5 Protein ID conversion

If you have handled proteomics or metabolomics data (e.g. mass spectrometry), you may need to convert protein to gene id before downstream analysis.

5.1 Example data

For example, in this data article Dataset from proteomic analysis of rat, mouse, and human liver microsomes and S9 fractions , we could get rat proteomic analysis data

Firstly, take a look at the data:

colnames(rat_prodata)
## [1] "GI"       "Acc"      "Gene"     "Name"     "GRAVY"    "Length"   "Sequence"
head(rat_prodata, 5)
##       GI    Acc      Gene
## 1 112774 P27364 3BHS5_RAT
## 2 112889 P17475  A1AT_RAT
## 3 112893 P14046  A1I3_RAT
## 4 112987 P00507  AATM_RAT
## 5 113016 P15650 ACADL_RAT
##                                                        Name      GRAVY Length
## 1                3 beta-hydroxysteroid dehydrogenase type 5 -0.2168901    373
## 2                                    Alpha-1-antiproteinase -0.1576642    411
## 3                                       Alpha-1-inhibitor 3 -0.2164523   1477
## 4                 Aspartate aminotransferase, mitochondrial -0.2295349    430
## 5 Long-chain specific acyl-CoA dehydrogenase, mitochondrial -0.2227907    430
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Sequence
## 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 MPGWSCLVTGAGGFLGQRIVQMLVQEKELQEVRVLYRTFSPKHKEELSKLQTKAKVTVLRGDIVDAQFLRRACQGMSVIIHTAAALDIAGFLPRQTILDVNVKGTQLLLDACVEASVPAFIYSSSTGVAGPNSYKETILNDREEEHRESTWSNPYPYSKRMAEKAVLAANGSILKNGGTFHTCALRLPFIYGEESQIISTMVNRALKNNSIIKRHATFSIANPVYVGNAAWAHILAARGLRDPEKSQSIQGQFYYISDDTPHQSYDDLNYTLSKEWGFCLDSSWSLPLPLLYWLAFLLETVSFLLRPFYNYRPPFNRFMVTILNSVFTISYKKAQRDLGYEPLVSWEEAKQKTSEWIGTLVEQHRETLDTKSQ
## 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           MAPSISRGLLLLAALCCLAPSFLAEDAQETDTSQQDQSPTYRKISSNLADFAFSLYRELVHQSNTSNIFFSPMSITTAFAMLSLGSKGDTRKQILEGLEFNLTQIPEADIHKAFHHLLQTLNRPDSELQLNTGNGLFVNKNLKLVEKFLEEVKNNYHSEAFSVNFADSEEAKKVINDYVEKGTQGKIVDLMKQLDEDTVFALVNYIFFKGKWKRPFNPEHTRDADFHVDKSTTVKVPMMNRLGMFDMHYCSTLSSWVLMMDYLGNATAIFLLPDDGKMQHLEQTLTKDLISRFLLNRQTRSAILYFPKLSISGTYNLKTLLSSLGITRVFNNDADLSGITEDAPLKLSQAVHKAVLTLDERGTEAAGATVVEAVPMSLPPQVKFDHPFIFMIVESETQSPLFVGKVIDPTR
## 3 