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# Pbase example data

Laurent Gatto

The original data is a 10 fmol Peptide Retention Time Calibration Mixture spiked into 50 ng HeLa background acquired on a Thermo Orbitrap Q Exactive instrument. A restricted set of high scoring human proteins from the UniProt release 2014_06 were searched using the MSGF+ engine.

## The fasta database

    library("Biostrings")

    ## Loading required package: XVector

    fafile <- system.file("extdata/HUMAN_2014_06-09prots.fasta", package = "Pbase")
    fa <- readAAStringSet(fafile)
    fa

    ##   A AAStringSet instance of length 9
    ##     width seq                                          names
    ## [1]   375 MDDDIAALVVDNGSGMCKAGF...WISKQEYDESGPSIVHRKCF sp|P60709|ACTB_HU...
    ## [2]   664 METPSQRRATRSGAQASSTPL...SYLLGNSSPRTQSPQNCSIM sp|P02545|LMNA_HU...
    ## [3]   417 MSLSNKLTLDKLDVKGKRVVM...ASLELLEGKVLPGVDALSNI sp|P00558|PGK1_HU...
    ## [4]  2602 MPVTEKDLAEDAPWKKIQQNT...LAVKWGEEHIPGSPFHVTVP sp|O75369|FLNB_HU...
    ## [5]   911 MVDYHAANQSYQYGPSSAGNG...VPGALDYKSFSTALYGESDL sp|O43707|ACTN4_H...
    ## [6]  2624 MFRRARLSVKPNVRPGVGARG...ATTVSEYFFNDIFIEVDETE sp|A6H8Y1|BDP1_HU...
    ## [7]  3374 MSPESGHSRIFEATAGPNKPE...TLSKDSLSNGVPSGRQAEFS sp|A4UGR9|XIRP2_H...
    ## [8]   364 MPYQYPALTPEQKKELSDIAH...PSGQAGAAASESLFVSNHAY sp|P04075|ALDOA_H...
    ## [9]   418 MARRKPEGSSFNMTHLSMAMA...PSGQAGAAASESLFVSNHAY sp|P04075-2|ALDOA...

## The PSM data

    library("mzID")
    idfile <- system.file("extdata/Thermo_Hela_PRTC_1_selected.mzid", package = "Pbase")
    id <- flatten(mzID(idfile))

    ## reading Thermo_Hela_PRTC_1_selected.mzid... DONE!

    dim(id)

    ## [1] 137  41

    head(id)

