I am trying to do a "classical" match of uniprot ids, using protein IDs identified in a Zebrafish mass-spec experiment, to find the corresponding ensembl gene ids. However, there are several proteins for which my biomaRt query fails to retrive any information, although they are present in the Uniprot database and with an attributed ensembl gene id. Am I missing something?

Here is my code:

prot_ids = c("F1QCB4", "F1R8H7", "A0JMF6", "F1QU18", "A0JMK7", "A0MTA1")

uniProt <- useMart("unimart", dataset="uniprot")

getBM(
        attributes =c("accession" ,"name","ensembl_id", "gene_name"),
        filter="accession",
        values=prot_ids,
        mart=uniProt)

[1] accession  name       ensembl_id gene_name
<0 rows> (or 0-length row.names)

sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] biomaRt_2.22.0     VennDiagram_1.6.9  RColorBrewer_1.1-2

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1 Biobase_2.26.0       BiocGenerics_0.12.1
 [4] bitops_1.0-6         DBI_0.3.1            GenomeInfoDb_1.2.3  
 [7] IRanges_2.0.0        parallel_3.1.2       RCurl_1.95-4.5      
[10] RSQLite_1.0.0        S4Vectors_0.4.0      stats4_3.1.2        
[13] tcltk_3.1.2          tools_3.1.2          XML_3.98-1.1 

Some of the accessions you are trying to map have been deleted from UniProt e.g. F1QCB4 your code should return results with the for example the accession P05067. However, it is likely that you will need to rerun the protein ACC mapping to using the Zebrafish mass-spec results.

See this example from the Biomart that shows the basic query is correct but no value exists for F1QCB4.