MKKDREAQLCLFSALLAFLPFASLLNGNSKYMVLVPSQLYTETPEKICLHLYHLNETVTVTASLISQRGTRKLFDELVVDKDLFHCVSFTIPRLPSSEEEESLDINIEGAKHKFSERRVVLVKNKESVVFVQTDKPMYKPGQSVKFRVVSMDKNLHPLNELFPLAYIEDPKMNRIMQWQDVKTENGLKQLSFSLSAEPIQGPYKIVILKQSGVKEEHSFTVMEFVLPRFGVDVKVPNAISVYDEIINVTACATYTYGKPVPGHVKISLCHGNPTFSSETKSGCKEEDSRLDNNGCSTQEVNITEFQLKENYLKMHQAFHVNATVTEEGTGSEFSGSGRIEVERTRNKFLFLKADSHFRHGIPFFVKVRLVDIKGDPIPNEQVLIKARDAGYTNATTTDQHGLAKFSIDTNGISDYSLNIKVYHKEESSCIHSSCTAERHAEAHHTAYAVYSLSKSYIYLDTEAGVLPCNQIHTVQAHFILKGQVLGVLQQIVFHYLVMAQGSILQTGNHTHQVEPGESQVQGNFALEIPVEFSMVPVAKMLIYTILPDGEVIADSVKFQVEKCLRNKVHLSFSPSQSLPASQTHMRVTASPQSLCGLRAVDQSVLLQKPEAELSPSLIYDLPGMQDSNFIASSNDPFEDEDYCLMYQPIAREKDVYRYVRETGLMAFTNLKIKLPTYCNTDYDMVPLAVPAVALDSSTDRGMYESLPVVAVKSPLPQEPPRKDPPPKDPVIETIRNYFPETWIWDLVTVNSSGVTELEMTVPDTITEWKAGALCLSNDTGLGLSSVASFQAFQPFFVELTMPYSVIRGEAFTLKATVLNYLPTSLPMAVLLEASPDFTAVPVENNQDSYCLGANGRHTSSWLVTPKSLGNVNFSVSAEARQSPGPCGSEVATVPETGRKDTVVKVLIVEPEGIKKEHTFSSLLCASDAELSETLSLLLPPTVVKDSARAHFSVMGDILSSAIKNTQNLIQMPYGCGEQNMVLFAPNIYVLKYLNETQQLTEKIKSKALGYLRAGYQRELNYKHKDGSYSAFGDHNGQGQGNTWLTAFVLKSFAQARAFIFIDESHITDAFTWLSKQQKDSGCFRSSGSLLNNAMKGGVDDEITLSAYITMALLESSLPDTDPVVSKALSCLESSWENIEQGGNGSFVYTKALMAYAFALAGNQEKRNEILKSLDKEAIKEDNSIHWERPQKPTKSEGYLYTPQASSAEVEMSAYVVLARLTAQPAPSPEDLALSMGTIKWLTKQQNSYGGFSSTQDTVVALDALSKYGAATFSKSQKTPSVTVQSSGSFSQKFQVDKSNRLLLQQVSLPYIPGNYTVSVSGEGCVYAQTTLRYNVPLEKQQPAFALKVQTVPLTCNNPKGQNSFQISLEISYMGSRPASNMVIADVKMLSGFIPLKPTVKKLERLGHVSRTEVTTNNVLLYLDQVTNQTLSFSFIIQQDIPVKNLQPAIVKVYDYYETDEVAFAEYSSPCSSDDQNV
## 4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        MALLHSGRVLSGMAAAFHPGLAAAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAGKNLDKEYLPIGGLADFCKASAELALGENSEVLKSGRFVTVQTISGTGALRVGASFLQRFFKFSRDVFLPKPSWGNHTPIFRDAGMQLQGYRYYDPKTCGFDFSGALEDISKIPEQSVLLLHACAHNPTGVDPRPEQWKEMAAVVKKKNLFAFFDMAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSYAKNMGLYGERVGAFTVVCKDAEEAKRVESQLKILIRPLYSNPPLNGARIAATILTSPDLRKQWLQEVKGMADRIISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSVYMTKDGRISVAGVTSGNVGYLAHAIHQVTK
## 5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        MAARLLLRSLRVLSARSATLPPPSARCSHSGAEARLETPSAKKLTDIGIRRIFSSEHDIFRESVRKFFQEEVIPYHEEWEKAGEVSRELWEKAGKQGLLGINIAEKHGGIGGDLLSTAVTWEEQAYSNCTGPGFSLHSDIVMPYIANYGTKEQIEQFIPQMTAGKCIGAIAMTEPGAGSDLQGVRTNAKRSGSDWILNGSKVFITNGWLSDLVIVVAVTNREARSPAHGISLFLVENGMKGFIKGKKLHKMGMKAQDTAELFFEDVRLPASALLGEENKGFYYLMQELPQERLLIADLAISACEFMFEETRNYVRQRKAFGKTVAHIQTVQHKLAELKTNICVTRAFVDSCLQLHETKRLDSASASMAKYWASELQNTVAYQCVQLHGGWGYMWEYPIAKAYVDARVQPIYGGTNEIMKELIARQIVSDS

The second column is rat protein id, and the third one is gene name.