    ##     spectrumid scan number(s)
    ## 1    index=173          12256
    ## 1.1  index=173          12256
    ## 2    index=163          11860
    ## 2.1  index=163          11860
    ## 3    index=200          13408
    ## 3.1  index=200          13408
    ##                                                                                spectrum title
    ## 1   msLevel 2; retentionTime 2094.56706; scanNum 12256; precMz 1137.06665029649; precCharge 2
    ## 1.1 msLevel 2; retentionTime 2094.56706; scanNum 12256; precMz 1137.06665029649; precCharge 2
    ## 2   msLevel 2; retentionTime 2039.84424; scanNum 11860; precMz 1136.57450195803; precCharge 2
    ## 2.1 msLevel 2; retentionTime 2039.84424; scanNum 11860; precMz 1136.57450195803; precCharge 2
    ## 3   msLevel 2; retentionTime 2258.27868; scanNum 13408; precMz 703.038108542133; precCharge 3
    ## 3.1 msLevel 2; retentionTime 2258.27868; scanNum 13408; precMz 703.038108542133; precCharge 3
    ##     acquisitionnum passthreshold rank calculatedmasstocharge
    ## 1              173          TRUE    1               1136.574
    ## 1.1            173          TRUE    1               1136.574
    ## 2              163          TRUE    1               1136.574
    ## 2.1            163          TRUE    1               1136.574
    ## 3              200          TRUE    1                703.037
    ## 3.1            200          TRUE    1                703.037
    ##     experimentalmasstocharge chargestate ms-gf:denovoscore ms-gf:evalue
    ## 1                  1137.0667           2               132 2.597097e-18
    ## 1.1                1137.0667           2               132 2.597097e-18
    ## 2                  1136.5745           2               230 4.942664e-17
    ## 2.1                1136.5745           2               230 4.942664e-17
    ## 3                   703.0381           3               145 4.080429e-10
    ## 3.1                 703.0381           3               145 4.080429e-10
    ##     ms-gf:rawscore ms-gf:specevalue assumeddissociationmethod
    ## 1              118     2.276758e-22                       CID
    ## 1.1            118     2.276758e-22                       CID
    ## 2              186     4.333009e-21                       CID
    ## 2.1            186     4.333009e-21                       CID
    ## 3               98     3.578068e-14                       CID
    ## 3.1             98     3.578068e-14                       CID
    ##     ctermioncurrentratio explainedioncurrentratio isotopeerror
    ## 1              0.5061673                0.5888804            1
    ## 1.1            0.5061673                0.5888804            1
    ## 2             0.48202217               0.57532895            0
    ## 2.1           0.48202217               0.57532895            0
    ## 3             0.32245573                0.5909792            0
    ## 3.1           0.32245573                0.5909792            0
    ##     ms2ioncurrent meanerrorall meanerrortop7 meanrelerrorall
    ## 1        526864.0    17.757027     4.3787823     -15.7646885
    ## 1.1      526864.0    17.757027     4.3787823     -15.7646885
    ## 2       3342169.2    18.029726     5.0083427       -16.59046
    ## 2.1     3342169.2    18.029726     5.0083427       -16.59046
    ## 3       5008038.0    22.256987      8.589616       -17.53643
    ## 3.1     5008038.0    22.256987      8.589616       -17.53643
    ##     meanrelerrortop7 ntermioncurrentratio nummatchedmainions stdeverrorall
    ## 1          -3.255431           0.08271315                 25     23.135044
    ## 1.1        -3.255431           0.08271315                 25     23.135044
    ## 2          -3.333969           0.09330681                 30     28.647552
    ## 2.1        -3.333969           0.09330681                 30     28.647552
    ## 3         -1.7168152            0.2685235                 22      38.71648
    ## 3.1       -1.7168152            0.2685235                 22      38.71648
    ##     stdeverrortop7 stdevrelerrorall stdevrelerrortop7 isdecoy post pre end
    ## 1         3.582861         24.53603          4.627396   FALSE    C   K 134
    ## 1.1       3.582861         24.53603          4.627396   FALSE    C   K 188
    ## 2        2.9929223        29.504406          4.788082   FALSE    C   K 134
    ## 2.1      2.9929223        29.504406          4.788082   FALSE    C   K 188
    ## 3        2.4928854        41.070827          8.777729   FALSE    Y   K 173
    ## 3.1      2.4928854        41.070827          8.777729   FALSE    Y   K 227
    ##     start               accession length
    ## 1     112   sp|P04075|ALDOA_HUMAN    364
    ## 1.1   166 sp|P04075-2|ALDOA_HUMAN    418
    ## 2     112   sp|P04075|ALDOA_HUMAN    364
    ## 2.1   166 sp|P04075-2|ALDOA_HUMAN    418
    ## 3     154   sp|P04075|ALDOA_HUMAN    364
    ## 3.1   208 sp|P04075-2|ALDOA_HUMAN    418
    ##                                                                description
    ## 1      Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA PE=1 SV=2
    ## 1.1 Isoform 2 of Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA
    ## 2      Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA PE=1 SV=2
    ## 2.1 Isoform 2 of Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA
    ## 3      Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA PE=1 SV=2
    ## 3.1 Isoform 2 of Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA
    ##                      pepseq modified modification
    ## 1   GVVPLAGTNGETTTQGLDGLSER    FALSE         <NA>
    ## 1.1 GVVPLAGTNGETTTQGLDGLSER    FALSE         <NA>
    ## 2   GVVPLAGTNGETTTQGLDGLSER    FALSE         <NA>
    ## 2.1 GVVPLAGTNGETTTQGLDGLSER    FALSE         <NA>
    ## 3      IGEHTPSALAIMENANVLAR    FALSE         <NA>
    ## 3.1    IGEHTPSALAIMENANVLAR    FALSE         <NA>
    ##                      spectrumFile                databaseFile
    ## 1   Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta
    ## 1.1 Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta
    ## 2   Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta
    ## 2.1 Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta
    ## 3   Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta
    ## 3.1 Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta

## The Proteins object

    library("Pbase")
    p <- Proteins(fafile)
    p <- addIdentificationData(p, idfile)

    ## Reading 1 identification files:
    ##   1. D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ## done.

    p

    ## S4 class type     : Proteins
    ## Class version     : 0.1
    ## Created           : Mon Oct 13 22:08:59 2014
    ## Number of Proteins: 9
    ## Sequences:
    ##   [1] A4UGR9 [2] A6H8Y1 ... [8] P04075-2 [9] P60709
    ## Sequence features:
    ##   [1] DB [2] AccessionNumber ... [11] Filename [12] npeps
    ## Peptide features:
    ##   [1] DB [2] AccessionNumber ... [25] DatabaseSeq [26] filenames

A `Proteins` object is composed of a set of protein sequences accessible with the `aa` accessor as well as an optional set of peptides features that are mapped as coordinates along the proteins, available with `pranges`. The actual peptide sequences can be extraced with `pfeatures`.

    aa(p)

    ##   A AAStringSet instance of length 9
    ##     width seq                                          names
    ## [1]  3374 MSPESGHSRIFEATAGPNKPE...TLSKDSLSNGVPSGRQAEFS A4UGR9
    ## [2]  2624 MFRRARLSVKPNVRPGVGARG...ATTVSEYFFNDIFIEVDETE A6H8Y1
    ## [3]   911 MVDYHAANQSYQYGPSSAGNG...VPGALDYKSFSTALYGESDL O43707
    ## [4]  2602 MPVTEKDLAEDAPWKKIQQNT...LAVKWGEEHIPGSPFHVTVP O75369
    ## [5]   417 MSLSNKLTLDKLDVKGKRVVM...ASLELLEGKVLPGVDALSNI P00558
    ## [6]   664 METPSQRRATRSGAQASSTPL...SYLLGNSSPRTQSPQNCSIM P02545
    ## [7]   364 MPYQYPALTPEQKKELSDIAH...PSGQAGAAASESLFVSNHAY P04075
    ## [8]   418 MARRKPEGSSFNMTHLSMAMA...PSGQAGAAASESLFVSNHAY P04075-2
    ## [9]   375 MDDDIAALVVDNGSGMCKAGF...WISKQEYDESGPSIVHRKCF P60709

    pranges(p)

    ## IRangesList of length 9
    ## $A4UGR9
    ## IRanges of length 36
    ##      start  end width  names
    ## [1]   2743 2760    18 A4UGR9
    ## [2]    307  318    12 A4UGR9
    ## [3]   1858 1870    13 A4UGR9
    ## [4]   1699 1708    10 A4UGR9
    ## [5]   2622 2637    16 A4UGR9
    ## ...    ...  ...   ...    ...
    ## [32]    20   31    12 A4UGR9
    ## [33]  1712 1729    18 A4UGR9
    ## [34]    48   61    14 A4UGR9
    ## [35]  2082 2094    13 A4UGR9
    ## [36]  2743 2756    14 A4UGR9
    ##
    ## ...
    ## <8 more elements>

    pfeatures(p)

    ## AAStringSetList of length 9
    ## [["A4UGR9"]] QEITQNKSFFSSVKESQR LPVPKDVYSKQR ... QEITQNKSFFSSVK
    ## [["A6H8Y1"]] EDAEQVALEVDLNQKKRR ETGKENFR ... ARLSVKPNVRPGVGARGSTASNPQRGR
    ## [["O43707"]] QQRKTFTAWCNSHLR CQKICDQWDALGSLTHSR ... VGWEQLLTTIAR
    ## [["O75369"]] DLDIIDNYDYSHTVK PFDLVIPFAVRK ... VQAQGPGLKEAFTNK
    ## [["P00558"]] ELNYFAKALESPER DLMSKAEK QIVWNGPVGVFEWEAFAR FHVEEEGKGKDASGNK GTKALMDEVVK
    ## [["P02545"]] METPSQRRATR DTSRRLLAEKEREMAEMR ... RATRSGAQASSTPLSPTR
    ## [["P04075"]] GVVPLAGTNGETTTQGLDGLSER ... YTPSGQAGAAASESLFVSNHAY
    ## [["P04075-2"]] GVVPLAGTNGETTTQGLDGLSER ... YTPSGQAGAAASESLFVSNHAY
    ## [["P60709"]] DLTDYLMKILTER

