Analytical Chemistry
ARTICLE
coupled to an LTQ LIT mass spectrometer (Thermo Fisher, San
Jose, CA). The peptide separation (1 μg) was performed on a
0.18 mm  150 mm BioBasic-18 RP column (ThermoHypersil-
Keystone) using 0.5% acetic acid in Milli-Q water and in 80%
acetonitrile (ACN) as mobile phases A and B, respectively. A 60 min
linear gradient from 5% to 40% B, at a flow rate of 1.5À1.7 μL/min,
was used. ESI parameters were as follows: spray voltage, 3.5 kV; N2
flow, 10 arbitrary units; capillary temperature, 200 °C. Peptides were
analyzed in positive mode from 400 to 1600 amu (three micro-
scans), followed by four data-dependent MS/MS scans (three
microscans), using an isolation width of 3 amu and a normalized
collision energy of 35%. Fragmented masses were set in dynamic
exclusion for 3 min after the second fragmentation event, and singly
charged ions were excluded from MS/MS analysis.
Selected MS/MS Ion Monitoring. SMIM analysis was per-
formed using a Surveyor LC system coupled to an LTQ LIT mass
spectrometer (Thermo Fisher, San Jose, CA), as described
previously8 with minor modifications. The peptide separation
(1 μg) was performed on a 0.18 mm  150 mm BioBasic-18 RP
column (ThermoHypersil-Keystone) using 0.5% acetic acid in
water and in 80% ACN as mobile phases A and B, respectively.
A 45 min linear gradient from 5% to 40% B, at a flow rate of 1.5À
1.7 μL/min, was used. ESI parameters were as described
previously. Peptides were detected in the positive ion mode
using SMIM.8 For this method, the MS instrument was pro-
grammed to perform continuous MS/MS scans (five micro-
scans) of doubly charged precursor ions from all candidate
peptide biomarkers along the complete chromatographic separa-
tion. The normalized collision energy was set to 35%, and a 3 amu
mass window was used to fragment selected parent ions.
Mass Spectrometry Data Processing. MS/MS spectra were
searched using SEQUEST (Bioworks 3.1 package, Thermo Fisher)
againsttheTeleosteiUniProt/TrEMBLdatabase(release2010_12;
158.545 entries), which also included their respective decoy
sequences. The following constraints were used for the searches:
semitryptic cleavage with up to two missed cleavage sites and
tolerances of 1.8 Da for precursor ions and 0.8 Da for MS/MS
fragment ions. The variable modifications allowed were methio-
nine oxidation (Mox), carbamidomethylation of Cys (C*), and
acetylation of the N-terminus of the protein (N-Acyl). The
database search results were subjected to statistical analysis with
the PeptideProphet algorithm (v.4.4).20 The false discovery rate
(FDR) was kept below 1%.
using HIFU (time 2 min), and (c) monitoring of 11 species-
specific PRVB peptide biomarkers by SMIM using an LIT mass
spectrometer (time 60 min). With this strategy, all relevant
commercial fish species belonging to the Merlucciidae family
can be unequivocally identified in any seafood product, including
precooked, in less than 2 h. The detailed results for each step and
the validation of this new fast monitoring strategy using un-
known hake commercial products are shown in the following
sections.
PRVB Purification and Enzymatic Digestion Accelerated
by HIFU. PRVBs, considered as the best protein biomarker for
the authentication of Merluciidae species,10,21 were purified from
the sarcoplasmic extracts, taking advantage of their thermo-
stability.10 Figure S-1 in the Supporting Information shows a
summary of the protein composition in the extracts before and
after the treatment with heat (70 °C for 5 min). The complete list
of proteins and peptides for both samples, identified by
LCÀMS/MS and Sequest search after a conventional overnight
trypsin digestion,22 are presented in the Supporting Information.
Protein composition of the original sarcoplasmic extracts re-
vealed more than 125 different proteins involved in 10 relevant
functional pathways (Table S-1 in the Supporting Information).
After treatment with heat, the majority of identified peptides
corresponded to PRVBs (77.87%) (Figure S-1). These results
demonstrated that the treatment with heat is a simple, fast,
and effective procedure to purify and enrich the samples in
only PRVBs.
Purified PRVBs were digested with trypsin using either the
conventional overnight procedure or the fast procedure acceler-
ated by HIFU. As reported previously,14 HIFU-assisted digestion
produced results comparable to those obtained by the conven-
tional overnight incubation methods, but in a fraction of time.
Moreover, the absence of urea in the digestion buffer prevented
undesired peptide side reactions, such as carbamylation of
N-termini and Lys residues, which may occur when HIFU is
applied in the presence of urea.23,24
The combination of a fast and easy protein purification
procedure (time 45 min) with the use of HIFU for the protein
digestion (ime 2 min) considerably simplified and reduced the
time needed for the sample preparation, reflected in the overall
time needed for monitoring.
Selection of the Species-Specific Peptide Biomarkers. The
next step in the proposed strategy consisted in selecting the
smaller number of species-specific peptides, which must be
monitored, to effectively identify all the species from the Merluc-
ciidae family. Parvalbumin peptide sequences with a high inter-
specific variability, obtained afterthe extensive de novo sequencing
of PRVBs previously published,10 were used for this purpose.
Eleven tryptic peptides were selected on the basis of the informa-
tion that their combined presence or absence could provide to
confidently identify all of the species under study (Table 2). A
Basic Local Alignment Search Tool (BLAST) search was per-
formed using the UniProtKB database to validate the uniqueness
of the peptide sequences selected. Four of them were present in
only one specific species and can be considered as a canonical
peptide for each of these Merlucciidae species (S-MER794,
S-MER612, S-MER721, S-MER973). The sequences of the rest
were shared by PRVBs from several Merlucciidae species or other
organisms. However, their use following a specific and systematic
combination avoids interferences and allows for a correct discri-
mination of all the hake species under study. Figure 2 shows the
flow diagram for the unambiguous systematic discrimination
The proteins identified in the original and heated sarcoplasmic
extracts were submitted to ingenuity pathway analysis (IPA;
Ingenuity Systems, Redwood City, CA). Only pathways scoring
Àlog(p) g 2, which have >99% confidence of not being
generated by chance, were selected.
For the SMIM mode, virtual chromatogram traces were plotted
and optimized using QualBrowser software (Thermo Fisher) to
show the selected transitions for each parent ion. In addition, MS/
MS spectra collected in the SMIM mode were used to validate the
peptide identities using SEQUEST as described before.
’ RESULTS AND DISCUSSION
Strategy for the Fast Monitoring of Species-Specific Pep-
tide Biomarkers. The strategy for the fast monitoring of peptide
biomarkers proposed in this work is summarized in Figure 1. This
strategy integrates three steps: (a) purification of thermostable
proteins (PRVBs) by short heat treatment followed by centrifu-
gation (time 45 min), (b) in-solution trypsin digestion accelerated
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dx.doi.org/10.1021/ac200890w |Anal. Chem. 2011, 83, 5688–5695