5.2 Id conversion

Here we will convert protein id to gene symbol and compare with the original one.

protein_id <- rat_prodata[, "Acc"]
gname <- transId(protein_id, "symbol", "rat", unique = T)

new_res <- merge(rat_prodata, gname,
  by.x = "Acc", by.y = "input_id", all.x = T
) %>%
  dplyr::relocate(symbol, .after = Gene)

head(new_res, 5)
##      Acc        GI      Gene       symbol
## 1 A0FKI7 123797828 ACBD5_RAT        Acbd5
## 2 A0JPQ8 158512263 ALKMO_RAT         Agmo
## 3 A0JPQ9 134035401 CHID1_RAT LOC100911881
## 4 A1L134 221222583  AUP1_RAT         Aup1
## 5 A1L1J9 171704593  LMF2_RAT         Lmf2
##                                           Name       GRAVY Length
## 1 Acyl-CoA-binding domain-containing protein 5 -0.81245059    506
## 2                  Alkylglycerol monooxygenase  0.23579418    447
## 3        Chitinase domain-containing protein 1 -0.20229008    393
## 4                 Ancient ubiquitous protein 1 -0.09902439    410
## 5                   Lipase maturation factor 2  0.04757835    702
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Sequence
## 1                                                                                                                                                                                                     MLFLSFYAGSWESWICCCCVIPVDRPWDRGRRWQLEMADTRSVYETRFEAAVKVIQSLPKNGSFQPTNEMMLRFYSFYKQATEGPCKLSRPGFWDPIGRYKWDAWSSLGDMTKEEAMIAYVEEMKKIIETMPMTEKVEELLHVIGPFYEIVEDKKNSKSSDLTSDLGNVLTSSNAKAVNGKAESSDSGAESEEEEAQEELKGAEQSGSDDKKMMTKSTDKNLEIIVTNGYKDSFAQDSDIHTDSSRSARRSEDKKPTDQSSQQTGNTVLCVHQDTNEDPGEDASGVHHLTSDSDSEVYCDSMEQFGQEEYYLGGDPAQHLEGSGFCEDAQLSPGNGSIGKMQMRAVKGKGEVKHGGEDGRSSSGTPHREKRGGESEDISGVRRGRGHRMPHLSEGTKGRQVGSGGDGERWGSDRGSRGSLNEQIALVLIRLQEDMQNVLQRLHKLETLTASQAKLSWQTSNQPSSQRPSWWPFEMSPGALAFAIIWPFIAQWLVHLYYQRRRRKLN
## 2                                                                                                                                                                                                                                                                MRNPGAQDNVSVSQGMRAMFYMMKPSETAFQTVEEVPDYVKKATPFFIFLILLELVVSWILKGKPSGRLDDILTSMSAGVVSRLPNLFFRSLEVTSYIYIWENYRVCELPWDSPWTWYLTFLGVDFGYYWFHRMAHEINIIWAAHQAHHSSEDYNLSTALRQSVLQQYSSWVFYCPLALFVPPSVFAVHIQFNLLYQFWIHTEVIRTLGPLELVLNTPSHHRVHHGRNRYCIDKNYAGTLIIWDRIFGTFEAENEQVIYGLTHPIGTFEPFKVQFHHLLYIWTTFWATPGFCHKFSVLFKGPGWGPGKPRLGLSEEIPEVTGQEVPFTSSASQFLKIYAVLQFAVMLVFYEETFANTAVLSQVTILLRICFIILTLTSIGFLLDQRPKAAIVETLRCLLFLTLYRFGHLKPLIESLSFAFEIFFSVCIAFWGVRSITHLASGSWKKP
## 3                                                                                                                                                                                                                                                                                                                      