katz, Z., Novotná, L., Blount, A. L., & Lillemeier, B. F. (2016) · Nature Immunology · doi:10.1038/ni.3631 · Cited by 79
Park, D. E., Cheng, J., McGrath, J. P., Lim, M. Y., Cushman, C. H., Swanson, S. K., Tillgren, M. L., Paulo, J. A., Gokhale, P. C., Florens, L. A., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0503-2 · Cited by 77
Across intra-mammalian stages of the liver f luke Fasciola hepatica: a proteomic study
Maggio, L. S. D., Tirloni, L., Pinto, A. F. M., Diedrich, J. K., Yates, J. R., Benavides, U., Carmona, C., Vaz, I. D. S., & Berasain, P. (2016) · Scientific Reports · doi:10.1038/srep32796 · Cited by 77
Self-citationSimple, efficient and thorough shotgun proteomic analysis with PatternLab V
Santos, M. D. M., Lima, D. B., Fischer, J. D. S. D. G., Clasen, M. A., Kurt, L. U., Camillo-Andrade, A. C., Monteiro, L. C., de Aquino, P. F., Neves‐Ferreira, A. G. C., Valente, R. H., et al. (2022) · Nature Protocols · doi:10.1038/s41596-022-00690-x · Cited by 77
Self-citationMutlu, B., Chen, H.-M., Moresco, J. J., Orelo, B. D., Yang, B., Gaspar, J. M., Keppler‐Ross, S., Yates, J. R., Hall, D. H., Maine, E. M., et al. (2018) · Science Advances · doi:10.1126/sciadv.aat6224 · Cited by 77
Self-citationBenjamin, D. I., Both, P., Benjamin, J. S., Nutter, C. W., Tan, J. H., Kang, J., Machado, L. A., Klein, J. D. D., de Morree, A., Kim, S., et al. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.04.012 · Cited by 79
Multiomics reveals glutathione metabolism as a driver of bimodality during stem cell aging
Benjamin, D. I., Brett, J. O., Both, P., Benjamin, J. S., Ishak, H. D., Kang, J., Kim, S., Chung, M., Arjona, M., Nutter, C. W., et al. (2023) · Cell Metabolism · doi:10.1016/j.cmet.2023.02.001 · Cited by 80
Wang, L., Collings, C. K., Zhao, Z., Cozzolino, K., Ma, Q., Liang, K., Marshall, S. A., Sze, C. C., Hashizume, R., Savas, J. N., et al. (2017) · Genes & Development · doi:10.1101/gad.306092.117 · Cited by 78
“…al. 2015), and the tandem mass spectra were searched against the UniProt humanprotein databaseandmatched to sequences using the ProLuCID/SEQUEST algorithm (ProLuCID version 3.1) (Eng et al. 1994; Xu et al. 2015) with peptide mass tolerance of 50 ppm for precursorions and 600 ppm forfragment ions.”
InfluentialNievas, Y. R., Cóceres, V. M., Midlej, V. D. V. P., de Souza, W., Benchimol, M., Pereira‐Neves, A., Vashisht, A. A., Wohlschlegel, J. A., Johnson, P. J., & de Miguel, N. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2726-3 · Cited by 81
“Spectra were analyzed using the ProLuCID [27] algorithm and searching against a fasta protein database consisting of all predicted open reading frames downloaded from TrichDB on January 4, 2015 [28] concatenated to a decoy database in which the amino acid sequence of each entry was reversed.”
MethodSelf-citationSelenium-Encoded Isotopic Signature Targeted Profiling
Gao, J., Yang, F., Che, J., Han, Y., Wang, Y., Chen, N., Bak, D. W., Lai, S., Xie, X., Weerapana, E., et al. (2018) · ACS Central Science · doi:10.1021/acscentsci.8b00112 · Cited by 73
Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman, M., & Hetzer, M. W. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.10.008 · Cited by 73
A Dimethyl-Labeling-Based Strategy for Site-Specifically Quantitative Chemical Proteomics
Yang, F., Gao, J., Che, J., Jia, G., & Wang, C. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b02426 · Cited by 74
Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates
Steichen, J. M., Phung, I., Salcedo, E., Ozorowski, G., Willis, J. R., Baboo, S., Liguori, A., Cottrell, C. A., Torres, J. L., Madden, P. J., et al. (2024) · Science · doi:10.1126/science.adj8321 · Cited by 74
“Tan-demmassspectra were extracted from raw files using RawConverter ( 61 ) and searched with ProLuCID ( 62 ) against a database comprising the UniProt reviewed (Swiss-Prot) proteome for Homo sapiens (UP000005640); UniProt amino acid sequences for Endo H (P04067), PNGase F (Q9XBM8), and proteinase K…”
MethodSelf-citationdCas9-targeted locus-specific protein isolation method identifies histone gene regulators
Tsui, C., Inouye, C. J., Levy, M. J., Lu, A. C., Florens, L. A., Washburn, M. P., & Tjian, R. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1718844115 · Cited by 74
“3) on the fly dataset (59) and were searched against a nonredundant protein D.”
