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. 2024 May 29;23(7):2518–2531. doi: 10.1021/acs.jproteome.4c00187

Table 1. Tolerance Parameters Used for Comet Search for Each Data Set.

Original data set identifier Tissue Instrument Count of. RAW files Count MS2 spectra Peptide mass tolerance (ppm) Fragment tolerance (Da) Count of observed sites reported Statistical control method used (Peptides) Statistical control method used (Sites)
PXD00092327 Flower TripleTOF 5600 10 97388 20 0.02 2347 ion score >34 (p < 0.05) Ascore ≥ 19, p ≤ 0.01
PXD00222229 Leaf Q Exactive 6 121117 20 0.02 2367 filtered for peptide rank 1 and high identification confidence, corresponding to 1% FDR PhosphoRS probability >90%, in at least 2 of 3 biological replicates
                Mascot score >20
PXD00275634 Anther LTQ Orbitrap Elite 5 225674 20 1.0005 8973 Expectation value p < 0.05 phosphoRS (no threshold given)
PXD00470533 Leaf Q Exactive 9 208050 20 0.02 3412 Protein Discoverer <1% FDR PhosphoRS probability >90% in at least 2 of 3 biological replicates
PXD00493931 Leaf Q Exactive 9 212875 20 0.02 2271 Protein Discoverer <1% FDR PhosphoRS probability >90%
                Mascot score >20  
PXD00524132 Shoot, Leaf, Panicles (Young and Mature) Q Exactive 18 1040757 20 1.0005 5523 Protein Discoverer <1% FDR PhosphoRS probability >90% in at least 2 of 3 biological replicates
PXD01276435 Root Q Exactive 6 260560 10 0.02 2674 Protein Discoverer <1% FDR PhosphoRS score ≥50; PhosphoRS site probability ≥75%
PXD01929138 Pollen Q Exactive 4 110117 10 0.02 2246 Not reported Not reported