Klaus Hollemeyer,*, Wolfgang Altmeyer, and Elmar Heinzle

Size: px
Start display at page:

Download "Klaus Hollemeyer,*, Wolfgang Altmeyer, and Elmar Heinzle"

Transcription

1 Anal. Chem. 2002, 74, Identification and Quantification of Feathers, Down, and Hair of Avian and Mammalian Origin Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Klaus Hollemeyer,*, Wolfgang Altmeyer, and Elmar Heinzle Biochemical Engineering Institute, Im Stadtwald, Saarland University, D Saarbrücken, Germany, and GENE-FACTS GbR, Science Park Saar, Stuhlsatzenweg 69, D Saarbrücken, Germany We describe a fast method for the identification of the origin of native and chemically processed feathers, down, and hair and for distinguishing closely related using enzyme digestion and MALDI-TOF mass spectrometry. Additionally we present two methods for the quantification of different identified bird and mammalian samples, respectively, in binary mixtures. Without any prior cleaning or isolation of single proteins, enzymatical digests of feathers, down, and hair are performed. Fragments generated are analyzed by MALDI-TOF mass spectrometry, and peak groups of different selectivity are established for every animal. For the identification of individual animal, only unique -specific peaks are accepted while for classification of tinted or bleached hair, the group of semispecific peaks (SEMPs) is used. Samples from native animal show a higher coincidence of digest peak masses of SEMPs than far-related, indicating a phylogenetical relationship of the investigated structure proteins. Quantification of mixed binary avian samples is performed by identification of preweighed single feathers and down, followed by calculation of the gravimetric mass fractions. The composition of mixed binary mammalian samples is calculated from correlation of the quotient of the relative peak intensities or areas of these and the quotient of corresponding gravimetric mass fractions. High accuracy is achieved by both quantification methods. The fast methods are well suited for industrial quality control for example. * Corresponding author. Fax: ++49-(0) Phone: ++49-(0) k.hollemeyer@mx.uni-saarland.de. Saarland University. GENE-FACTS GbR. For the identification of the origin of biological samples, several methods analyzing proteins, DNA, RNA, or lipids are commonly used. In the quality control of food, where usually soluble proteins are present, electrophoretic methods are applied under denaturing or nondenaturing conditions (PAGE) 1 as well as isoelectric focusing (IEF). 2,3 Electrophoretic methods use whole proteins in mixtures from native samples and separate these proteins. The isolated single proteins are digested, and the amino acid sequences are determined by comparisons with known sequences from several. All these methods are time-consuming and limited to a relative small number of parallel samples. A further disadvantage is the limited number of with known amino acid sequences. Enzyme-linked immunoassays (ELISA) are also often used for the determination of animal. 4 All these methods essentially depend on the presence of soluble proteins. A nonprotein method for the determination of is capillary gas chromatography of derivatized fatty acids, normally as fatty acid methyl esters (FAME). This method is limited to samples containing a relatively high content of fat. 5 The most sensitive method is the nucleic acid-based polymerase chain reaction analysis (PCR) 6 that is able to detect -specific differences in the DNA and RNA pool. It is a powerful method in differentiating, and even single individuals can be identified. This is done by amplifying the nucleic acids present in almost unlimited (1) Bundesinstitut für gesundheitlichen Verbraucherschutz und Veterinärmedizin, Band I/3, Lebensmittel (L), Teil 2, Beuth Verlag GmbH, Berlin, Köln, Wien, Zürich, Nachweis der Tierart bei nativem Muskelfleisch in Polyacrylamid- Gelen mit Hilfe der Standard- Elektrophorese (PAGE), Amtliche Sammlung von Untersuchungsverfahren nach 35 LMBG, Methode , Dezember (2) Bundesinstitut für gesundheitlichen Verbraucherschutz und Veterinärmedizin, Band I/3, Lebensmittel (L), Teil 1a, Beuth Verlag GmbH, Berlin, Köln, Wien, Zürich, Nachweis der Tierart bei Milch, Milchprodukten und Käse mit Hilfe der isoelektrischen Fokussierung (PAGIF), Amtliche Sammlung von Untersuchungsverfahren nach 35 LMBG, Methode , January (3) Bundesinstitut für gesundheitlichen Verbraucherschutz und Veterinärmedizin, Band I/1b, Lebensmittel (L), Teil 1b, Beuth Verlag GmbH, Berlin, Köln, Wien, Zürich, Nachweis von Kuhmilchkasein in Käse aus Schaf- Ziegen- oder Büffelmilch oder aus Gemischen von Schaf- Ziegen oder Büffelmilch, Referenzmethode,. Amtliche Sammlung von Untersuchungsverfahren nach 35 LMBG, Methode (EG), September (4) Bundesinstitut für gesundheitlichen Verbraucherschutz und Veterinärmedizin, Band I/1c, Lebensmittel (L), Teil 1c, Beuth Verlag GmbH, Berlin, Köln, Wien, Zürich, Immunoenzymatischer Nachweis der Tierart bei erhitzten Fleisch- und Fleischerzeugnissen; ELISA- Verfahren im Mikrotitertestsystem, Amtliche Sammlung von Untersuchungsverfahren nach 35 LMBG, Methode , November (5) Bundesinstitut für gesundheitlichen Verbraucherschutz und Veterinärmedizin, Band I/3, Lebensmittel (L), Teil 2, Beuth Verlag GmbH, Berlin, Köln, Wien, Zürich, Nachweis von rohem und erhitztem Rind- und Schweinefleisch in Fleisch und Fleisch-Erzeugnissen, Screening Verfahren, Amtliche Sammlung von Untersuchungsverfahren nach 35 LMBG, Methode , January (6) Genetisches Analyseverfahren zur Abstammungsüberprüfung biologischer Materialien durch Verwendung artspezifischer Primer, Patent DE A1, Analytical Chemistry, Vol. 74, No. 23, December 1, /ac020347f CCC: $ American Chemical Society Published on Web 11/01/2002

