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lgatto / MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics
http://lgatto.github.io/MSnbase/
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addIdentificationData() gives no errors, but idFile is NA #268

Closed meilumcdermott closed 7 years ago

meilumcdermott commented 7 years ago

I tried to do some troubleshooting but couldn't figure out why this was happening.

The MSnExp is loading from the mzML file, but the corresponding mzID file is not adding the identifications.

My code:

> myquantFile <- dir(system.file(package = "MSnbase", dir = "extdata"), full.name = TRUE, pattern = "33data.mzML")
> myidentFile <- dir(system.file(package = "MSnbase", dir = "extdata"), full.name = TRUE, pattern = "33data.mzid")

> mymsexp <- readMSData(myquantFile, centroided. = TRUE, verbose = TRUE)

mzML seems to be read in perfectly fine:

> head(fData(mymsexp), n = 2)

        spectrum
X0001.1        1
X0002.1        2

> mymsexp[["X0001.1"]]

Object of class "Spectrum2"
 Precursor: 890.5841 
 Retention time: 10:3 
 Charge: 4 
 MSn level: 2 
 Peaks count: 11 
 Total ion count: 63290.32

And then the issue in addIdentificationData():

> mymsexp1 <- addIdentificationData(mymsexp, id = myidentFile, verbose = TRUE)
reading 33data.mzid... DONE!

> head(fData(mymsexp1), n = 2)
        spectrum scan number(s) passthreshold rank
X0001.1        1             NA            NA   NA
X0002.1        2             NA            NA   NA
        calculatedmasstocharge experimentalmasstocharge chargestate
X0001.1                     NA                       NA          NA
X0002.1                     NA                       NA          NA
        ms-gf:denovoscore ms-gf:evalue ms-gf:pepqvalue ms-gf:qvalue
X0001.1                NA           NA              NA           NA
X0002.1                NA           NA              NA           NA
        ms-gf:rawscore ms-gf:specevalue assumeddissociationmethod
X0001.1             NA               NA                      <NA>
X0002.1             NA               NA                      <NA>
        isotopeerror isdecoy post  pre end start accession length
X0001.1         <NA>      NA <NA> <NA>  NA    NA      <NA>     NA
X0002.1         <NA>      NA <NA> <NA>  NA    NA      <NA>     NA
        description pepseq modified modification idFile databaseFile
X0001.1        <NA>   <NA>       NA         <NA>   <NA>         <NA>
X0002.1        <NA>   <NA>       NA         <NA>   <NA>         <NA>
        nprot npep.prot npsm.prot npsm.pep
X0001.1    NA        NA        NA       NA
X0002.1    NA        NA        NA       NA

> idSummary(mymsexp1)
  spectrumFile idFile coverage
1 33data.mzML   <NA>        0

I tried to see if maybe MSnbase wasn't just wasn't reading the mzID, but seems as if it can (sorry for the scrolling):

