Table 1.
Raw-datafiles in PXD001608 and PXD003082. All samples were analyzed in technical triplicates, and all raw-files are named accordingly (e.g. Ctrl_10_3 is the third repeat of control 10). “Poor R” signifies a Pearson's correlation coefficient R<0.95 between the technical repeats, and additional data validation is recommended for studies including these datafiles. The number of identified proteins in each replicate is given, wo/w the MaxQuant match between runs feature which transfer MS/MS information between different LC-MS/MS analysis. RA: Rheumatoid arthritis, UC: ulcerative colitis, NA: Not available.
| Filename | Sample | #Proteins matching OFF | #Proteins matching ON | Dataset ID | Comment |
|---|---|---|---|---|---|
| Ctrl_1 | Control | 4362, 4279, 4241 | 5967, 5903, 5897 | PXD001608 | |
| Ctrl_2 | Control | 3613, 3607, 3595 | 5657, 5664, 5723 | PXD001608 | |
| Ctrl_3 | Control | 4203, 4203, 4188 | 5936, 5952, 5939 | PXD001608 | |
| Ctrl_4 | Control | 4245, 4268, 4191 | 5863, 5865, 5849 | PXD001608 | |
| Ctrl_5 | Control | 3961, 3881, 3903 | 5694, 5683, 5632 | PXD001608 | |
| Ctrl_6 | Control | 4290, 4281, 4242 | 5966, 5959, 5932 | PXD001608 | |
| Ctrl_7 | Control | 4080, 4099, 4097 | 5856, 5822, 5817 | PXD001608 | |
| Ctrl_8 | Control | 4269, 4325, 4336 | 5968, 5986, 5966 | PXD001608 | |
| Ctrl_9 | Control | 4560, 4549, 3974 | 6103, 6126, 6103 | PXD001608 | |
| Ctrl_10 | Control | 3974, 3993, 3972 | 5781, 5817, 5779 | PXD001608 | |
| UC_1 | UC | 4290, 4229, 4363 | 5870, 5852, 5907 | PXD001608 | |
| UC_2 | UC | 3328, 3285, 3328 | 5148, 5101, 5139 | PXD001608 | |
| UC_3 | UC | 4455, 4472, 4482 | 6068, 6082, 6041 | PXD001608 | |
| UC_4 | UC | 4236, 4005, NA | 5685, 5773, NA | PXD001608 | UC_4_3 poor R |
| UC_5 | UC | 3097, 3174, NA | 5051, 5017, NA | PXD001608 | UC_5_3 poor R |
| UC_6 | UC | 4458, 4424, 4482 | 6118, 6108, 6115 | PXD001608 | |
| UC_7 | UC | 3657, 3686, 3693 | 5647, 5626, 5575 | PXD001608 | |
| UC_8 | UC | 3356, 3288, 3303 | 5237, 5207, 5164 | PXD001608 | |
| UC_9 | UC | 4681, 4700, 4703 | 6220, 6233, 6223 | PXD001608 | |
| UC_10 | UC | 3762, 3688, 3674 | 5587, 5557, 5562 | PXD001608 | |
| RA_1 | RA | 3900, 3789, 3755 | 5658, 5644, 5632 | PXD003082 | |
| RA_2 | RA | 4347, 4141, 4285 | 6023, 5997, 5973 | PXD003082 | |
| RA_3 | RA | 4654, 4678, 4629 | 6204, 6179, 6180 | PXD003082 | |
| RA_4 | RA | 4298, 4287, 4267 | 5933, 5925, 5899 | PXD003082 | |
| RA_5 | RA | 3472, 3521, 3491 | 5402, 5390, 5344 | PXD003082 | |
| RA_6 | RA | 3545, 3485, 3526 | 5735, 5742, 5728 | PXD003082 | |
| RA_7 | RA | 4538, 4476, 4459 | 6057, 6062, 6071 | PXD003082 | |
| RA_8 | RA | 3619, 3439 NA | 5317, 5310, NA | PXD003082 | RA_8_3 poor R |
| RA_9 | RA | 3361, NA, 3427, | 5256, NA, 5187 | PXD003082 | RA_9_2 poor R |
| RA_10 | RA | 4417, 4354, 4361 | 5991, 6010, 6023 | PXD003082 | |
| RA_11 | RA | 3094, 3055, 3051 | 5005, 5050, 5006 | PXD003082 |