2 (7) Frasier, R. D. B.; MacRae, T. P.; Rogers, G. E. Keratins: Their Composition, Structure and Biosysnthesis; Charles C. Thomas Publ.: Springfield, IL, (8) Powell, B.; Crocker, L. A.; Rogers, G. E. Development 1992, 114, (9) Wilson, B. W.; Edwards, K. J.; Sleigh, M. J.; Bryne, C. R.; Ward, K. A. Gene 1988, 73, (10) Powell, B. C.; Rogers, G. E. In Formation and Structure of Human Hair; Jollès, P., Kahn, H., Höcker, H., Eds.; Birkhäuser Verlage: Basel, 1977; pp (11) Winter, H.; Hofmann, I.; Langbein, L.; Rogers, M. A.; Schweizer, J., Jr. J. Biol. Chem. 1997, 272, (12) Butler, D. J.; De Forest, P. R.; Kobilinsky, L., Jr. Forensic Sci. 1990, 35 (2), (13) Langbein, L.; Rogers, M. A.; Winter, H.; Praetzel, S.; Schweizer, J., Jr. J. Biol. Chem. 2001, 276, (14) Langbein, L.; Rogers, M. A.; Winter, H.; Praetzel, S.; Beckhaus, U.; Rackwitz, H. R.; Schweizer, J., Jr. J. Biol. Chem. 1999, 274, (15) Plowman, J. E.; Bryson, W. G.; Jordan, T. W. Electrophoresis 2000, 17, copies and subsequent electrophoresis of the highly specific oligonucleotides created by enzymatic cleavage of the amplified nucleic acids. Thus, using infinitesimal traces of original samples, the method is mainly used in science and in forensic medicine. However, it essentially depends on the presence of amplifiable nucleic acid sequences. Furthermore, the quantification with PCR is still very difficult to perform. Feathers, down, hairs, nails, scales, beaks, horns, and hooves mainly consist of keratin structures. Keratins are almost insoluble, highly fibrous, cysteine-rich intracellular structure proteins of the land vertebrates. In feathers and down, 95% of the total material is composed of β-keratin forming a twisted sheet secondary structure. Two β-keratin chains are arranged antiparallel, forming a left-twisting helical superstructure cross-linked by amino acid side chains. 7 Hair is mainly composed of intermediate filament proteins (IFPs), which can be divided into two protein families (type I and type II), each consisting of four proteins. 8 One protein from type I and one protein from type II, respectively, form a dimeric structure and 16 dimers form an intermediate filament. 9 The matrix proteins embedding these filaments and creating bicomponent polymers are classified in several groups according to their content of glycine and cysteine, respectively. High-sulfur proteins (HSP) are cysteine-rich matrix proteins with a content of sulfur less than 30%; ultrahigh-sulfur proteins (UHSP) have a higher sulfur content. 10 Glycine- and tyrosine-rich keratin-associated proteins are called high-glycine tyrosine proteins (HGTPs). Some of these proteins show a high degree of sequence homology and oligopeptide repeats reaching homologies up to 96%, whereas other proteins exhibit distinctive amino acid compositions, which can be used for the identification of. After keratinization, the producing cells die and the nuclei and the other cell organelles are reabsorbed. This absorption of nucleic acids is one of the reasons why it is difficult to perform PCR analysis. Keratins, although mostly insoluble, can be extracted from native hair using a high concentration of urea and a high content of thiols, reducing disulfide bridges. 11 Separation by electrophoresis 11 and isoelectric focusing was successfully used to identify -specific keratins, 12 and sequencing data from many different types of keratins are known. 13,14 Although these methods can be used for identifying animal, 15 they are suitable for neither fast analysis nor quantification in mixed samples. So far, native and chemically processed feathers, down, and hair are mostly determined by several macroscopic and microscopic visual methods. These methods need a high degree of experience and often fail because of the lack of differing morphological patterns, 16 especially in juvenile animals. Our newly developed analytical method for the determination of cell-free biological material like feathers, down, and hair overcomes all these drawbacks because the samples do not require soluble proteins, fat, nucleic acids, or visible different morphological patterns. A modified enzymatic digest of a wellknown standard protocol 17 with very high contents of trypsin and 2-mercaptoethanol delivered a mixture containing -specific and -unspecific digest peptides. The peptides were measured by MALDI-TOF mass spectrometry, and -specific peptide masses of certified animal were identified and used as standards for unknown samples. The method was used to identify chemically degreased duck and goose feathers, down, and native feathers from dove, chicken, and turkey as well as hair from several mammalian such as rabbit, sheep, camel, llama, cashmere goat, mohair goat, mink, red fox, dog, yak, and human. Tinted or bleached hair samples showed a reduced number of original -specific peptide masses. Additionally, new peaks were observed. It was even possible to recognize a phylogenetical tendency of the relationship within the determined avian and mammalian, respectively, by comparing the percentage of coincident peptide masses. The closer the relationship, the larger the number of coincident peptide masses that could be detected. Quantification data led to reliable results for mixtures in binary animal sample systems. With high accuracy, even small amounts of contaminating feathers, down, and hair, foreign to the investigated, could be estimated. In binary avian test systems, quantification was done by identifying each single feather or down and summing the masses of both. In binary mammalian test systems, mass fractions of one were determined by calculating the ratios of the relative intensities or the peak areas of two suitable peptide masses, being specific for the two selected. The measurement of large numbers of samples can be investigated in a short analysis time making automatic runs. EXPERIMENTAL SECTION Chemicals and Analyzed Samples. Trypsin from hog pancreas with an activity of 1645 units/mg was purchased from Fluka (Deisenhofen, Germany). Trifluoroacetic acid (TFA), R-cyano-4- hydroxycinnamic acid (CCA), 2-mercaptoethanol, and the calibration peptides human angiotensin II, substance P, human neurotensin, and the human adenocorticotropic hormone fragments ACTH(1-17) and ACTH(18-39) were obtained from Sigma (Deisenhofen, Germany). Ammonium bicarbonate and acetonitrile p.a. were obtained from Merck (Darmstadt, Germany). Certified feathers and down from eider and several races of duck and goose were provided from Forschungsinstitut Hohenstein (Bönnigheim, Germany) and from H. Brinkhaus GmbH & Co. KG (Warendorf, Germany). Chicken and turkey feathers were self-collected from poultry farming, and dove feathers were delivered from a breeder. Hair samples from the mammalian (16) IDFB Handbook, Determination of Feather and Down Species; proposed IDFB Method 1, (17) Kellner, R.; Houthaeve, T. In Microcharacterization of Proteins, 2nd ed.; Kellner, R., Lottspeich, F., Meyer, H. E., Eds.; Wiley-VCH Verlag: Weinheim, 1999; pp Analytical Chemistry, Vol. 74, No. 23, December 1,

3 llama, camel, cashmere goat, mohair goat, sheep, yak, and human, partly chemically tinted or bleached, were obtained from the group of Prof. Dr. F. J. Wortmann, Deutsches Wollforschungsinstitut an der RWTH Aachen e.v., Germany. Rabbit, merino sheep, mink, and fox samples were obtained from Pelzatelier Hildegard Pick, Dreieich, Germany. Dog hair samples were self-collected. Sample Preparation. Feathers and down from certified and unknown samples were weighed individually. Each feather and down was taken by tweezers; extraneous fibers were mechanically removed. A single sample was composed of up to 100 individual feathers and down. About mg of yak, mohair, camel, sheep, and cashmere hair standards were weighed separately, and for the mixed binary samples, they were put together in various weight percentages. The weighed feathers, down, and hair were transferred into eight-well PCR strips (Biozym Diagnostik GmbH, Hessisch Oldendorf, Germany) containing 50 µl of 25 mmol/l NH 4 HCO 3 with 5% 2-mercaptoethanol (v/v) and carefully wetted. Caps were sealed, and after transferring into a boiling water bath for 20 min, the samples were cooled on ice and 50 µl of25 mmol/l NH 4 HCO 3, containing 5 mg of trypsin/ml was added to each tube. Incubation took place for 2 h in a water bath at 37 C. A5-µL aliquot of each sample was transferred into a fresh tube, containing 45 µl of saturated CCA solution in 50% acetonitrile, 1% TFA, and mixed by pipetting. One microliter of each sample was manually pipetted on a polished steel MALDI-TOF target plate and allowed to dry (Figure 1). Mass Spectrometry. Analysis was performed on a Bruker Reflex III time-of-flight mass spectrometer (Bruker-Daltonic, Bremen, Germany) equipped with the SCOUT 384 probe ion source. The system uses a pulsed nitrogen laser (337 nm, model VSL-337ND, Laser Science Inc., Boston, MA) with energy of 400 µj/pulse. The ions were accelerated under delayed extraction conditions in the positive mode with an acceleration voltage of 20 kv and a reflector voltage of 22.5 kv. A 6.9-kV potential difference between target and the extraction lens was applied with a time delay of 1000 ns. A Lecroy 9384C, 1-GHz digital storage oscilloscope was used for data acquisition (Lecroy Corp., Chestnut Ridge, NY). The detector signals were amplified in two stages, digitized, and transferred to the XACQ program on a SUN work station (Sun Microsystems Inc. Palo Alto, CA). Autoexecute mode was chosen for automated measurement with 68-62% attenuation of the laser intensity, a resolution better than 1400, a signal-tonoise ratio (S/N) better than 4, and a noise range of 100. Spectra with one or more peaks, larger than the measurement range, were not used. For one stored spectrum, 200 successful laser shots arising from more than three spots were summed. Saved m/zintensity data were processed with the program XMASS 5.1 (Bruker Daltonics, Bremen, Germany) using the SNAP algorithm for exclusive detection of monoisotopic masses. The 99 most intensive peaks in the range of Da were collected. Relative intensities and peak areas were calculated, and the data were stored as report files. Relative intensities are always related to the maximum peak intensity of the measured spectral range. Identification of Useful Mass Spectral Peaks for the Characterization of Avian and Mammalian Samples. The procedure of data treatment is depicted in Figure 2. From each report file containing one mass spectrum, collected from 200 laser Figure 1. Flow diagram of sample preparation for MALDI-TOF mass spectrometry. shots, significant peaks with intensities of >2% of the maximum peak were selected and the accepted monoisotopic peak masses were rounded to integer values. For each determined, the frequency of occurrence of peaks was determined by inspection of 8-83 spectra. The more spectra of a taken into account, the better was the reliability of statistical predictions of occurring peaks. Eight mass spectra per were the minimum number required, while 16 spectra per were a useful compromise between accuracy and simplicity of analysis. From the collected spectra, only those peaks were further used that occurred at least twice. Peaks originating from trypsin were identified from blank samples containing only trypsin. These peaks were discarded as well. This led to the absolute and percentage frequencies of avian and mammalian peak occurrences for each. In a next step, nonspecific peaks, occurring in all investigated avian and in more than 80% of all mammalian, respectively, were removed. We called the remaining peaks semispecific peaks (SEMPs). A part of these peaks occurred in other as well, but they were significantly more frequently detected with one than with others. These peaks were the more frequent peaks (MFPs). Another part was unique for one in a set of the investigated and was therefore called the unique -specific peaks (USSPs). USSPs were exclusively observed in one but were not always detectable. Both subgroups 5962 Analytical Chemistry, Vol. 74, No. 23, December 1, 2002