> id <- openIDfile(myidentFile)
> score(id)
                                          spectrumID MS.GF.RawScore
1     controllerType=0 controllerNumber=1 scan=65157            160
2     controllerType=0 controllerNumber=1 scan=65157            160
3     controllerType=0 controllerNumber=1 scan=34834            145
4     controllerType=0 controllerNumber=1 scan=30923            131
5     controllerType=0 controllerNumber=1 scan=63684            116
6     controllerType=0 controllerNumber=1 scan=63829            116
7     controllerType=0 controllerNumber=1 scan=34704            128
8     controllerType=0 controllerNumber=1 scan=35705            160
9     controllerType=0 controllerNumber=1 scan=27170            156
10    controllerType=0 controllerNumber=1 scan=61250            140
11    controllerType=0 controllerNumber=1 scan=61250            140
12    controllerType=0 controllerNumber=1 scan=65228            177
13    controllerType=0 controllerNumber=1 scan=65228            177
14    controllerType=0 controllerNumber=1 scan=30784            114
15    controllerType=0 controllerNumber=1 scan=32710            123
16    controllerType=0 controllerNumber=1 scan=65230            126
17    controllerType=0 controllerNumber=1 scan=65230            126
18    controllerType=0 controllerNumber=1 scan=26516            168
19    controllerType=0 controllerNumber=1 scan=31964            148
20    controllerType=0 controllerNumber=1 scan=31964            148
21    controllerType=0 controllerNumber=1 scan=28536            103
22    controllerType=0 controllerNumber=1 scan=27320            109
23    controllerType=0 controllerNumber=1 scan=27018            115
24    controllerType=0 controllerNumber=1 scan=36085            116
25    controllerType=0 controllerNumber=1 scan=28402            105
26    controllerType=0 controllerNumber=1 scan=31106            103
27    controllerType=0 controllerNumber=1 scan=27600             95
28    controllerType=0 controllerNumber=1 scan=29873             86
29    controllerType=0 controllerNumber=1 scan=29873             86
30    controllerType=0 controllerNumber=1 scan=29329             97
31    controllerType=0 controllerNumber=1 scan=33169             89
32    controllerType=0 controllerNumber=1 scan=27848            121
33    controllerType=0 controllerNumber=1 scan=27848            121
34    controllerType=0 controllerNumber=1 scan=27848            121
35    controllerType=0 controllerNumber=1 scan=27848            121
36    controllerType=0 controllerNumber=1 scan=26973             73
37    controllerType=0 controllerNumber=1 scan=26973             73
38    controllerType=0 controllerNumber=1 scan=26973             73
39    controllerType=0 controllerNumber=1 scan=26973             73
40    controllerType=0 controllerNumber=1 scan=26973             73
41    controllerType=0 controllerNumber=1 scan=26973             73
42    controllerType=0 controllerNumber=1 scan=27124             96
43    controllerType=0 controllerNumber=1 scan=27124             96
44    controllerType=0 controllerNumber=1 scan=27124             96
45    controllerType=0 controllerNumber=1 scan=27124             96
46    controllerType=0 controllerNumber=1 scan=27124             96
47    controllerType=0 controllerNumber=1 scan=27124             96
48    controllerType=0 controllerNumber=1 scan=27468             99
49    controllerType=0 controllerNumber=1 scan=27468             99
50    controllerType=0 controllerNumber=1 scan=27468             99
51    controllerType=0 controllerNumber=1 scan=27468             99
52    controllerType=0 controllerNumber=1 scan=27468             99
53    controllerType=0 controllerNumber=1 scan=27468             99
54    controllerType=0 controllerNumber=1 scan=28039             90
55    controllerType=0 controllerNumber=1 scan=28039             90
56    controllerType=0 controllerNumber=1 scan=28039             90
57    controllerType=0 controllerNumber=1 scan=28039             90
58    controllerType=0 controllerNumber=1 scan=28039             90
59    controllerType=0 controllerNumber=1 scan=28039             90
60    controllerType=0 controllerNumber=1 scan=28182             96
61    controllerType=0 controllerNumber=1 scan=28182             96
62    controllerType=0 controllerNumber=1 scan=28182             96
63    controllerType=0 controllerNumber=1 scan=28182             96
64    controllerType=0 controllerNumber=1 scan=28182             96
65    controllerType=0 controllerNumber=1 scan=28182             96