A Proteins instance is further described by general `metadata`. Protein sequence and peptide features annotations can be accessed with `ametadata` and `pmetadata` (or `acols` and `pcols`) respectively.

    metadata(p)

    ## $created
    ## [1] "Mon Oct 13 22:08:59 2014"

    head(acols(p))

    ## DataFrame with 6 rows and 12 columns
    ##      DB AccessionNumber   EntryName IsoformName
    ##   <Rle>     <character> <character>       <Rle>
    ## 1    sp          A4UGR9 XIRP2_HUMAN          NA
    ## 2    sp          A6H8Y1  BDP1_HUMAN          NA
    ## 3    sp          O43707 ACTN4_HUMAN          NA
    ## 4    sp          O75369  FLNB_HUMAN          NA
    ## 5    sp          P00558  PGK1_HUMAN          NA
    ## 6    sp          P02545  LMNA_HUMAN          NA
    ##                                         ProteinName OrganismName GeneName
    ##                                         <character>        <Rle>    <Rle>
    ## 1     Xin actin-binding repeat-containing protein 2 Homo sapiens    XIRP2
    ## 2 Transcription factor TFIIIB component B'' homolog Homo sapiens     BDP1
    ## 3                                   Alpha-actinin-4 Homo sapiens    ACTN4
    ## 4                                         Filamin-B Homo sapiens     FLNB
    ## 5                         Phosphoglycerate kinase 1 Homo sapiens     PGK1
    ## 6                                      Prelamin-A/C Homo sapiens     LMNA
    ##            ProteinExistence SequenceVersion Comment
    ##                       <Rle>           <Rle>   <Rle>
    ## 1 Evidence at protein level               2      NA
    ## 2 Evidence at protein level               3      NA
    ## 3 Evidence at protein level               2      NA
    ## 4 Evidence at protein level               2      NA
    ## 5 Evidence at protein level               3      NA
    ## 6 Evidence at protein level               1      NA
    ##                                                                                               Filename
    ##                                                                                                  <Rle>
    ## 1 D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/HUMAN_2014_06-09prots.fasta
    ## 2 D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/HUMAN_2014_06-09prots.fasta
    ## 3 D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/HUMAN_2014_06-09prots.fasta
    ## 4 D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/HUMAN_2014_06-09prots.fasta
    ## 5 D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/HUMAN_2014_06-09prots.fasta
    ## 6 D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/HUMAN_2014_06-09prots.fasta
    ##       npeps
    ##   <integer>
    ## 1        36
    ## 2        23
    ## 3         6
    ## 4        13
    ## 5         5
    ## 6        12

    head(pcols(p))