4 of peaks higher than 50% was necessary. The closer the relationship is, the more common peaks were expected. (4) Quantification of Mixed Feather and Down Samples in Avian Binary Systems. The quantification of duck and goose feather and down content of an unknown mixture was achieved by first identifying each single weighed feather or down using a minimum of six USSPs, occurring in more than 50% of all investigated spectra and, second, summing up the masses of the weighed and identified feathers or down. The final results were mass weight fractions of both. (5) Quantification of Mixed Hair Samples in Binary Mammalian Species. The binary sample pairs, yak wool contamination in cashmere wool, yak wool contamination in mohair wool, and sheep wool contamination in camel wool, were analyzed using pure samples of each and mixed samples of known composition as standards. Each sample was treated as described and 10 spots for every sample were put onto the target plate. For the identification of the digest peaks suitable for the quantification, peaks with a frequency of occurrence of more than 80% were selected. It was not essential that these peaks were USSPs; the chosen peaks had to be unique in this present binary test system only. For quantification over a large range of ratios in mixtures, the intensities of the selected mass peaks in a 1:1 mixture should be about equal but not less than 0.3 or larger than 3. The reason for this is the limited intensity resolution caused by the 8-bit analog-digital converter of the MALDI-ToF detector. From 10 measurements, those with the largest and the smallest intensity ratios were discarded. The average of the residual eight measurements was used for quantification. Figure 2. Flow diagram for processing raw data from report files for avian and mammalian. The semispecific peaks (SEMPs) were divided into two subgroups, the unique -specific (USSPs), occurring exclusively in one, and the more frequent peaks (MFPs), occurring in more than one, both essential for identification and distinguishing and quantification of. of the SEMPs were used for solving the following analytical problems as also summarized in Table 1. (1) Identification of Native Species. For the identification of a native, only those USSPs were taken into account that occurred in more than 50% of all investigated spectra of the. These remaining peaks were compared to the peaks of all other avian or mammalian, respectively. For each, a set of USSP masses was established. (2) Recognition of Tinted or Bleached Species. For the identification of a tinted or bleached, it was necessary to identify the native first and to estimate the SEMPs. In a second step, remaining SEMPs, not derivatized by tinting or bleaching, were searched for. The required frequency of occurrence for these peaks was more than 50% of the investigated spectra of the derivatized. The final result was the identification of tinted or bleaches. (3) Determination of the Relationship of Two Species. Two avian or mammalian, respectively, were compared by estimating the fraction of coincident SEMPs, including both the MFPs and the USSPs. For both, a frequency of occurrence RESULTS AND DISCUSSION The use of the high concentration of 5% (v/v) 2-mercaptoethanol was essential for the effectiveness of the following enzymatic digest. Only poor digest was achieved if 2-mercaptoethanol was used with a concentration of e1% (v/v). The high trypsin/substrate ratio ranged from 50:1 (w/w) for feathers and down to 2.5:1-0.25:1 (w/w) for hair samples. Standard trypsin protocols for cleaving proteins in polyacrylamide gels or bound to a membrane requires a maximum ratio of 1:1 (w/w) to get meaningful mass spectra. Although a high concentration of trypsin was used, no visible decay or complete digestion of even small down or hair samples was observed in the digest wells. Therefore, we can assume that only the outer protein layers of the samples were digested. As expected, the high concentration of trypsin produced many autoproteolytic digest fragments in sample free negative standards. These fragments originated from trypsin itself and from possible impurities contained in the trypsin preparation. Nevertheless, these peptide fragments did not disturb the identification or quantification of individual. The mass range of peptide detection reaching from 1000 to 3400 Da was suitable for identifying all investigated avian and mammalian. Several matrixes were tested, and CCA acid gave best spectra. It also gave the most homogeneous sample spots, which were necessary for automated MALDI-TOF runs. Identification and Comparison of Mammalian and Avian Species. Samples of both classes of animals, avian and mammalian, showed many identical digest fragments each. We assume this is because of the genetic relationship of feathers, down, and hair, respectively. After peak processing, the number of remaining Analytical Chemistry, Vol. 74, No. 23, December 1,

5 Table 1. Use of the MFPs and the USSPs for Identification of Species and Quantitative Determination of Mass Fractions in Binary Avian and Mammalian Systems, Respectively purpose identification of a native recognition of a tinted or bleached determination of relationship of two quantitative determination of mass fractions in binary avian systems quantitative determination of mass fractions in binary mammalian systems parameters of differentiation differences to all other tested remaining semispecific native peaks fraction of coincident peaks minimum six specific peaks two selected peaks being unique only for the tested system FoO a (%) more frequent peaks (MFPs) -specific peaks (USSPs) >50 not used essential >50 essential essential >50 essential essential >50 not used essential >80 sufficient not essential a Frequency of occurrence of mass spectral peaks. All peaks, further used, had to be detected in more than 50% or more than 80% of the individual measured spectra. SEMPs varied from to. In most cases, a sufficient number of MFPs and USSPs, occurring in more than 50% of the investigated spectra, could be detected (Table 2). For human hair, only 3 USSPs and 1 MFP could be detected, while for the fur of red fox, 54 USSPs and 39 MFPs could be established. On average, 9 of 11 remaining mammalian showed 7 USSPs and 14 MFPs and correspondingly 21 SEMPs. For the estimation of identity of a native, it was essential to use only the USSPs with a frequency of appearance of more than 50% of the investigated spectra. These USSPs were also the basis for the quantification of avian binary systems, described later. For comparison of two different and for the recognition of tinted or bleached, the additional use of the MFPs was essential. For quantification purposes of avian, the occurrence of the USSPs had to be higher than 50% of the investigated spectra. For the quantification of mammals, two selected SEMPs occurring in more than 80% of the investigated spectra of that were sufficient. We did not find significant differences in the spectra of feathers, down, and hair of juvenile and adult animals. Plowman et al. 15 noted that the quality of wool is a function not only of but also of nutrition, age, and environmental conditions and could discover differences in 2Dgel electrophoresis and MALDI-TOF studies. With our new method for identification, we did not detect any significant differences of mass spectra related to nutrition, age, or environmental conditions. Figure 3 shows the fraction (% match) of common SEMPs of the investigated mammalian pairs. Very closely related animals had a high degree of peak conformity: Cashmere goat and mohair goat had 57.1% common SEMPs. Sheep and mohair goat were identical in 43.8% of the SEMPs and sheep, compared with cashmere goat, were also identical in 43.8% of the investigated peaks. Llama and camel, two closely related too, had peak conformity of 46.7%. The comparison of several of herbivores resulted in a different degree of peak identity reaching from 18.8 to 22.8% for cloven hoofed animals. Comparison of the cloven-hoofed sheep with rabbits, vegetarian rodents, showed only a small degree of peak identity of 6.3%. Carnivores among themselves also had peak conformity of 22%, whereas the comparison of herbivores with carnivores, including human, varied from 0 to 4.9% peak identity. For the avian, similar results were obtained (Table 3). Waterfowl such as goose, duck, and eider had degrees of mass conformities reaching from 17.9 to 29.4%, the latter for the comparison of Chinese duck with Pyrenees duck, two biological races. In contrast, land fowls, free of down, showed a maximum degree of peak identity of 13.7% for the comparison of chicken with turkey. All other comparisons of land fowls among each other or against waterfowls resulted in smaller degrees ranging from 5 to 11.1%. Like the mammalian, the avian also showed higher conformity of SEMPs for closer zoological relationship. A clear tendency of relationship and coincident peaks is visible: The closer the zoological relationship, the more common peaks could be detected. The new method confirms that at least some proteins derived from keratin structures vary in their amino acid sequences depending on the genetic relationship. The fast method described here is well suited for identification of a from a possible set. The uniqueness of the USSPs was only determined for the tested and should not be seen as absolute values. It is possible that other birds or mammals, not investigated here, show some of the USSPs of the studied here. The probability of finding coincident digest peaks grows with the number of investigated. To overcome this problem and for the creation of a digest mass library it could be necessary to calculate the match of identity with clusters of SEMPs. This will be useful for the simultaneous differentiation of a large number of. However, in practical cases of industrial quality control, there are only a few of commercial interest and only a few for possible adulteration. Influence of Chemical Treatment of Hair in Identifying Mammalian Species. Coloring or bleaching hair drastically reduced the number of detected SEMP identities within one. Some SEMPs were lost and some new peaks appeared. This was expected because the chemical derivatizations of amino acid side chains dramatically changed the properties of the keratin structures and the masses of digest peptides. Tinted rabbit fur only showed 8 remaining SEMPs, from 20 original SEMPs, of the 5964 Analytical Chemistry, Vol. 74, No. 23, December 1, 2002

6 Table 2. List of SEMPs of 11 Mammals a a For each determined the list contains rounded monoisotopic m/z values, the number of investigated spectra, and the sum of the SEMPs, consisting of MFPs and the USSPs. The gray background marks the USSPs. Boldface numbers in boldface, framed boxes show the SEMPs used for quantification. native fur (Table 4). In comparison of tinted mink fur with native mink fur, only 5 peaks of 15 were left, while in bleached human hair 3 of original 4 SEMPs were conserved. The remaining peaks, however, were sufficient for recognition in all three pairs Analytical Chemistry, Vol. 74, No. 23, December 1,

