PVIEW is a tool to analyze and visualize high-resolution LC-MS/MS Data. The PVIEW algorithm has functions for
1. Isotope-labeled heavy vs. light quantification,
2. 5N heavy vs. light quantification,
3. Isotope-labeled heavy vs. medium vs. light (e.g., pulsed SILAC) quantification,
4. Nonlinear alignment label-free quantification,
5. Label-free XIC-based quantification,
6. XIC-based quantification (XICs are cross-referenced based on peptide sequence),
7. MS/MS database search,
8. Internal reverse concatenated decoy database construction,
9. FDR and q-value estimation utilizing a reverse decoy database,
10. Support for external search engines, such as Mascot, SEQUEST, X! Tandem,
11. Protein grouping of isoforms and peptides,
12. Support for data from Orbitrap, FTICR, and high resolution QTOF instruments.
PVIEW is multi-threaded.
Proteomics; Proteomics experiment
Khan Z, Bloom JS, Garcia BA, Singh M, Kruglyak L "Protein quantification across hundreds of experimental conditions." Proc. Natl. Acad. Sci. U.S.A. 2009; 106(37):15544-8 https://doi.org/10.1073/pnas.0904100106
PMID: 19717460
PMCID: PMC2732709
Khan Z, Amini S, Bloom JS, Ruse C, Caudy AA, Kruglyak L, Singh M, Perlman DH, Tavazoie S "Accurate proteome-wide protein quantification from high-resolution 15N mass spectra." Genome Biol, 2011 https://doi.org/10.1186/gb-2011-12-12-r122
PMID: 22182234
PMCID: PMC3334617
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