    ## SplitDataFrameList of length 6
    ## $A4UGR9
    ## DataFrame with 36 rows and 26 columns
    ##        DB AccessionNumber   EntryName IsoformName
    ##     <Rle>     <character> <character>       <Rle>
    ## 1      sp          A4UGR9 XIRP2_HUMAN          NA
    ## 2      sp          A4UGR9 XIRP2_HUMAN          NA
    ## 3      sp          A4UGR9 XIRP2_HUMAN          NA
    ## 4      sp          A4UGR9 XIRP2_HUMAN          NA
    ## 5      sp          A4UGR9 XIRP2_HUMAN          NA
    ## ...   ...             ...         ...         ...
    ## 32     sp          A4UGR9 XIRP2_HUMAN          NA
    ## 33     sp          A4UGR9 XIRP2_HUMAN          NA
    ## 34     sp          A4UGR9 XIRP2_HUMAN          NA
    ## 35     sp          A4UGR9 XIRP2_HUMAN          NA
    ## 36     sp          A4UGR9 XIRP2_HUMAN          NA
    ##                                                             ProteinName
    ##                                                             <character>
    ## 1   sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
    ## 2   sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
    ## 3   sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
    ## 4   sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
    ## 5   sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
    ## ...                                                                 ...
    ## 32  sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
    ## 33  sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
    ## 34  sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
    ## 35  sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
    ## 36  sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
    ##     OrganismName GeneName          ProteinExistence SequenceVersion
    ##            <Rle>    <Rle>                     <Rle>           <Rle>
    ## 1   Homo sapiens    XIRP2 Evidence at protein level               2
    ## 2   Homo sapiens    XIRP2 Evidence at protein level               2
    ## 3   Homo sapiens    XIRP2 Evidence at protein level               2
    ## 4   Homo sapiens    XIRP2 Evidence at protein level               2
    ## 5   Homo sapiens    XIRP2 Evidence at protein level               2
    ## ...          ...      ...                       ...             ...
    ## 32  Homo sapiens    XIRP2 Evidence at protein level               2
    ## 33  Homo sapiens    XIRP2 Evidence at protein level               2
    ## 34  Homo sapiens    XIRP2 Evidence at protein level               2
    ## 35  Homo sapiens    XIRP2 Evidence at protein level               2
    ## 36  Homo sapiens    XIRP2 Evidence at protein level               2
    ##     Comment spectrumID chargeState      rank passThreshold
    ##       <Rle>   <factor>   <integer> <integer>     <logical>
    ## 1        NA  index=124           3         1          TRUE
    ## 2        NA   index=28           2         1          TRUE
    ## 3        NA   index=20           2         1          TRUE
    ## 4        NA  index=187           2         1          TRUE
    ## 5        NA  index=211           3         1          TRUE
    ## ...     ...        ...         ...       ...           ...
    ## 32       NA   index=99           2         1          TRUE
    ## 33       NA    index=9           2         1          TRUE
    ## 34       NA  index=122           2         1          TRUE
    ## 35       NA   index=87           2         1          TRUE
    ## 36       NA   index=77           2         1          TRUE
    ##     experimentalMassToCharge calculatedMassToCharge           sequence
    ##                    <numeric>              <numeric>           <factor>
    ## 1                   715.0305               715.0308 QEITQNKSFFSSVKESQR
    ## 2                   715.9177               715.4117       LPVPKDVYSKQR
    ## 3                   786.9066               786.9081      EQNNDALEKSLRR
    ## 4                   629.8380               629.3386         SLKESSHRWK
    ## 5                   645.3429               645.3511   LKMVPRKQREFSGSDR
    ## ...                      ...                    ...                ...
    ## 32                  619.2888               618.7782       PESGFAEDSAAR
    ## 33                 1014.0198              1013.5117 QPDAIPGDIEKAIECLEK
    ## 34                  821.4005               820.8909     MARYQAAVSRGDCR
    ## 35                  720.3445               720.3527      TNTSTGLKMAMER
    ## 36                  821.9231               821.9254     QEITQNKSFFSSVK
    ##        modNum   isDecoy     post      pre     start       end
    ##     <integer> <logical> <factor> <factor> <integer> <integer>
    ## 1           0     FALSE        D        K      2743      2760
    ## 2           0     FALSE        N        R       307       318
    ## 3           0     FALSE        L        R      1858      1870
    ## 4           0     FALSE        E        K      1699      1708
    ## 5           0     FALSE        G        K      2622      2637
    ## ...       ...       ...      ...      ...       ...       ...
    ## 32          0     FALSE        G        K        20        31
    ## 33          1     FALSE        A        K      1712      1729
    ## 34          1     FALSE        S        R        48        61
    ## 35          0     FALSE        S        K      2082      2094
    ## 36          0     FALSE        E        K      2743      2756
    ##            DatabaseAccess DatabaseSeq
    ##                  <factor>    <factor>
    ## 1   sp|A4UGR9|XIRP2_HUMAN
    ## 2   sp|A4UGR9|XIRP2_HUMAN
    ## 3   sp|A4UGR9|XIRP2_HUMAN
    ## 4   sp|A4UGR9|XIRP2_HUMAN
    ## 5   sp|A4UGR9|XIRP2_HUMAN
    ## ...                   ...         ...
    ## 32  sp|A4UGR9|XIRP2_HUMAN
    ## 33  sp|A4UGR9|XIRP2_HUMAN
    ## 34  sp|A4UGR9|XIRP2_HUMAN
    ## 35  sp|A4UGR9|XIRP2_HUMAN
    ## 36  sp|A4UGR9|XIRP2_HUMAN
    ##                                                                                                     filenames
    ##                                                                                                         <Rle>
    ## 1   D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ## 2   D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ## 3   D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ## 4   D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ## 5   D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ## ...                                                                                                       ...
    ## 32  D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ## 33  D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ## 34  D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ## 35  D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ## 36  D:/biocbld/bbs-3.0-bioc/tmpdir/Rtmpcbjd6Q/Rinst222c75c5483/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
    ##
    ## ...
    ## <5 more elements>