66    controllerType=0 controllerNumber=1 scan=27743             92
67    controllerType=0 controllerNumber=1 scan=27608             66
68    controllerType=0 controllerNumber=1 scan=27608             66
69    controllerType=0 controllerNumber=1 scan=27608             66
70    controllerType=0 controllerNumber=1 scan=27608             66
71    controllerType=0 controllerNumber=1 scan=27608             66
72    controllerType=0 controllerNumber=1 scan=27608             66
73    controllerType=0 controllerNumber=1 scan=27278             91
74    controllerType=0 controllerNumber=1 scan=27278             91
75    controllerType=0 controllerNumber=1 scan=27278             91
76    controllerType=0 controllerNumber=1 scan=27278             91
77    controllerType=0 controllerNumber=1 scan=27278             91
78    controllerType=0 controllerNumber=1 scan=27278             91
79    controllerType=0 controllerNumber=1 scan=27751             70
80    controllerType=0 controllerNumber=1 scan=27751             70
81    controllerType=0 controllerNumber=1 scan=27751             70
82    controllerType=0 controllerNumber=1 scan=27751             70
83    controllerType=0 controllerNumber=1 scan=27751             70
84    controllerType=0 controllerNumber=1 scan=27751             70
85    controllerType=0 controllerNumber=1 scan=33785            134
86    controllerType=0 controllerNumber=1 scan=33785            134
87    controllerType=0 controllerNumber=1 scan=33385             78
88    controllerType=0 controllerNumber=1 scan=64225             93
89    controllerType=0 controllerNumber=1 scan=29195             92
90    controllerType=0 controllerNumber=1 scan=33684             93
91    controllerType=0 controllerNumber=1 scan=33684             93
92    controllerType=0 controllerNumber=1 scan=33505             88
93    controllerType=0 controllerNumber=1 scan=27323             77
94    controllerType=0 controllerNumber=1 scan=28266             81
95    controllerType=0 controllerNumber=1 scan=27894             80
96    controllerType=0 controllerNumber=1 scan=27894             80
97    controllerType=0 controllerNumber=1 scan=27894             80
98    controllerType=0 controllerNumber=1 scan=27894             80
99    controllerType=0 controllerNumber=1 scan=27894             80
100   controllerType=0 controllerNumber=1 scan=27894             80
101   controllerType=0 controllerNumber=1 scan=35681             89
102   controllerType=0 controllerNumber=1 scan=27085             84
103   controllerType=0 controllerNumber=1 scan=27085             84
104   controllerType=0 controllerNumber=1 scan=27085             84
105   controllerType=0 controllerNumber=1 scan=36231            107
106   controllerType=0 controllerNumber=1 scan=26588             88
107   controllerType=0 controllerNumber=1 scan=33814             94
108   controllerType=0 controllerNumber=1 scan=33814             94
109   controllerType=0 controllerNumber=1 scan=27245             89
110   controllerType=0 controllerNumber=1 scan=27245             89
111   controllerType=0 controllerNumber=1 scan=27530             93
112   controllerType=0 controllerNumber=1 scan=27530             93
113   controllerType=0 controllerNumber=1 scan=27530             93
114   controllerType=0 controllerNumber=1 scan=33296             63
115   controllerType=0 controllerNumber=1 scan=63944             79
116   controllerType=0 controllerNumber=1 scan=63944             79
117   controllerType=0 controllerNumber=1 scan=23392             95
118   controllerType=0 controllerNumber=1 scan=23533            100
119   controllerType=0 controllerNumber=1 scan=24074            101
120   controllerType=0 controllerNumber=1 scan=24203             99
121   controllerType=0 controllerNumber=1 scan=33635             90
122   controllerType=0 controllerNumber=1 scan=33028             80
123   controllerType=0 controllerNumber=1 scan=33551             93
124   controllerType=0 controllerNumber=1 scan=33551             93
125   controllerType=0 controllerNumber=1 scan=31777             98
126   controllerType=0 controllerNumber=1 scan=19555             62
127   controllerType=0 controllerNumber=1 scan=19555             62
128   controllerType=0 controllerNumber=1 scan=19555             62
129   controllerType=0 controllerNumber=1 scan=19555             62
130   controllerType=0 controllerNumber=1 scan=19555             62
131   controllerType=0 controllerNumber=1 scan=19555             62