7 Table 4. Comparison of Semispecific Peaks (SEMPs) of Native and Tinted Rabbit Hair from Eight Individual Spectra a Figure 3. Match of coincident semispecific peaks (SEMPs) of compared pairs of mammals (in percent). Only native hair and fur samples were used. Closely related animals show a significantly higher match than distently related. Above 57% of the SEMPs were common in two goat. Sheep and goat showed 44% conformity similar to camel and llama with 47%. Table 3. Percentage of Common SEMPs of Feathers and down of Several Avian Pairs native rabbit tinted rabbit FO b mass pfo c FO b mass pfo c a Boldface numbers indicate SEMPs occurring in both native and tinted rabbit hair. b Absolute number peak occurrence. c Frequency of peak occurrence in percent. goose Pyrenee duck Chinese duck eider turkey chicken Pyrenee duck 21.7 Chinese duck eider turkey chicken dove of comparison. This makes the method described suitable for the identification of tinted or bleached hair and fur, which may be of interest in the field of hair fashion, the identification of adulteration, and for forensic medicine, respectively. Quantitative Determination of Mixtures Containing Duck and Goose Feathers and Down. The quantification of mixtures of feathers and down is presently done by sampling 100 single feathers or down, weighing and identifying each of them. 16 In the presently accepted standard method, identification is made visually using microscopy. In our method, we exactly follow the same procedure, but identification is made by MALDI-TOF measurement. Calibration is only required for the identification that is carried out using feathers and down of known origin. We found that six USSPs were sufficient for proper identification. Figure 4 shows parts of two spectra with four selected USSPs from goose and two from duck being used for differentiation. In total, the following USSPs were detected for goose: 1237, 1293, 1313, 1828, 1884, 1918, and 1994 Da. For duck, we found the following USSPs: 1527, 1543, 1727, and 1743 Da. However, not all of the possible USSPs could be detected in all samples, but it was found that the numbers of detected USSPs were sufficient for identification in all cases. Both, the existence and nonexistence of peaks were used for identification, enhancing the fidelity of identification. The quantification of binary avian systems was simply performed by adding up the weighed gravimetric masses of the identified Figure 4. Two tryptic digest mass spectra from 1700 to 2100 Da of feathers from goose (A) and duck (B). The tagged (/) mass peaks 1828, 1884, 1918, and 1984 were USSPs for goose while the mass peaks 1727 and 1743 were USSPs for duck. feathers and down. The agreement with hand-sorted reference samples was better than 98%. The new method is therefore straightforwardly applicable for routine analyses. Quantitative Determination of Mixed Binary Sample Pairs of Hair. Suitable USSPs for the quantification of the three mammalian test pairs were estimated as 1432 Da for yak and 1622 Da for cashmere goat (Figure 5), 1085 Da for mohair goat, 1109 Da for camel, and 1226 Da for sheep. All of these peptide masses had larger relative intensities than 0.3 for the equally weighed mixed samples. The quotient of the relative intensity or area of the USSP of one to the sum of the relative intensities of both tested was compared to the quotient of the weight of that to the total weight of both, respectively. The tested mammalian pairs showed a linear relationship between relative intensity ratios and weight ratios. Instead of the ratios of relative 5966 Analytical Chemistry, Vol. 74, No. 23, December 1, 2002

8 Table 5. Statistical Parameters of Linear Regression Analyses of Quantitative Determinations in Binary, Mammalian Sample Pairs a 1 sample pairs 2 selected peaks (integer m/z values) 1 max SD (n ) 8) b of individual samples R 2 of linear regression slope (a) intercept (b) 2 int c rel area d rel int c rel area d rel int c rel area d rel int c rel area d rel yak cashmere goat yak mohair goat sheep camel a The calculations showed the linear relationship of the quotients of weighed mass fractions of each sample pair and the quotients of detected relative peak intensities or detected peak areas of the SEMPs, respectively: (rel intensity peak 1)/[(rel intensity peak 1) + (rel intensity peak 2)] ) a(weight 1)/[(weight 1) + (weight 2)] + b and (area peak 1)/[(area peak 1) + (area peak 2)] ) a(weight 1)/ [(weight 1) + (weight 2)] + b. b Maximum standard deviation of 8 of 10 parallel measurements for each mass fraction of each value pair. The two values deviating most from the mean were removed. c Calculation based on relative peak intensities. d Calculations based on peak areas. Figure 5. Two tryptic digest mass spectra from 1400 to 1700 Da of hair from yak (A) and cashmere goat (B). The tagged (/) SEMPs 1432 and 1622 respectively were used for quantification of mixed binary samples. peak intensities, the ratios of peak area could also be used, yielding almost identical results (Table 5). Correlation coefficients better than 0.99 were calculated for all of the three tested pairs. Standard deviations smaller than 4% for each of the eight parallel measurements for each measured mass fraction were calculated. It was possible to determine unknown samples with 98% accuracy. The detection limits of contaminants varied from 1 to 14.2% (w/w). Quantitative estimations of contaminants in binary mammalian systems could be measured with the necessary accuracy for all of the three compared pairs. In practical cases of commercial samples, a possible adulteration can be expected with the addition of 10% up to 40% of foreign hair to be of economic interest. In this expected range, our method can accurately quantify these foreign feathers, down, and hair. The only limiting conditions for the application of the new method are the knowledge of the contaminating. Ternary systems of contaminations are not tested yet but can most likely be analyzed analogously. Further investigations showed that two almost arbitrarily chosen individual peaks fulfilling the conditions described above are sufficient for quantitative estimation of mixed mammalian samples. The only differences using other suited pairs of peaks are the different slopes and intercepts of the calculated linear regression straight lines. Usually the slope was 1.0 and the intercept was close to 0, of two peaks showing very similar relative intensities or areas, respectively, in sample pairs with equal mass fractions. In our method, the selected SEMPs of one serve as a kind of internal standard for the other. This is a surprising fact for MALDI-TOF mass spectrometry. During the past few years, MALDI-TOF mass spectrometry was increasingly used for quantification particularly of low molecular weight molecules, 18,20 but in all these cases, internal standards, preferably isotopomers, were required to get reasonable accuracy. In our newly developed method for the quantitative determination of hair in binary samples, we do not need isotopically labeled internal standards. These findings suggest that similar quantification procedures might be used for quantification of other proteins and peptides. Our new method has proven its applicability not only for qualitative identification purposes but also for quantitative use in discrimination of binary mixed samples of avian and mammalian origin. The high data accuracy and the high speed of data acquisition make this method interesting for routine analyses in a wide field of applications. Quality assurance of raw material as well as from ready-to-use products is of great interest in industrial quality management systems. The feather-processing industries producing bed linen as well as down jackets, etc., and the textile industries producing high-priced canvas such as cashmere and mohair textiles, for example, have to use quantitative methods to guarantee the product identity. This is of fundamental interest, but up to now, difficult to perform, due to the physical and biochemical properties of the original materials. Our newly developed method can help to satisfy the requested demands. Another field of application may be the possibility to recognize furs from protected animals and to help animal welfare in this way. For forensic medicine there also may be some applications to identify the origin of native and chemically processed feathers, down, and hair. Because hair and feathers are made from materials very similar to horn or scales, it should also be possible to identify animal on the basis of these materials. Easily performed sample preparation and digest as well as simple transfer to MALDI targets make this method straightfor- (18) Kang, M.-J.; Tholey, A.; Heinzle, E. Rapid Commun. Mass Spectrom. 2001, 15, (19) Wittmann, C.; Heinzle, E. Biotechnol. Bioeng. 2001, 72, (20) Kang, M.-J.; Tholey, A.; Heinzle, E. Rapid Commun. Mass Spectrom. 2000, 14, Analytical Chemistry, Vol. 74, No. 23, December 1,

9 wardly applicable. The short measuring time in the automated mode of 80 s/sample and the application of 384 samples/target plate upgradeable to 1536 samples/target make this method ideal for measuring large numbers of samples. ACKNOWLEDGMENT We thank Forschungsinstitut Hohenstein, Bönnigheim, Germany, and Fa. Brinkhaus GmbH & Co. KG, Warendorf, Germany, for the certified duck, eider, and goose samples and the group of Prof. Dr. F. J. Wortmann and Pelzatelier Hildegard Pick, Dreieich, Germany, for the mammalian hair samples. Received for review May 24, Accepted September 11, AC020347F 5968 Analytical Chemistry, Vol. 74, No. 23, December 1, 2002

Effects of Intelligent Data Acquisition and Fast Laser Speed on Analysis of Complex Protein Digests

Effects of Intelligent Data Acquisition and Fast Laser Speed on Analysis of Complex Protein Digests Effects of Intelligent Data Acquisition and Fast Laser Speed on Analysis of Complex Protein Digests AB SCIEX TOF/TOF 5800 System with DynamicExit Algorithm and ProteinPilot Software for Robust Protein

More information

TECHNICAL BULLETIN. ProteoMass Peptide & Protein MALDI-MS Calibration Kit. Catalog Number MSCAL1 Store at Room Temperature

TECHNICAL BULLETIN. ProteoMass Peptide & Protein MALDI-MS Calibration Kit. Catalog Number MSCAL1 Store at Room Temperature ProteoMass Peptide & Protein MALDI-MS Calibration Kit Catalog Number MSCAL1 Store at Room Temperature TECHNICAL BULLETIN Description This kit provides a range of standard peptides and proteins for the

More information

Pesticide Analysis by Mass Spectrometry

Pesticide Analysis by Mass Spectrometry Pesticide Analysis by Mass Spectrometry Purpose: The purpose of this assignment is to introduce concepts of mass spectrometry (MS) as they pertain to the qualitative and quantitative analysis of organochlorine