Specific proteins can be extracted by index of name using `[` and proteins and their peptide features can be plotted with the default plot method.

    seqnames(p)

    ## [1] "A4UGR9"   "A6H8Y1"   "O43707"   "O75369"   "P00558"   "P02545"
    ## [7] "P04075"   "P04075-2" "P60709"

    plot(p[c(1,9)])

More details can be found in `?Proteins`. The object generated above is also directly available as `data(p)`.

## Session information

    sessionInfo()

    ## R version 3.1.1 Patched (2014-09-24 r66678)
    ## Platform: i386-w64-mingw32/i386 (32-bit)
    ##
    ## locale:
    ## [1] LC_COLLATE=C
    ## [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] stats4    grid      parallel  stats     graphics  grDevices utils
    ##  [8] datasets  methods   base
    ##
    ## other attached packages:
    ##  [1] mzID_1.4.0           Biostrings_2.34.0    XVector_0.6.0
    ##  [4] Pbase_0.4.0          Gviz_1.10.0          GenomicRanges_1.18.0
    ##  [7] GenomeInfoDb_1.2.0   IRanges_2.0.0        S4Vectors_0.4.0
    ## [10] Rcpp_0.11.3          BiocGenerics_0.12.0  BiocStyle_1.4.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] AnnotationDbi_1.28.0     BBmisc_1.7
    ##  [3] BSgenome_1.34.0          BatchJobs_1.4
    ##  [5] Biobase_2.26.0           BiocInstaller_1.16.0
    ##  [7] BiocParallel_1.0.0       DBI_0.3.1
    ##  [9] Formula_1.1-2            GenomicAlignments_1.2.0
    ## [11] GenomicFeatures_1.18.0   Hmisc_3.14-5
    ## [13] MALDIquant_1.11          MASS_7.3-35
    ## [15] MSnbase_1.14.0           Pviz_1.0.0
    ## [17] R.methodsS3_1.6.1        RColorBrewer_1.0-5
    ## [19] RCurl_1.95-4.3           RSQLite_0.11.4
    ## [21] Rsamtools_1.18.0         VariantAnnotation_1.12.0
    ## [23] XML_3.98-1.1             acepack_1.3-3.3
    ## [25] affy_1.44.0              affyio_1.34.0
    ## [27] base64enc_0.1-2          biomaRt_2.22.0
    ## [29] biovizBase_1.14.0        bitops_1.0-6
    ## [31] brew_1.0-6               checkmate_1.4
    ## [33] chron_2.3-45             cleaver_1.4.0
    ## [35] cluster_1.15.3           codetools_0.2-9
    ## [37] colorspace_1.2-4         data.table_1.9.4
    ## [39] dichromat_2.0-0          digest_0.6.4
    ## [41] doParallel_1.0.8         evaluate_0.5.5
    ## [43] fail_1.2                 foreach_1.4.2
    ## [45] foreign_0.8-61           formatR_1.0
    ## [47] ggplot2_1.0.0            gtable_0.1.2
    ## [49] impute_1.40.0            iterators_1.0.7
    ## [51] knitr_1.7                lattice_0.20-29
    ## [53] latticeExtra_0.6-26      limma_3.22.0
    ## [55] matrixStats_0.10.0       munsell_0.4.2
    ## [57] mzR_2.0.0                nnet_7.3-8
    ## [59] pcaMethods_1.56.0        plyr_1.8.1
    ## [61] preprocessCore_1.28.0    proto_0.3-10
    ## [63] reshape2_1.4             rpart_4.1-8
    ## [65] rtracklayer_1.26.0       scales_0.2.4
    ## [67] sendmailR_1.2-1          splines_3.1.1
    ## [69] stringr_0.6.2            survival_2.37-7
    ## [71] tools_3.1.1              vsn_3.34.0
    ## [73] zlibbioc_1.12.0