132   controllerType=0 controllerNumber=1 scan=27168             92
133   controllerType=0 controllerNumber=1 scan=33675             45
134   controllerType=0 controllerNumber=1 scan=23745             83
135   controllerType=0 controllerNumber=1 scan=23745             83
136   controllerType=0 controllerNumber=1 scan=23745             83
137   controllerType=0 controllerNumber=1 scan=23745             83
138   controllerType=0 controllerNumber=1 scan=23745             83
139   controllerType=0 controllerNumber=1 scan=23745             83
140   controllerType=0 controllerNumber=1 scan=23745             83
141   controllerType=0 controllerNumber=1 scan=23745             83
142   controllerType=0 controllerNumber=1 scan=18063             71
      MS.GF.DeNovoScore MS.GF.SpecEValue MS.GF.EValue MS.GF.QValue
1                   164     5.048283e-26 1.380117e-17  0.000000000
2                   164     5.048283e-26 1.380117e-17  0.000000000
3                   153     1.495029e-24 4.026016e-16  0.000000000
4                   144     6.597571e-24 1.776683e-15  0.000000000
5                   119     2.109424e-22 5.528301e-14  0.000000000
6                   118     6.297963e-22 1.650547e-13  0.000000000
7                   140     7.532981e-22 2.028583e-13  0.000000000
8                   168     1.388551e-21 3.674789e-13  0.000000000
9                   165     1.186795e-20 3.077427e-12  0.000000000
10                  165     9.924275e-20 2.713133e-11  0.000000000
11                  165     9.924275e-20 2.713133e-11  0.000000000
12                  194     1.386281e-19 3.553187e-11  0.000000000
13                  194     1.386281e-19 3.553187e-11  0.000000000
14                  152     5.253944e-19 1.414853e-10  0.000000000
15                  134     1.139322e-18 2.985893e-10  0.000000000
16                  129     1.321433e-18 3.386973e-10  0.000000000
17                  129     1.321433e-18 3.386973e-10  0.000000000
18                  170     3.445967e-18 8.598315e-10  0.000000000
19                  148     4.470375e-18 1.115440e-09  0.000000000
20                  148     4.470375e-18 1.115440e-09  0.000000000
21                  111     7.754547e-18 1.987574e-09  0.000000000
22                  147     2.356443e-17 6.395386e-09  0.000000000
23                  139     3.399041e-17 8.813911e-09  0.000000000
24                  136     7.644390e-17 2.023081e-08  0.000000000
25                  118     1.658833e-16 4.251767e-08  0.000000000
26                  120     1.682156e-16 4.311546e-08  0.000000000
27                  134     4.011710e-16 1.088778e-07  0.000000000
28                   98     5.268238e-16 1.314521e-07  0.000000000
29                   98     5.268238e-16 1.314521e-07  0.000000000
30                  109     6.108490e-16 1.500419e-07  0.000000000
31                  119     8.296573e-16 2.174336e-07  0.000000000
32                  126     1.046761e-15 2.611859e-07  0.000000000
33                  126     1.046761e-15 2.611859e-07  0.000000000
34                  126     1.046761e-15 2.611859e-07  0.000000000
35                  126     1.046761e-15 2.611859e-07  0.000000000
36                   73     1.153023e-15 2.782639e-07  0.000000000
37                   73     1.153023e-15 2.782639e-07  0.000000000
38                   73     1.153023e-15 2.782639e-07  0.000000000
39                   73     1.153023e-15 2.782639e-07  0.000000000
40                   73     1.153023e-15 2.782639e-07  0.000000000
41                   73     1.153023e-15 2.782639e-07  0.000000000
42                   96     1.153023e-15 2.782639e-07  0.000000000
43                   96     1.153023e-15 2.782639e-07  0.000000000
44                   96     1.153023e-15 2.782639e-07  0.000000000
45                   96     1.153023e-15 2.782639e-07  0.000000000
46                   96     1.153023e-15 2.782639e-07  0.000000000
47                   96     1.153023e-15 2.782639e-07  0.000000000
48                   99     1.153023e-15 2.782639e-07  0.000000000
49                   99     1.153023e-15 2.782639e-07  0.000000000
50                   99     1.153023e-15 2.782639e-07  0.000000000
51                   99     1.153023e-15 2.782639e-07  0.000000000
52                   99     1.153023e-15 2.782639e-07  0.000000000
53                   99     1.153023e-15 2.782639e-07  0.000000000
54                   90     1.153023e-15 2.782639e-07  0.000000000
55                   90     1.153023e-15 2.782639e-07  0.000000000