More information

Protein Purification and Analysis

Protein Purification and Analysis Protein Purification and Analysis Numbers of genes: Humans ~40,000 genes Yeast ~6000 genes Bacteria ~3000 genes Solubility of proteins important for purification: 60-80% soluble, 20-40% membrane Some proteins

More information

Electrospray Ion Trap Mass Spectrometry. Introduction

Electrospray Ion Trap Mass Spectrometry. Introduction Electrospray Ion Source Electrospray Ion Trap Mass Spectrometry Introduction The key to using MS for solutions is the ability to transfer your analytes into the vacuum of the mass spectrometer as ionic

More information

SpikeTides TM Peptides for relative and absolute quantification in SRM and MRM Assays

SpikeTides TM Peptides for relative and absolute quantification in SRM and MRM Assays Protocol SpikeTides TM Peptides for relative and absolute quantification in SRM and MRM Assays Contact us: InfoLine: +49-30-6392-7878 Order per fax: +49-30-6392-7888 or e-mail: www: peptide@jpt.com www.jpt.com

More information

Mass Spectrometry for Chemists and Biochemists

Mass Spectrometry for Chemists and Biochemists Erasmus Intensive Program SYNAPS Univ. of Crete - Summer 2007 Mass Spectrometry for Chemists and Biochemists Spiros A. Pergantis Assistant Professor of Analytical Chemistry Department of Chemistry University

More information

Proteomics in Practice

Proteomics in Practice Reiner Westermeier, Torn Naven Hans-Rudolf Höpker Proteomics in Practice A Guide to Successful Experimental Design 2008 Wiley-VCH Verlag- Weinheim 978-3-527-31941-1 Preface Foreword XI XIII Abbreviations,

More information

Analytical Testing Methods

Analytical Testing Methods Analytical Testing Methods Updated: February 2005 Background The Mandatory Guidelines for Federal Workplace Drug Testing Programs require a laboratory to conduct two analytical tests before a urine specimen

More information

AB SCIEX TOF/TOF 4800 PLUS SYSTEM. Cost effective flexibility for your core needs

AB SCIEX TOF/TOF 4800 PLUS SYSTEM. Cost effective flexibility for your core needs AB SCIEX TOF/TOF 4800 PLUS SYSTEM Cost effective flexibility for your core needs AB SCIEX TOF/TOF 4800 PLUS SYSTEM It s just what you expect from the industry leader. The AB SCIEX 4800 Plus MALDI TOF/TOF

More information

Molecular Spectroscopy

Molecular Spectroscopy Molecular Spectroscopy UV-Vis Spectroscopy Absorption Characteristics of Some Common Chromophores UV-Vis Spectroscopy Absorption Characteristics of Aromatic Compounds UV-Vis Spectroscopy Effect of extended

More information

13C NMR Spectroscopy

13C NMR Spectroscopy 13 C NMR Spectroscopy Introduction Nuclear magnetic resonance spectroscopy (NMR) is the most powerful tool available for structural determination. A nucleus with an odd number of protons, an odd number

More information

Tutorial for Proteomics Data Submission. Katalin F. Medzihradszky Robert J. Chalkley UCSF

Tutorial for Proteomics Data Submission. Katalin F. Medzihradszky Robert J. Chalkley UCSF Tutorial for Proteomics Data Submission Katalin F. Medzihradszky Robert J. Chalkley UCSF Why Have Guidelines? Large-scale proteomics studies create huge amounts of data. It is impossible/impractical to

More information

Milk protein analysis with the Agilent 2100 Bioanalyzer and the Agilent Protein 80 kit

Milk protein analysis with the Agilent 2100 Bioanalyzer and the Agilent Protein 80 kit Milk protein analysis with the Agilent 21 Bioanalyzer and the Agilent Protein 8 kit Application Note Food Analysis Author Rainer Nitsche Agilent Technologies, Inc. Waldbronn, Germany Abstract Protein content

More information

Disaccharides consist of two monosaccharide monomers covalently linked by a glycosidic bond. They function in sugar transport.

Disaccharides consist of two monosaccharide monomers covalently linked by a glycosidic bond. They function in sugar transport. 1. The fundamental life processes of plants and animals depend on a variety of chemical reactions that occur in specialized areas of the organism s cells. As a basis for understanding this concept: 1.

More information

Mass Spectrometry Signal Calibration for Protein Quantitation

Mass Spectrometry Signal Calibration for Protein Quantitation Cambridge Isotope Laboratories, Inc. www.isotope.com Proteomics Mass Spectrometry Signal Calibration for Protein Quantitation Michael J. MacCoss, PhD Associate Professor of Genome Sciences University of

More information

Aiping Lu. Key Laboratory of System Biology Chinese Academic Society APLV@sibs.ac.cn

Aiping Lu. Key Laboratory of System Biology Chinese Academic Society APLV@sibs.ac.cn Aiping Lu Key Laboratory of System Biology Chinese Academic Society APLV@sibs.ac.cn Proteome and Proteomics PROTEin complement expressed by genome Marc Wilkins Electrophoresis. 1995. 16(7):1090-4. proteomics

More information

Application Note FTMS-55 Laser/Desorption Ionization FT-ICR Mass Spectrometry as a Tool for Statistical Analysis of Crude Oils

Application Note FTMS-55 Laser/Desorption Ionization FT-ICR Mass Spectrometry as a Tool for Statistical Analysis of Crude Oils Application Note FTMS-55 Laser/Desorption Ionization FT-ICR Mass Spectrometry as a Tool for Statistical Analysis of Crude Oils Introduction Crude oil is an extremely complex mixture of hydrocarbons and

More information

Rubisco; easy Purification and Immunochemical Determination

Rubisco; easy Purification and Immunochemical Determination Rubisco; easy Purification and Immunochemical Determination Ulrich Groß Justus-Liebig-Universität Gießen, Institute of Plant Nutrition, Department of Tissue Culture, Südanlage 6, D-35390 Giessen e-mail:

More information

Functional Data Analysis of MALDI TOF Protein Spectra

Functional Data Analysis of MALDI TOF Protein Spectra Functional Data Analysis of MALDI TOF Protein Spectra Dean Billheimer dean.billheimer@vanderbilt.edu. Department of Biostatistics Vanderbilt University Vanderbilt Ingram Cancer Center FDA for MALDI TOF

More information

Methods for Protein Analysis

Methods for Protein Analysis Methods for Protein Analysis 1. Protein Separation Methods The following is a quick review of some common methods used for protein separation: SDS-PAGE (SDS-polyacrylamide gel electrophoresis) separates

More information

Standard Mixture. TOF/TOF Calibration Mixture. Calibration Mixture 1 (Cal Mix 1, 1:10) Calibration Mixture 1 (Cal Mix 1, 1:100)

Standard Mixture. TOF/TOF Calibration Mixture. Calibration Mixture 1 (Cal Mix 1, 1:10) Calibration Mixture 1 (Cal Mix 1, 1:100) Mass Standards Kit for Calibration of AB SCIEX TOF/TOF Instruments Protocol 1 Product Description The Mass Standards Kit includes reagents needed to test instrument function, optimize instrument parameters,

More information

Experimental workflow

Experimental workflow Experimental workflow Pg. 3 Lysis Protein quant Protein precipitation Pg. 4 Digest Pgs. 5&6 Label Peptides Peptide quant Ratio check Search, filter & compile data Pgs. 9-12 Combine Samples LC-MS3 Pg. 8

More information

Isotope distributions

Isotope distributions Isotope distributions This exposition is based on: R. Martin Smith: Understanding Mass Spectra. A Basic Approach. Wiley, 2nd edition 2004. [S04] Exact masses and isotopic abundances can be found for example

More information

Enhanced Diode Array Detector Sensitivity and Automated Peak Purity Control

Enhanced Diode Array Detector Sensitivity and Automated Peak Purity Control Enhanced Diode Array Detector Sensitivity and Automated Peak Purity Control Technical Note Introduction The most widely used detection technique for HPLC analysis is UV absorption. Over the decades, single

More information

Master course KEMM03 Principles of Mass Spectrometric Protein Characterization. Exam

Master course KEMM03 Principles of Mass Spectrometric Protein Characterization. Exam Exam Master course KEMM03 Principles of Mass Spectrometric Protein Characterization 2010-10-29 kl 08.15-13.00 Use a new paper for answering each question! Write your name on each paper! Aids: Mini calculator,

More information

Laboration 1. Identifiering av proteiner med Mass Spektrometri. Klinisk Kemisk Diagnostik

Laboration 1. Identifiering av proteiner med Mass Spektrometri. Klinisk Kemisk Diagnostik Laboration 1 Identifiering av proteiner med Mass Spektrometri Klinisk Kemisk Diagnostik Sven Kjellström 2014 kjellstrom.sven@gmail.com 0702-935060 Laboration 1 Klinisk Kemisk Diagnostik Identifiering av

More information

Application Note # MT-90 MALDI-TDS: A Coherent MALDI Top-Down-Sequencing Approach Applied to the ABRF-Protein Research Group Study 2008

Application Note # MT-90 MALDI-TDS: A Coherent MALDI Top-Down-Sequencing Approach Applied to the ABRF-Protein Research Group Study 2008 Bruker Daltonics Application Note # MT-90 MALDI-TDS: A Coherent MALDI Top-Down-Sequencing Approach Applied to the ABRF-Protein Research Group Study 2008 In the ABRF-PRG study 2008 [*] the ability to characterize

More information

LABORATÓRIUMI GYAKORLAT SILLABUSZ SYLLABUS OF A PRACTICAL DEMONSTRATION. financed by the program

LABORATÓRIUMI GYAKORLAT SILLABUSZ SYLLABUS OF A PRACTICAL DEMONSTRATION. financed by the program TÁMOP-4.1.1.C-13/1/KONV-2014-0001 projekt Az élettudományi-klinikai felsőoktatás gyakorlatorientált és hallgatóbarát korszerűsítése a vidéki képzőhelyek nemzetközi versenyképességének erősítésére program

More information

A disaccharide is formed when a dehydration reaction joins two monosaccharides. This covalent bond is called a glycosidic linkage.

