raw.mine.RdExample of SpectroMine PSM sheet. It is the output of SpectroMine and the input for SpectroMinetoMSstatsTMTFormat function, with annotation file. Annotation file should be made by users. It includes peak intensities for 10 proteins among 12 MS runs with TMT-6plex. The important variables are as follows:
raw.mine
A data frame with 170 rows and 28 variables.
PG.ProteinAccessions
P.MoleculeID
PP.Charge
R.FileName
PG.QValue
PSM.Qvalue
Channels : PSM.TMT6_126..Raw., ..., PSM.TMT6_131..Raw.
#> R.MS3.Used R.BlockName R.QuantificationMethod #> 1 True All Runs TMT6Plex #> 2 True All Runs TMT6Plex #> 3 True All Runs TMT6Plex #> 4 True All Runs TMT6Plex #> 5 True All Runs TMT6Plex #> 6 True All Runs TMT6Plex #> R.FileName PG.Genes PG.Organisms #> 1 ch_19Jan2017_SM-1-1_Sp-6-2_CID-OT-MS3-Short_HpH_1.raw EGLN1 Homo sapiens #> 2 ch_19Jan2017_SM-1-1_Sp-6-2_CID-OT-MS3-Short_HpH_1.raw SEPT11 Homo sapiens #> 3 ch_19Jan2017_SM-1-1_Sp-6-2_CID-OT-MS3-Short_HpH_1.raw SEPT11 Homo sapiens #> 4 ch_19Jan2017_SM-1-1_Sp-6-2_CID-OT-MS3-Short_HpH_1.raw SEPT11 Homo sapiens #> 5 ch_19Jan2017_SM-1-1_Sp-6-2_CID-OT-MS3-Short_HpH_1.raw SEPT11 Homo sapiens #> 6 ch_19Jan2017_SM-1-1_Sp-6-2_CID-OT-MS3-Short_HpH_1.raw NAP1L4 Homo sapiens #> PG.ProteinAccessions PG.ProteinDescriptions PG.ProteinNames #> 1 Q9GZT9 Egl nine homolog 1 EGLN1_HUMAN #> 2 Q9NVA2 Septin-11 SEP11_HUMAN #> 3 Q9NVA2 Septin-11 SEP11_HUMAN #> 4 Q9NVA2 Septin-11 SEP11_HUMAN #> 5 Q9NVA2 Septin-11 SEP11_HUMAN #> 6 Q99733 Nucleosome assembly protein 1-like 4 NP1L4_HUMAN #> PG.UniprotIds PG.Coverage PG.QValue PEP.IsProteinGroupSpecific #> 1 Q9GZT9 5.6% 0 TRUE #> 2 Q9NVA2 9.1% 0 TRUE #> 3 Q9NVA2 9.1% 0 FALSE #> 4 Q9NVA2 9.1% 0 TRUE #> 5 Q9NVA2 9.1% 0 TRUE #> 6 Q99733 5.1% 0 TRUE #> PEP.IsProteotypic PEP.StrippedSequence PEP.QValue #> 1 TRUE AAAGGQGSAVAAEAEPGKEEPPAR 0.0000000000 #> 2 TRUE KELEEEVNNFQK 0.0001986492 #> 3 FALSE SLDLVTMK 0.0000000000 #> 4 TRUE AAAQLLQSQAQQSGAQQTK 0.0000000000 #> 5 TRUE AAAQLLQSQAQQSGAQQTK 0.0000000000 #> 6 TRUE VLAALQER 0.0024595109 #> PEP.IsUsedForQuantification PP.Charge #> 1 True 3 #> 2 True 3 #> 3 True 2 #> 4 True 3 #> 5 True 2 #> 6 True 2 #> P.MoleculeID PSM.TMT6_126..Raw. #> 1 _[TMT_Nter]AAAGGQGSAVAAEAEPGK[TMT_Lys]EEPPAR_ 382.1107 #> 2 _[TMT_Nter]K[TMT_Lys]ELEEEVNNFQK[TMT_Lys]_ 33554.1900 #> 3 _[TMT_Nter]SLDLVTMK[TMT_Lys]_ 44713.6300 #> 4 _[TMT_Nter]AAAQLLQSQAQQSGAQQTK[TMT_Lys]_ 20877.8700 #> 5 _[TMT_Nter]AAAQLLQSQAQQSGAQQTK[TMT_Lys]_ 506.1669 #> 6 _[TMT_Nter]VLAALQER_ 17143.5200 #> PSM.TMT6_127..Raw. PSM.TMT6_128..Raw. PSM.TMT6_129..Raw. PSM.TMT6_130..Raw. #> 1 392.9243 477.7064 989.6951 695.7537 #> 2 33671.5400 40525.3900 43739.8600 40697.4400 #> 3 51052.8400 58457.6400 47213.1300 58004.6700 #> 4 19930.0100 24963.5400 29021.8300 19510.8600 #> 5 1019.8020 543.2091 555.3629 501.8123 #> 6 4284.8930 26957.7100 15610.6900 21208.9500 #> PSM.TMT6_131..Raw. PSM.IsUsedForQuantification PSM.NrOfMatchedChannelIons #> 1 107.6282 True 6 #> 2 17299.1300 True 6 #> 3 23622.9500 True 6 #> 4 15952.0600 True 6 #> 5 268.5246 True 6 #> 6 7701.3510 True 6 #> PSM.Qvalue #> 1 0.000000e+00 #> 2 2.146015e-04 #> 3 0.000000e+00 #> 4 5.613247e-05 #> 5 0.000000e+00 #> 6 1.951193e-03