Abstract: The invention provides a method of separating proteins and peptides of a sample comprising contacting the sample with a Pd coordination compound. The Pd coordination compound binds to sulfur and/or nitrogen groups and thus is useful for purifying biomolecules comprising cysteine, methionine, histidine amino acids or derivatized amino acids/residues comprising sulfur or nitrogen groups which bind to coordination sites on the Pd coordination compounds. The invention also relates to methods, systems and kits for using the Pd coordination compound.

Abstract: Multiple derivatization by chemical reactions of analytes for mass spectrometry is disclosed. The derivatizations enhance the use of MS techniques for analyzing protein samples, particularly when the sequence of a polypeptide is determined by tandem MS/MS. Accurate mass analysis techniques are described for use in sequencing polypeptides, together with the use of sequencing data in protein analysis. An apparatus and method for calibrating a mass spectrometer by internally introducing calibration masses at a post-source stage of the mass spectrometer is also provided. Lock mass ions mix with the derivatized polypeptide analyte ions prior to mass analysis.

Abstract: Serial derivatization by chemical reactions of analytes for mass spectrometry is disclosed. The derivatizations enhance the use of MS techniques for analyzing protein samples, particularly when the sequence of a polypeptide is determined by tandem MS/MS. Accurate mass analysis techniques are described for use in sequencing polypeptides, together with the use of sequencing data in protein analysis.

Abstract: A method of analyzing a polynucleotide using matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) is described. The method includes obtaining the polynucleotide bound to a substrate via a linker moiety having a triaryl methyl linker group. The polynucleotide bound to the substrate is then contacted with a matrix material and analyzed by MALDI-MS. During the MALDI-MS analysis, laser radiation is directed at the matrix material, thereby exciting the matrix material and causing cleavage of the linker moiety. Ions generated as a result of this excitation and cleavage process are then analyzed to provide information about the polynucleotide.

Abstract: A method of analyzing an array during and/or after fabrication to obtain information relating to the quality of the array manufacturing process is described. The method includes providing an array of features on a substrate, wherein each feature has one or more polynucleotides bound to the substrate. At least one of the features of the provided array is a cleavable feature. The cleavable feature has one or more polynucleotides bound to the substrate via a cleavable linker. The cleavable feature is then contacted with a matrix material, and a MALDI-MS protocol is used to obtain information about the one or more polynucleotides of the cleavable feature. This information may then be used to evaluate the manufacturing process.

Abstract: Methods, systems and device for performing analytical protocols are provided. Embodiments of the subject methods include sequentially contacting a sample with at least a first stationary phase and a second stationary phase under chromatographic conditions to at least determine the binding identity of the at least one constituent, where the specificity of the first stationary phase for at least one constituent present in the sample is at least uncertain and the specificity of the second stationary phase for the at least one constituent is certain. Also provided are systems and devices that include at least the first and second stationary phases. Kits for use in practicing the subject methods are also provided.