A disaccharide is formed when a dehydration reaction joins two monosaccharides. This covalent bond is called a glycosidic linkage. CH 5 Structure & Function of Large Molecules: Macromolecules Molecules of Life All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic

More information

In-Depth Qualitative Analysis of Complex Proteomic Samples Using High Quality MS/MS at Fast Acquisition Rates

In-Depth Qualitative Analysis of Complex Proteomic Samples Using High Quality MS/MS at Fast Acquisition Rates In-Depth Qualitative Analysis of Complex Proteomic Samples Using High Quality MS/MS at Fast Acquisition Rates Using the Explore Workflow on the AB SCIEX TripleTOF 5600 System A major challenge in proteomics

More information

Quantitative & Qualitative HPLC

Quantitative & Qualitative HPLC Quantitative & Qualitative HPLC i Wherever you see this symbol, it is important to access the on-line course as there is interactive material that cannot be fully shown in this reference manual. Contents

More information

Introduction to Proteomics 1.0

Introduction to Proteomics 1.0 Introduction to Proteomics 1.0 CMSP Workshop Tim Griffin Associate Professor, BMBB Faculty Director, CMSP Objectives Why are we here? For participants: Learn basics of MS-based proteomics Learn what s

More information

Annex to the Accreditation Certificate D-PL-13372-01-00 according to DIN EN ISO/IEC 17025:2005

Annex to the Accreditation Certificate D-PL-13372-01-00 according to DIN EN ISO/IEC 17025:2005 Deutsche Akkreditierungsstelle GmbH German Accreditation Body Annex to the Accreditation Certificate D-PL-13372-01-00 according to DIN EN ISO/IEC 17025:2005 Period of validity: 26.03.2012 to 25.03.2017

More information

The Techniques of Molecular Biology: Forensic DNA Fingerprinting

The Techniques of Molecular Biology: Forensic DNA Fingerprinting Revised Fall 2011 The Techniques of Molecular Biology: Forensic DNA Fingerprinting The techniques of molecular biology are used to manipulate the structure and function of molecules such as DNA and proteins

More information

ProteinScape. Innovation with Integrity. Proteomics Data Analysis & Management. Mass Spectrometry

ProteinScape. Innovation with Integrity. Proteomics Data Analysis & Management. Mass Spectrometry ProteinScape Proteomics Data Analysis & Management Innovation with Integrity Mass Spectrometry ProteinScape a Virtual Environment for Successful Proteomics To overcome the growing complexity of proteomics

More information

Separation of Amino Acids by Paper Chromatography

Separation of Amino Acids by Paper Chromatography Separation of Amino Acids by Paper Chromatography Chromatography is a common technique for separating chemical substances. The prefix chroma, which suggests color, comes from the fact that some of the

More information

Common Course Topics Biology 1414: Introduction to Biotechnology I

Common Course Topics Biology 1414: Introduction to Biotechnology I Common Course Topics Biology 1414: Introduction to Biotechnology I Assumptions Students may be enrolled in this course for several reasons; they are enrolled in the Biotechnology Program, they need a science

More information

Scientific Working Group on DNA Analysis Methods. Validation Guidelines for DNA Analysis Methods. Table of Contents

Scientific Working Group on DNA Analysis Methods. Validation Guidelines for DNA Analysis Methods. Table of Contents Scientific Working Group on DNA Analysis Methods Validation Guidelines for DNA Analysis Methods Table of Contents Introduction.2 1. Definitions. 2 2. General Considerations 3 3. Developmental Validation..5

More information

STANDARD 2 Students will demonstrate appropriate safety procedures and equipment use in the laboratory.

STANDARD 2 Students will demonstrate appropriate safety procedures and equipment use in the laboratory. BIOTECHNOLOGY Levels: 11-12 Units of Credit: 1.0 CIP Code: 51.1201 Prerequisite: Biology or Chemistry Skill Certificates: #708 COURSE DESCRIPTION is an exploratory course designed to create an awareness

More information

Real-time PCR: Understanding C t

Real-time PCR: Understanding C t APPLICATION NOTE Real-Time PCR Real-time PCR: Understanding C t Real-time PCR, also called quantitative PCR or qpcr, can provide a simple and elegant method for determining the amount of a target sequence

More information

PosterREPRINT AN LC/MS ORTHOGONAL TOF (TIME OF FLIGHT) MASS SPECTROMETER WITH INCREASED TRANSMISSION, RESOLUTION, AND DYNAMIC RANGE OVERVIEW

PosterREPRINT AN LC/MS ORTHOGONAL TOF (TIME OF FLIGHT) MASS SPECTROMETER WITH INCREASED TRANSMISSION, RESOLUTION, AND DYNAMIC RANGE OVERVIEW OVERVIEW Exact mass LC/MS analysis using an orthogonal acceleration time of flight (oa-tof) mass spectrometer is a well-established technique with a broad range of applications. These include elemental

More information

Choices, choices, choices... Which sequence database? Which modifications? What mass tolerance?

Choices, choices, choices... Which sequence database? Which modifications? What mass tolerance? Optimization 1 Choices, choices, choices... Which sequence database? Which modifications? What mass tolerance? Where to begin? 2 Sequence Databases Swiss-prot MSDB, NCBI nr dbest Species specific ORFS

More information

Prior to release, the following tests are carried out on each batch of the final substances.

Prior to release, the following tests are carried out on each batch of the final substances. Insulin Lispro C 257 H 383 N 65 O 77 S 6 Mol. Wt. 5808 28 B -L-Lysine-29 B -L-proline insulin (human) Insulin Lispro is a 2-chain peptide containing 51 amino acids. The A- chain is composed of 21 amino

More information

Graphite Furnace AA, Page 1 DETERMINATION OF METALS IN FOOD SAMPLES BY GRAPHITE FURNACE ATOMIC ABSORPTION SPECTROSCOPY (VERSION 1.

Graphite Furnace AA, Page 1 DETERMINATION OF METALS IN FOOD SAMPLES BY GRAPHITE FURNACE ATOMIC ABSORPTION SPECTROSCOPY (VERSION 1. Graphite Furnace AA, Page 1 DETERMINATION OF METALS IN FOOD SAMPLES BY GRAPHITE FURNACE ATOMIC ABSORPTION SPECTROSCOPY I. BACKGROUND (VERSION 1.0) Atomic absorption spectroscopy (AAS) is a widely used

More information

1. The diagram below represents a biological process

1. The diagram below represents a biological process 1. The diagram below represents a biological process 5. The chart below indicates the elements contained in four different molecules and the number of atoms of each element in those molecules. Which set

More information

PROTEIN SEQUENCING. First Sequence

PROTEIN SEQUENCING. First Sequence PROTEIN SEQUENCING First Sequence The first protein sequencing was achieved by Frederic Sanger in 1953. He determined the amino acid sequence of bovine insulin Sanger was awarded the Nobel Prize in 1958

More information

Troubleshooting Sequencing Data

Troubleshooting Sequencing Data Troubleshooting Sequencing Data Troubleshooting Sequencing Data No recognizable sequence (see page 7-10) Insufficient Quantitate the DNA. Increase the amount of DNA in the sequencing reactions. See page

More information

TOTAL PROTEIN FIBRINOGEN

TOTAL PROTEIN FIBRINOGEN UNIT: Proteins 16tproteins.wpd Task Determination of Total Protein, Albumin and Globulins Objectives Upon completion of this exercise, the student will be able to: 1. Explain the ratio of albumin and globulin

More information

ProteinPilot Report for ProteinPilot Software

ProteinPilot Report for ProteinPilot Software ProteinPilot Report for ProteinPilot Software Detailed Analysis of Protein Identification / Quantitation Results Automatically Sean L Seymour, Christie Hunter SCIEX, USA Pow erful mass spectrometers like

More information

Development of Headspace Gas Chromatography-Mass Spectrometry for Determination of Residual Monomer in Polymer Latex