MWPLLHVLWLALVCGSVHTTLSKSDAKKAASKTLLEKTQFSDKPVQDRGLVVTDIKAEDVVLEHRSYCSARARERNFAGEVLGYVTPWNSHGYDVAKVFGSKFTQISPVWLQLKRRGREMFEITGLHDVDQGWMRAVKKHAKGVRIVPRLLFEDWTYDDFRSVLDSEDEIEELSKTVVQVAKNQHFDGFVVEVWSQLLSQKHVGLIHMLTHLAEALHQARLLVILVIPPAVTPGTDQLGMFTHKEFEQLAPILDGFSLMTYDYSTSQQPGPNAPLSWIRACVQVLDPKSQWRSKILLGLNFYGMDYAASKDAREPVIGARYIQTLKDHRPRVVWDSQAAEHFFEYKKNRGGRHVVFYPTLKSLQVRLELARELGVGVSIWELGQGLDYFYDLL
## 4                                                                                                                                                                                                                                                                                                     MEPPPAPGPERLFDSHRLPSDGFLLLALLLYAPVGLCLLVLRLFLGLHVFLVSCALPDSVLRRFVVRTMCAVLGLVARQEDSGLRDHRVRVLISNHVTPFDHNIVNLLTTCSTPLLNSPPSFVCWSRGFMEMDRRVELVESLKKFCASTRLPPTPLLLFPEEEATNGREGLLRFSSWPFSIQDVVQPLTLQVQRPLVSVTVSDASWVSELLWSLFVPFTVYQVRWLHPIRRQLGEENEEFALRVQQLVAKELGQIGTRLTPADKAEHMKRQRHPRLRPQSVQSSFPSPPSPSSDVQLTILAQRVKEVLPHVPLNVIQRDLARTGCVDLTITNLLEGAVAFMPEDVTEGSQSLPTASAPKFPSSGLVTPQPTALTFAKSSWARQESLQERKQALYEYARRRFRERQAQEAE
## 5 MASARVPQQLFLQGVAAVYLFAFASLYTQIPGLYGPEGILPARRTLRPQGKGRWQQLWETPTILWEAPRLGLDTAQGLDLLTLLGTVLALGALLLNSLRHPFIYLLLWAAYLSACQVGQVFLYFQWDSLLLETGFLAILVAPLRRPSKHKIPQGGLAGALPHEDLPFWLVRWLLFRLMFASGVVKLTSRCPAWWGLTALTYHYETQCLPTPAAWFAHHLPVWLHRLSVVATFLIEIAVPPLFFAPIRRLRLSAFYAQALLQILIIITGNYNFFNLLTLVLTTALLDDRHLSAEPELRCHKKMPTSWPKTLLTSLSLMLELTVYGLLAYGTIYYFGLEVDWQQQIVLSKTTFTFHQFSQWLKMVTLPTVWLGTASLAWELLIALWRWIQVQGWSRKFFAGIQLSVLGTATVFLFLISLVPYSYVEPGTHGRLWTGAHRLFSSVEHLQLANSYGLFRRMTGLGGRPEVVLEGSHDGHHWTEIEFMYKPGNVSRPPPFLIPHQPRLDWQMWFAALGPHTHSPWFTSLVLRLLQGKEPVIRLIQNQVANYPFREQPPTYLRAQRYKYWFSKPGDQSRWWHRQWVEEFFPSVSLGDPTLETLLQQFGLKDKSPPRARSSKNALAQTLNWVRAQLSPLEPSILLWGLLGAVVAIRVVRTLLTPRPLQSSKQTREEKRKQAPKKDSRAVSEQTAPNSNSNGSWAPRRKK

Maybe you have noticed that some gene names are different from the original data. For example, the second one: A0JPQ8 is called Alkmo before, but the latest name is Agmo.

Some proteins have new gene names like above, while some may have no names for now.

old_name <- unique(new_res$Gene) %>%
  stringr::str_remove_all("_RAT")
new_name <- unique(toupper(new_res$symbol))
new_res[which(is.na(new_res$symbol)), ] %>%
  dplyr::select(Acc, Gene, symbol)
##        Acc      Gene symbol
## 103 P01835  KACB_RAT   <NA>
## 215 P0C169 H2A1C_RAT   <NA>
## 305 P16391  HA12_RAT   <NA>
## 485 P50169  RDH3_RAT   <NA>
## 544 P62161  CALM_RAT   <NA>
## 620 P81828   UP2_RAT   <NA>
## 623 P83121   UP3_RAT   <NA>
## 950 Q6P6G2 CF089_RAT   <NA>

We could see the result above: the protein id P01835 has replaced the gene name with NA.

The Venn plot shows that primary protein ids have changed their gene names. If users continue to use the old gene names, they may lose the latest gene information even enriched pathways.

plotVenn(list(old_name = old_name, new_name = na.omit(new_name)))