56                   90     1.153023e-15 2.782639e-07  0.000000000
57                   90     1.153023e-15 2.782639e-07  0.000000000
58                   90     1.153023e-15 2.782639e-07  0.000000000
59                   90     1.153023e-15 2.782639e-07  0.000000000
60                   98     1.561812e-15 3.769185e-07  0.000000000
61                   98     1.561812e-15 3.769185e-07  0.000000000
62                   98     1.561812e-15 3.769185e-07  0.000000000
63                   98     1.561812e-15 3.769185e-07  0.000000000
64                   98     1.561812e-15 3.769185e-07  0.000000000
65                   98     1.561812e-15 3.769185e-07  0.000000000
66                  134     1.630435e-15 4.424999e-07  0.000000000
67                   66     1.914265e-15 4.619774e-07  0.000000000
68                   66     1.914265e-15 4.619774e-07  0.000000000
69                   66     1.914265e-15 4.619774e-07  0.000000000
70                   66     1.914265e-15 4.619774e-07  0.000000000
71                   66     1.914265e-15 4.619774e-07  0.000000000
72                   66     1.914265e-15 4.619774e-07  0.000000000
73                   93     2.094666e-15 5.055144e-07  0.000000000
74                   93     2.094666e-15 5.055144e-07  0.000000000
75                   93     2.094666e-15 5.055144e-07  0.000000000
76                   93     2.094666e-15 5.055144e-07  0.000000000
77                   93     2.094666e-15 5.055144e-07  0.000000000
78                   93     2.094666e-15 5.055144e-07  0.000000000
79                   73     2.417917e-15 5.835258e-07  0.000000000
80                   73     2.417917e-15 5.835258e-07  0.000000000
81                   73     2.417917e-15 5.835258e-07  0.000000000
82                   73     2.417917e-15 5.835258e-07  0.000000000
83                   73     2.417917e-15 5.835258e-07  0.000000000
84                   73     2.417917e-15 5.835258e-07  0.000000000
85                  188     2.460216e-15 6.510940e-07  0.000000000
86                  188     2.460216e-15 6.510940e-07  0.000000000
87                   97     2.776130e-15 6.818967e-07  0.000000000
88                  127     4.354638e-15 1.141248e-06  0.000000000
89                  105     4.515503e-15 1.109136e-06  0.000000000
90                  138     6.603896e-15 1.747715e-06  0.000000000
91                  138     6.603896e-15 1.747715e-06  0.000000000
92                   99     7.872057e-15 1.933602e-06  0.000000000
93                  100     8.655920e-15 2.244531e-06  0.000000000
94                  101     8.680610e-15 2.224933e-06  0.000000000
95                   82     8.919169e-15 2.152500e-06  0.000000000
96                   82     8.919169e-15 2.152500e-06  0.000000000
97                   82     8.919169e-15 2.152500e-06  0.000000000
98                   82     8.919169e-15 2.152500e-06  0.000000000
99                   82     8.919169e-15 2.152500e-06  0.000000000
100                  82     8.919169e-15 2.152500e-06  0.000000000
101                 129     9.495772e-15 2.513048e-06  0.000000000
102                 131     1.078499e-14 2.948438e-06  0.000000000
103                 131     1.078499e-14 2.948438e-06  0.000000000
104                 131     1.078499e-14 2.948438e-06  0.000000000
105                 164     1.455696e-14 4.006889e-06  0.000000000
106                 128     1.464172e-14 3.973762e-06  0.000000000
107                 139     1.532094e-14 4.054673e-06  0.000000000
108                 139     1.532094e-14 4.054673e-06  0.000000000
109                 145     1.554014e-14 4.248417e-06  0.000000000
110                 145     1.554014e-14 4.248417e-06  0.000000000
111                 150     1.585002e-14 4.333133e-06  0.000000000
112                 150     1.585002e-14 4.333133e-06  0.000000000
113                 150     1.585002e-14 4.333133e-06  0.000000000
114                  85     1.770318e-14 4.639585e-06  0.000000000
115                 139     1.795291e-14 4.908028e-06  0.000000000
116                 139     1.795291e-14 4.908028e-06  0.000000000
117                  95     1.805502e-14 4.174394e-06  0.000000000
118                 100     1.805502e-14 4.174394e-06  0.000000000
119                 101     1.805502e-14 4.174394e-06  0.000000000
120                  99     1.805502e-14 4.174394e-06  0.000000000
121                  95     2.066531e-14 5.075989e-06  0.000000000
122                 105     2.075723e-14 5.439980e-06  0.000000000
123                 142     2.209994e-14 5.848730e-06  0.000000000
