Crux is a mass spectrometry analysis toolkit that combines state-of-the-art computational, machine learning, and statistical methods. The Crux toolkit includes the following tools:
1. bullseye
2. tide-index
3. tide-search
4. cascade-search
5. comet
6. percolator
7. q-ranker
8. barista
9. search-for-xlinks
10. spectral-counts
11. pipeline
Utilities:
1. assign-confidence
2. generate-peptides
3. get-ms2-spectrum
4. hardklör
5. make-pin
6. param-medic
7. predict-peptide-ions
8. print-processed-spectra
9. psm-convert
10. subtract-index
11. xlink-assign-ions
12. xlink-score-spectrum
13. localize-modification
Text file utilities:
1. extract-columns
2. extract-rows
3. stat-column
4. sort-by-column
Proteomics
McIlwain S, Tamura K, Kertesz-Farkas A, Grant CE, Diament B, Frewen B, Howbert JJ, Hoopmann MR, Käll L, Eng JK, MacCoss MJ, Noble WS "Crux: rapid open source protein tandem mass spectrometry analysis." J. Proteome Res. 2014; 13(10):4488-91 https://doi.org/10.1021/pr500741y
PMID: 25182276
PMCID: PMC4184452
Park CY, Klammer AA, Käll L, MacCoss MJ, Noble WS "Rapid and accurate peptide identification from tandem mass spectra." J Proteome Res, 2008 https://doi.org/10.1021/pr800127y
PMID: 18505281
PMCID: PMC2667385
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