Development of Headspace Gas Chromatography-Mass Spectrometry for Determination of Residual Monomer in Polymer Latex Journal of Metals, Materials and Minerals, Vol.20 No.3 pp.145-149, 2010 Development of Headspace Gas Chromatography-Mass Spectrometry for Determination of Residual Monomer in Polymer Latex Nopparat THAWEEWATTHANANON

More information

Application Note # EDS-10 Advanced light element and low energy X-ray analysis of a TiB 2 TiC SiC ceramic material using EDS spectrum imaging

Application Note # EDS-10 Advanced light element and low energy X-ray analysis of a TiB 2 TiC SiC ceramic material using EDS spectrum imaging Quantitative analysis Ceramics sample Peak deconvolution EDS map Phase analysis Application Note # EDS-10 Advanced light element and low energy X-ray analysis of a TiB 2 TiC SiC ceramic material using

More information

Chapter 3 Contd. Western blotting & SDS PAGE

Chapter 3 Contd. Western blotting & SDS PAGE Chapter 3 Contd. Western blotting & SDS PAGE Western Blot Western blots allow investigators to determine the molecular weight of a protein and to measure relative amounts of the protein present in different

More information

Nucleic Acid Quantification NUCLEIC dotmetric

Nucleic Acid Quantification NUCLEIC dotmetric PR060 G-Biosciences 1-800-628-7730 1-314-991-6034 technical@gbiosciences.com A Geno Technology, Inc. (USA) brand name Nucleic Acid Quantification NUCLEIC dotmetric Teacher s Guidebook (Cat. # BE-318) think

More information

Sample Analysis Design Step 2 Calibration/Standard Preparation Choice of calibration method dependent upon several factors:

Sample Analysis Design Step 2 Calibration/Standard Preparation Choice of calibration method dependent upon several factors: Step 2 Calibration/Standard Preparation Choice of calibration method dependent upon several factors: 1. potential matrix effects 2. number of samples 3. consistency of matrix across samples Step 2 Calibration/Standard

More information

La Protéomique : Etat de l art et perspectives

La Protéomique : Etat de l art et perspectives La Protéomique : Etat de l art et perspectives Odile Schiltz Institut de Pharmacologie et de Biologie Structurale CNRS, Université de Toulouse, Odile.Schiltz@ipbs.fr Protéomique et Spectrométrie de Masse

More information

Essentials of Real Time PCR. About Sequence Detection Chemistries

Essentials of Real Time PCR. About Sequence Detection Chemistries Essentials of Real Time PCR About Real-Time PCR Assays Real-time Polymerase Chain Reaction (PCR) is the ability to monitor the progress of the PCR as it occurs (i.e., in real time). Data is therefore collected

More information

# LCMS-35 esquire series. Application of LC/APCI Ion Trap Tandem Mass Spectrometry for the Multiresidue Analysis of Pesticides in Water

# LCMS-35 esquire series. Application of LC/APCI Ion Trap Tandem Mass Spectrometry for the Multiresidue Analysis of Pesticides in Water Application Notes # LCMS-35 esquire series Application of LC/APCI Ion Trap Tandem Mass Spectrometry for the Multiresidue Analysis of Pesticides in Water An LC-APCI-MS/MS method using an ion trap system

More information

Application Note # LCMS-81 Introducing New Proteomics Acquisiton Strategies with the compact Towards the Universal Proteomics Acquisition Method

Application Note # LCMS-81 Introducing New Proteomics Acquisiton Strategies with the compact Towards the Universal Proteomics Acquisition Method Application Note # LCMS-81 Introducing New Proteomics Acquisiton Strategies with the compact Towards the Universal Proteomics Acquisition Method Introduction During the last decade, the complexity of samples

More information

Monitoring Genetic and Metabolic Potential for In Situ Bioremediation: Mass Spectrometry. Progress Report

Monitoring Genetic and Metabolic Potential for In Situ Bioremediation: Mass Spectrometry. Progress Report Monitoring Genetic and Metabolic Potential for In Situ Bioremediation: Mass Spectrometry September 1997 Progress Report Principal Investigator Michelle V. Buchanan (423) 574-4868 (Phone) (423) 576-8559

More information

Forensic DNA Testing Terminology

Forensic DNA Testing Terminology Forensic DNA Testing Terminology ABI 310 Genetic Analyzer a capillary electrophoresis instrument used by forensic DNA laboratories to separate short tandem repeat (STR) loci on the basis of their size.

More information

Lab 2 Biochemistry. Learning Objectives. Introduction. Lipid Structure and Role in Food. The lab has the following learning objectives.

Lab 2 Biochemistry. Learning Objectives. Introduction. Lipid Structure and Role in Food. The lab has the following learning objectives. 1 Lab 2 Biochemistry Learning Objectives The lab has the following learning objectives. Investigate the role of double bonding in fatty acids, through models. Developing a calibration curve for a Benedict

More information

DNA Separation Methods. Chapter 12

DNA Separation Methods. Chapter 12 DNA Separation Methods Chapter 12 DNA molecules After PCR reaction produces many copies of DNA molecules Need a way to separate the DNA molecules from similar sized molecules Only way to genotype samples

More information

AMINO ACID ANALYSIS By High Performance Capillary Electrophoresis

AMINO ACID ANALYSIS By High Performance Capillary Electrophoresis AMINO ACID ANALYSIS By High Performance Capillary Electrophoresis Analysis of Amino Acid Standards Label free analysis using the HPCE-512 ABSTRACT Capillary electrophoresis using indirect UV detection

More information

Collagen analysis in fish tissue using the total collagen assay. Application note April 2013

Collagen analysis in fish tissue using the total collagen assay. Application note April 2013 Collagen analysis in fish tissue using the total collagen assay Application note April 2013 Summary The QuickZyme Total Collagen assay provides an easy and fast method to determine collagen quantities

More information

泛 用 蛋 白 質 體 學 之 質 譜 儀 資 料 分 析 平 台 的 建 立 與 應 用 Universal Mass Spectrometry Data Analysis Platform for Quantitative and Qualitative Proteomics

泛 用 蛋 白 質 體 學 之 質 譜 儀 資 料 分 析 平 台 的 建 立 與 應 用 Universal Mass Spectrometry Data Analysis Platform for Quantitative and Qualitative Proteomics 泛 用 蛋 白 質 體 學 之 質 譜 儀 資 料 分 析 平 台 的 建 立 與 應 用 Universal Mass Spectrometry Data Analysis Platform for Quantitative and Qualitative Proteomics 2014 Training Course Wei-Hung Chang ( 張 瑋 宏 ) ABRC, Academia

More information

Mass Spectra Alignments and their Significance

Mass Spectra Alignments and their Significance Mass Spectra Alignments and their Significance Sebastian Böcker 1, Hans-Michael altenbach 2 1 Technische Fakultät, Universität Bielefeld 2 NRW Int l Graduate School in Bioinformatics and Genome Research,

More information

Introduction To Real Time Quantitative PCR (qpcr)

Introduction To Real Time Quantitative PCR (qpcr) Introduction To Real Time Quantitative PCR (qpcr) SABiosciences, A QIAGEN Company www.sabiosciences.com The Seminar Topics The advantages of qpcr versus conventional PCR Work flow & applications Factors

More information

Chem 405 Biochemistry Lab I Experiment 2 Quantitation of an unknown protein solution.

Chem 405 Biochemistry Lab I Experiment 2 Quantitation of an unknown protein solution. Chem 405 Biochemistry Lab I Experiment 2 Quantitation of an unknown protein solution. Introduction: The determination of protein concentration is frequently required in biochemical work. Several methods

More information

Definition of the Measurand: CRP

Definition of the Measurand: CRP A Reference Measurement System for C-reactive Protein David M. Bunk, Ph.D. Chemical Science and Technology Laboratory National Institute of Standards and Technology Definition of the Measurand: Human C-reactive

More information

Cloning of genes from genomic DNA: Part 3-Restriction Enzyme Digestion and Agarose Gel Electrophoresis

Cloning of genes from genomic DNA: Part 3-Restriction Enzyme Digestion and Agarose Gel Electrophoresis Cloning of genes from genomic DNA: Part 3-Restriction Enzyme Digestion and Agarose Gel Electrophoresis Continuing from our isolation of genomic DNA and PCR amplification of either the evenskipped gene

More information

ANALYSIS OF ASPIRIN INFRARED (IR) SPECTROSCOPY AND MELTING POINT DETERMINATION

ANALYSIS OF ASPIRIN INFRARED (IR) SPECTROSCOPY AND MELTING POINT DETERMINATION Chem 306 Section (Circle) M Tu W Th Name Partners Date ANALYSIS OF ASPIRIN INFRARED (IR) SPECTROSCOPY AND MELTING POINT DETERMINATION Materials: prepared acetylsalicylic acid (aspirin), stockroom samples

More information

The Empirical Formula of a Compound

The Empirical Formula of a Compound The Empirical Formula of a Compound Lab #5 Introduction A look at the mass relationships in chemistry reveals little order or sense. The ratio of the masses of the elements in a compound, while constant,

More information

Chapter 3 Cell Processes and Energy

Chapter 3 Cell Processes and Energy Chapter 3 Cell Processes and Energy 1 Chapter 3 Objectives Section 1: Chemical Compounds in Cells 1. Define elements and compounds 2. Explain how water is important to the function of cells 3. Identify