MethodBhattacharya, S., Levy, M. J., Zhang, N., Li, H., Florens, L. A., Washburn, M. P., & Workman, J. L. (2021) · Nature Communications · doi:10.1038/s41467-021-21663-w · Cited by 77
Defining the functional targets of cap'n'collar transcription factors NRF1, NRF2, and NRF3
Ibrahim, L., Mesgarzadeh, J., Xu, I., Powers, E. T., Wiseman, R. L., & Bollong, M. J. (2020) · Antioxidants · doi:10.3390/antiox9101025 · Cited by 67
“Protein identification and quantification were performed using the Integrated Proteomics Pipeline (IP2) [21,22].”
MethodLong-lived mitochondrial cristae proteins in mouse heart and brain
Bomba-Warczak, E. K., Edassery, S. L., Hark, T. J., & Savas, J. N. (2021) · The Journal of Cell Biology · doi:10.1083/jcb.202005193 · Cited by 71
“MS data analysis and quantification Protein identification/quantification and analysis were performed with the Integrated Proteomics Pipeline–IP2 (Integrated Proteomics Applications) using ProLuCID (Eng et al., 1994; Xu et al., 2015), DTASelect2 (Cociorva et al.”
MethodInfluentialPedros, C., Zhang, Y., Hu, J. K., Choi, Y. S., Canonigo-Balancio, A. J., Yates, J. R., Altman, A., Crotty, S., & Kong, K. (2016) · Nature Immunology · doi:10.1038/ni.3463 · Cited by 76
Self-citationLee, H. J., Bartsch, D., Xiao, C., Guerrero, S. X., Ahuja, G., Schindler, C., Moresco, J. J., Yates, J. R., Gebauer, F., Bazzi, H., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01744-5 · Cited by 73
Self-citationBamberger, C., Pankow, S., Martínez-Bartolomé, S., Ma, M., Diedrich, J., Rissman, R. A., & Yates, J. R. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00912 · Cited by 70
Self-citationmRNA-LNP HIV-1 trimer boosters elicit precursors to broad neutralizing antibodies
Xie, Z., Lin, Y., Steichen, J. M., Ozorowski, G., Kratochvil, S., Ray, R., Torres, J. L., Liguori, A., Kalyuzhniy, O., Wang, X., et al. (2024) · Science · doi:10.1126/science.adk0582 · Cited by 71
Self-citationDimethyl Fumarate Disrupts Human Innate Immune Signaling by Targeting the IRAK4–MyD88 Complex
Zaro, B. W., Vinogradova, E. V., Lazar, D. C., Blewett, M. M., Suciu, R. M., Takaya, J., Studer, S., de la Torre, J. C., Casanova, J.-L., Cravatt, B. F., et al. (2019) · The Journal of Immunology · doi:10.4049/jimmunol.1801627 · Cited by 68
Chen, H., Victor, A. K., Klein, J. D., Tacer, K. F., Tai, D. J. C., de Esch, C. E. F., Nuttle, A., Temirov, J. P., Burnett, L. C., ROSENBAUM, M. S., et al. (2020) · JCI Insight · doi:10.1172/jci.insight.138576 · Cited by 66
“For peptide identification, tandem mass spectra were searched against a database including the UniProt mouse database 1 entry per gene (21,982 entries released December 1, 2019) with common contaminants and reversed sequences using ProLuCID (69).”
Self-citationTime-resolved proteomic profile of Amblyomma americanum tick saliva during feeding
Kim, T. K., Tirloni, L., Pinto, A. F. M., Diedrich, J. K., Moresco, J. J., Yates, J. R., Vaz, I. D. S., & Mulenga, A. (2020) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0007758 · Cited by 66
Self-citationAbiraami, T. V., Singh, S., & Nain, L. (2019) · Reviews in Environmental Science and Bio/Technology · doi:10.1007/s11157-019-09519-8 · Cited by 63
Song, Y., Zhou, H., Vo, M.-N., Shi, Y., Nawaz, M. H., Vargas‐Rodriguez, O., Diedrich, J. K., Yates, J. R., Kishi, S., Musier‐Forsyth, K., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-02201-z · Cited by 64
Self-citationStructural Basis of Karrikin and Non-natural Strigolactone Perception in Physcomitrella patens
Bürger, M., Mashiguchi, K., Lee, H. J., Nakano, M., Takemoto, K., Seto, Y., Yamaguchi, S., & Chory, J. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.01.003 · Cited by 65
“Tandem mass spectra were extracted from raw files using RawConverter (He et al., 2015) and searched with ProLuCID (Xu et al., 2015) against an E. coli protein database with recombinant proteins added.”
MethodInfluentialHark, T. J., Rao, N. R., Castillon, C., Basta, T., Smukowski, S. N., Bao, H., Upadhyay, A., Bomba-Warczak, E. K., Nomura, T., O'Toole, E. T., et al. (2020) · Cell Systems · doi:10.1016/j.cels.2020.11.007 · Cited by 60
Thompson, A. J., Cao, L., Ma, Y., Wang, X., Diedrich, J. K., Kikuchi, C., Willis, S., Worth, C. S., McBride, R., Yates, J. R., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.03.009 · Cited by 63
Self-citationDiscovery of Itaconate-Mediated Lysine Acylation
Liu, D., Xiao, W., Li, H., Zhang, Y., Yuan, S., Li, C., Dong, S., & Wang, C. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c02332 · Cited by 62
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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