124                 142     2.209994e-14 5.848730e-06  0.000000000
125                 110     2.394322e-14 5.881139e-06  0.000000000
126                  67     2.525810e-14 5.839774e-06  0.000000000
127                  67     2.525810e-14 5.839774e-06  0.000000000
128                  67     2.525810e-14 5.839774e-06  0.000000000
129                  67     2.525810e-14 5.839774e-06  0.000000000
130                  67     2.525810e-14 5.839774e-06  0.000000000
131                  67     2.525810e-14 5.839774e-06  0.000000000
132                 148     2.528773e-14 6.863091e-06  0.000000000
133                  89     2.773456e-14 7.634099e-06  0.000000000
134                  98     2.948115e-14 7.556335e-06  0.000000000
135                  98     2.948115e-14 7.556335e-06  0.000000000
136                  98     2.948115e-14 7.556335e-06  0.000000000
137                  98     2.948115e-14 7.556335e-06  0.000000000
138                  98     2.948115e-14 7.556335e-06  0.000000000
139                  98     2.948115e-14 7.556335e-06  0.000000000
140                  98     2.948115e-14 7.556335e-06  0.000000000
141                  98     2.948115e-14 7.556335e-06  0.000000000
142                  73     3.050985e-14 7.054000e-06  0.000000000
      MS.GF.PepQValue
1          0.00000000
2          0.00000000
3          0.00000000
4          0.00000000
5          0.00000000
6          0.00000000
7          0.00000000
8          0.00000000
9          0.00000000
10         0.00000000
11         0.00000000
12         0.00000000
13         0.00000000
14         0.00000000
15         0.00000000
16         0.00000000
17         0.00000000
18         0.00000000
19         0.00000000
20         0.00000000
21         0.00000000
22         0.00000000
23         0.00000000
24         0.00000000
25         0.00000000
26         0.00000000
27         0.00000000
28         0.00000000
29         0.00000000
30         0.00000000
31         0.00000000
32         0.00000000
33         0.00000000
34         0.00000000
35         0.00000000
36         0.00000000
37         0.00000000
38         0.00000000
39         0.00000000
40         0.00000000
41         0.00000000
42         0.00000000
43         0.00000000
44         0.00000000
45         0.00000000
46         0.00000000
47         0.00000000
48         0.00000000
49         0.00000000
50         0.00000000
51         0.00000000
52         0.00000000
53         0.00000000
54         0.00000000
55         0.00000000
56         0.00000000
57         0.00000000
58         0.00000000
59         0.00000000
60         0.00000000
61         0.00000000
62         0.00000000
63         0.00000000
64         0.00000000
65         0.00000000
66         0.00000000
67         0.00000000
68         0.00000000
69         0.00000000
70         0.00000000
71         0.00000000
72         0.00000000
73         0.00000000
74         0.00000000
75         0.00000000
76         0.00000000
77         0.00000000
78         0.00000000
79         0.00000000
80         0.00000000
81         0.00000000
82         0.00000000
83         0.00000000
84         0.00000000
85         0.00000000
86         0.00000000
87         0.00000000
88         0.00000000
89         0.00000000
90         0.00000000
91         0.00000000
92         0.00000000
93         0.00000000
94         0.00000000
95         0.00000000
96         0.00000000
97         0.00000000
98         0.00000000
99         0.00000000
100        0.00000000
101        0.00000000
102        0.00000000
103        0.00000000
104        0.00000000
105        0.00000000
106        0.00000000
107        0.00000000
108        0.00000000
109        0.00000000
110        0.00000000
111        0.00000000
112        0.00000000
113        0.00000000
114        0.00000000
115        0.00000000
116        0.00000000
117        0.00000000
118        0.00000000
119        0.00000000
120        0.00000000
121        0.00000000
122        0.00000000
123        0.00000000
124        0.00000000
125        0.00000000
126        0.00000000
127        0.00000000
128        0.00000000
129        0.00000000
130        0.00000000
131        0.00000000
132        0.00000000
133        0.00000000
134        0.00000000
135        0.00000000
136        0.00000000
137        0.00000000
138        0.00000000
139        0.00000000
140        0.00000000
141        0.00000000
142        0.00000000
 [ reached getOption("max.print") -- omitted 18349 rows ]