More information

The Molecules of Cells

The Molecules of Cells The Molecules of Cells I. Introduction A. Most of the world s population cannot digest milk-based foods. 1. These people are lactose intolerant because they lack the enzyme lactase. 2. This illustrates

More information

Lab 3 Organic Molecules of Biological Importance

Lab 3 Organic Molecules of Biological Importance Name Biology 3 ID Number Lab 3 Organic Molecules of Biological Importance Section 1 - Organic Molecules Section 2 - Functional Groups Section 3 - From Building Blocks to Macromolecules Section 4 - Carbohydrates

More information

Peptides: Synthesis and Biological Interest

Peptides: Synthesis and Biological Interest Peptides: Synthesis and Biological Interest Therapeutic Agents Therapeutic peptides approved by the FDA (2009-2011) 3 Proteins Biopolymers of α-amino acids. Amino acids are joined by peptide bond. They

More information

Affinity Chromatography

Affinity Chromatography PR100-02 G-Biosciences 1-800-628-7730 1-314-991-6034 technical@gbiosciences.com A Geno Technology, Inc. (USA) brand name Affinity Chromatography Teacher s Guidebook (Cat. # BE-417) think proteins! think

More information

7 Electrophoresis. µ proportional to Q

7 Electrophoresis. µ proportional to Q 7 Electrophoresis Objectives: A) To perform agarose gel electrophoresis of the proteins isolated in last week's experiment and B) to interpret the banding patterns produced by these proteins. Introduction:

More information

10.1 The function of Digestion pg. 402

10.1 The function of Digestion pg. 402 10.1 The function of Digestion pg. 402 Macromolecules and Living Systems The body is made up of more than 60 % water. The water is found in the cells cytoplasm, the interstitial fluid and the blood (5

More information

MASCOT Search Results Interpretation

MASCOT Search Results Interpretation The Mascot protein identification program (Matrix Science, Ltd.) uses statistical methods to assess the validity of a match. MS/MS data is not ideal. That is, there are unassignable peaks (noise) and usually

More information

Carbohydrates, proteins and lipids

Carbohydrates, proteins and lipids Carbohydrates, proteins and lipids Chapter 3 MACROMOLECULES Macromolecules: polymers with molecular weights >1,000 Functional groups THE FOUR MACROMOLECULES IN LIFE Molecules in living organisms: proteins,

More information

General Chemistry I (FC, 09-10) Lab #3: The Empirical Formula of a Compound. Introduction

General Chemistry I (FC, 09-10) Lab #3: The Empirical Formula of a Compound. Introduction General Chemistry I (FC, 09-10) Introduction A look at the mass relationships in chemistry reveals little order or sense. The ratio of the masses of the elements in a compound, while constant, does not

More information

ACID-BASE TITRATIONS: DETERMINATION OF CARBONATE BY TITRATION WITH HYDROCHLORIC ACID BACKGROUND

ACID-BASE TITRATIONS: DETERMINATION OF CARBONATE BY TITRATION WITH HYDROCHLORIC ACID BACKGROUND #3. Acid - Base Titrations 27 EXPERIMENT 3. ACID-BASE TITRATIONS: DETERMINATION OF CARBONATE BY TITRATION WITH HYDROCHLORIC ACID BACKGROUND Carbonate Equilibria In this experiment a solution of hydrochloric

More information

Two-Dimensional Gel Electrophoresis (2-DGE)

Two-Dimensional Gel Electrophoresis (2-DGE) - Introduction - Sample preparation - First dimension: Isoelectric focusing - Second dimension: SDS-PAGE - Detection of protein spots: staining - Imaging analysis & 2D Gel databases - Spot handling: excision,

More information

Application Guide... 2

Application Guide... 2 Protocol for GenomePlex Whole Genome Amplification from Formalin-Fixed Parrafin-Embedded (FFPE) tissue Application Guide... 2 I. Description... 2 II. Product Components... 2 III. Materials to be Supplied

More information

Nuclear Structure. particle relative charge relative mass proton +1 1 atomic mass unit neutron 0 1 atomic mass unit electron -1 negligible mass

Nuclear Structure. particle relative charge relative mass proton +1 1 atomic mass unit neutron 0 1 atomic mass unit electron -1 negligible mass Protons, neutrons and electrons Nuclear Structure particle relative charge relative mass proton 1 1 atomic mass unit neutron 0 1 atomic mass unit electron -1 negligible mass Protons and neutrons make up

More information

18.2 Protein Structure and Function: An Overview

18.2 Protein Structure and Function: An Overview 18.2 Protein Structure and Function: An Overview Protein: A large biological molecule made of many amino acids linked together through peptide bonds. Alpha-amino acid: Compound with an amino group bonded

More information

Pep-Miner: A Novel Technology for Mass Spectrometry-Based Proteomics

Pep-Miner: A Novel Technology for Mass Spectrometry-Based Proteomics Pep-Miner: A Novel Technology for Mass Spectrometry-Based Proteomics Ilan Beer Haifa Research Lab Dec 10, 2002 Pep-Miner s Location in the Life Sciences World The post-genome era - the age of proteome

More information

SPECTROPHOTOMETRY. Blue. Orange

SPECTROPHOTOMETRY. Blue. Orange Appendix I FV /26/5 SPECTROPHOTOMETRY Spectrophotometry is an analytical technique used to measure the amount of light of a particular wavelength absorbed by a sample in solution. This measurement is then

More information

Enzymes: Amylase Activity in Starch-degrading Soil Isolates

Enzymes: Amylase Activity in Starch-degrading Soil Isolates Enzymes: Amylase Activity in Starch-degrading Soil Isolates Introduction This week you will continue our theme of industrial microbiologist by characterizing the enzyme activity we selected for (starch

More information

MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification

MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification Gold Standard for Quantitative Data Processing Because of the sensitivity, selectivity, speed and throughput at which MRM assays can

More information

Analysis of proteins

Analysis of proteins Analysis of proteins Western blot Protein seperation (liqiuid chromatography) Mass spectrometry Assaying of protein in... Blood (e.g. viral infections, pregnancy test) Cells Tissue Urin (bladder infection)

More information

4. Which carbohydrate would you find as part of a molecule of RNA? a. Galactose b. Deoxyribose c. Ribose d. Glucose

4. Which carbohydrate would you find as part of a molecule of RNA? a. Galactose b. Deoxyribose c. Ribose d. Glucose 1. How is a polymer formed from multiple monomers? a. From the growth of the chain of carbon atoms b. By the removal of an OH group and a hydrogen atom c. By the addition of an OH group and a hydrogen

More information

Introduction. Chapter 12 Mass Spectrometry and Infrared Spectroscopy. Electromagnetic Spectrum. Types of Spectroscopy 8/29/2011

Introduction. Chapter 12 Mass Spectrometry and Infrared Spectroscopy. Electromagnetic Spectrum. Types of Spectroscopy 8/29/2011 Organic Chemistry, 6 th Edition L. G. Wade, Jr. Chapter 12 Mass Spectrometry and Infrared Spectroscopy Introduction Spectroscopy is an analytical technique which helps determine structure. It destroys

More information

the nature and importance of biomacromolecules in the chemistry of the cell: synthesis of biomacromolecules through the condensation reaction lipids

the nature and importance of biomacromolecules in the chemistry of the cell: synthesis of biomacromolecules through the condensation reaction lipids the nature and importance of biomacromolecules in the chemistry of the cell: synthesis of biomacromolecules through the condensation reaction lipids and their sub-units; the role of lipids in the plasma

More information

Simultaneous qualitative and quantitative analysis using the Agilent 6540 Accurate-Mass Q-TOF

Simultaneous qualitative and quantitative analysis using the Agilent 6540 Accurate-Mass Q-TOF Simultaneous qualitative and quantitative analysis using the Agilent 654 Accurate-Mass Q-TOF Technical Overview Authors Pat Perkins Anabel Fandino Lester Taylor Agilent Technologies, Inc. Santa Clara,

More information

An In-Gel Digestion Protocol

An In-Gel Digestion Protocol An In-Gel Digestion Protocol This protocol describes the digestion of a protein present in an SDS-PAGE gel band with trypsin. The band can be taken from either a 1D or 2D electrophoresis gel. Reagents

More information

Glycerol determination in biodiesel and biodiesel blends according to ASTM D 7591

Glycerol determination in biodiesel and biodiesel blends according to ASTM D 7591 Glycerol determination in biodiesel and biodiesel blends according to ASTM D 7591 J. Gandhi 1 and A. Wille 2 1 Metrohm USA Inc., Riverview FL 33578, USA 2 Metrohm International Headquarters, CH-9101 Herisau,

More information

General western blot protocol. Guidance for running an efficient and accurate experiment

General western blot protocol. Guidance for running an efficient and accurate experiment blot protocol Guidance for running an efficient and accurate experiment Contents Introduction Solution and reagents Sample lysis Sample preparation Loading and running the gel Antibody staining Useful

More information