DOI: 10.5061/dryad.vt4b8gtq5
title: Data from: Rapid species level identification of fish eggs by proteome fingerprinting using MALDI-TOF MS

description: Quantifying spawning biomass of commercially relevant fish species is
 important to generate fishing quotas. This will mostly rely on the annual
 or daily production of fish eggs. However, these have to be identified
 precisely to species level to obtain a reliable estimate of offspring
 production of the different species. Because morphological identification
 can be very difficult, recent developments are heading towards application
 of molecular tools. Methods such as COI barcoding have long handling times
 and cause high costs for single specimen identifications. In order to test
 MALDI-TOF MS, a rapid and cost-effective alternative for species
 identification, we identified fish eggs using COI barcoding and used the
 same specimens to set up a MALDI-TOF MS reference library. This library,
 constructed from two different MALDI-TOF MS instruments, was then used to
 identify unknown eggs from a different sampling occasion. By using a line
 of evidence from hierarchical clustering and different supervised
 identification approaches we obtained concordant species identifications
 for 97.5% of the unknown fish eggs, proving MALDI-TOF MS a good tool for
 rapid species level identification of fish eggs. At the same time we point
 out the necessity of adjusting identification scores of supervised methods
 for identification to optimize identification success.
description: Of the 40 µl mixture
 containing water and the crushed eggs, for all samples 5 µl were used for
 extraction of peptides and proteins (Fig. 2). To this mixture, 5 µl of 5%
 trifluoroacetic acid were added and incubated for 1h at room temperature
 (RT). After 1h, 1 µl of this solution was transferred to a MALDI-TOF
 target plate and dried at RT. The dried extract was covered with a layer
 of 1 µl α-Cyano-4-hydroxycinnamic acid (HCCA) as a saturated solution in
 50% acetonitrile, 47.5% molecular grade water and 2.5% trifluoroacetic
 acid. For each egg, the solution was applied to one spot and air dried for
 co-crystallization of proteins and peptides with the matrix.
 Measurements were carried
 out on a Microflex LT/SH System (Bruker Daltonics) using method MBTAuto
 with laser intensity between 50% and 60%. Peak evaluation during
 measurement was carried out in a mass peak range between 2k – 10k Dalton
 (Da) using a centroid peak detection algorithm, a signal to noise
 threshold of 2 and a minimum intensity threshold of 600, with a peak
 resolution higher than 400. Proteins/Oligonucleotide method was employed
 for fuzzy control with a maximal resolution ten times above the threshold.
 To create a sum spectrum, 240 satisfactory shots were summed up. Each spot
 was measured once. Before measurements, system calibration was carried out
 according to the Bruker default procedure using Bacterial standard
 (BTS).   Alongside raw data an Excel file
 containing meta data refering to sampling time and place is enclosed. In
 total raw data from 511 fish egg specimens is included. However, some of
 these were found to be of inferior quality and are not usefull for
 specimen identification. These are accordingly marked in the supplied meta
 data file.