mzML files are converted from Thermo RAW files using MSConvert and are centroided. mzID files were generated by MSGFplus (from the Bioconductor package). I used mzID package to convert the mzID to csv format if you want to look at that.

Dropbox link

I also tried to do the process with MGF files with readMgfData(), and the same thing happened (idFile was NA), but I did some further reading and realized the mzML was better to use anyway over MGF.

I also tried running the example files that came with the package (dummyiTRAQ.mzXML and dummyiTRAQ.mzid), and those were correct. So possibly something to do with my files? (I assumed MSGFplus output the current version of mzid, but perhaps not.)

And of course:

> sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets 
[7] methods   base     

other attached packages:
[1] MSnbase_2.2.0       ProtGenerics_1.8.0  BiocParallel_1.10.1
[4] mzR_2.10.0          Rcpp_0.12.13        Biobase_2.36.2     
[7] BiocGenerics_0.22.1

loaded via a namespace (and not attached):
 [1] compiler_3.4.2           BiocInstaller_1.26.1    
 [3] plyr_1.8.4               bitops_1.0-6            
 [5] iterators_1.0.8          tools_3.4.2             
 [7] zlibbioc_1.22.0          bit_1.1-12              
 [9] MALDIquant_1.16.4        biomaRt_2.32.1          
[11] digest_0.6.12            memoise_1.1.0           
[13] RSQLite_2.0              preprocessCore_1.38.1   
[15] tibble_1.3.4             gtable_0.2.0            
[17] lattice_0.20-35          rlang_0.1.2.9000        
[19] foreach_1.4.3            DBI_0.7                 
[21] S4Vectors_0.14.6         IRanges_2.10.4          
[23] bit64_0.9-7              stats4_3.4.2            
[25] grid_3.4.2               impute_1.50.1           
[27] AnnotationDbi_1.38.2     XML_3.98-1.9            
[29] limma_3.32.8             distr_2.6.2             
[31] blob_1.1.0               ggplot2_2.2.1           
[33] isobar_1.22.0            SweaveListingUtils_0.7.7
[35] sfsmisc_1.1-1            MASS_7.3-47             
[37] scales_0.5.0             pcaMethods_1.68.0       
[39] codetools_0.2-15         mzID_1.14.0             
[41] colorspace_1.3-2         startupmsg_0.9.4        
[43] affy_1.54.0              RCurl_1.95-4.8          
[45] lazyeval_0.2.0           munsell_0.4.3           
[47] doParallel_1.0.11        vsn_3.44.0              
[49] affyio_1.46.0

Let me know if you need any other info. Thank you!

sgibb commented 7 years ago

At least one of the problems is that the file names don't match. The mzML file is named 33data.mzML but the 33data.mzid refers to C:\\Users\\mmcdermott\\Documents\\Boston Data Runs\\mzML files\\2016-03-03-CD34-TMT-pST-Set1-3D-15-230.mzML.

If you just want to combine one single mzML file with one mzid file you could circumvent the file name problem by setting the fcol and icol argument of addIdentificationData manually (the default is spectrum id and acquisition number for both (unfortunately the column names of fcol and icol differ)):

mymsexp1 <- addIdentificationData(mymsnexp, myidentFile,
                                  # just match on acquisition number
                                  fcol="acquisition.number", icol="acquisitionNum")
meilumcdermott commented 7 years ago

Awesome - I didn't realize there was a reference within the mzID file itself. That fixed the issue. Thank you for your prompt reply, and for all the work you guys do on the package!