Waters Technologies Corporation

Micromass UK Limited

Cell Signaling Technology, Inc.

Microbia, Inc.

Jeffrey Cruz Silva

Scott Geromanos

Guo-Zhong Li

Marc Victor Gorenstein

Hans Vissers

Joshua Trueheart

Ailan Guo

G Todd Milne

Brian Cali

Douglas A Holtzman

Kevin T Madden

Jing Zhou

Amir Sherman

Martha Degen Stapels

Daniel Golick

Craig A Dorschel

Gregory Opiteck

Ashok Ramesh Dongre

Johannes P C Vissers

Hongbo Gu

Daniel Mulhern

Lixin Zhang

Asish B Chakraborty

Welbin Chen

Ashok Dongre

Scott J Geromanos

Li-Guo Zhong

Marths Degen Stapels

The disclosure features over 5000 methylation and acetylation sites identified in human cell line, human serum and mouse tissues, peptides (including AQUA peptides) comprising a methylation or acetylation site of the disclosure, antibodies specifically bind to a methylation or acetylation site of the disclosure, and diagnostic and therapeutic uses of the above.

Methylation and acetylation sites

LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.

System and method for grouping precursor and fragment ions using selected ion chromatograms

A method for matching a precursor ion with one or more related product ions includes providing input data sets obtained from sample injections, each of the data sets including a precursor ion and one or more product ions, normalizing the input data sets in accordance with a single retention time for the precursor ion, determining which product ions are within a predetermined retention time window with respect to the single retention time, and, if a product ion is within the predetermined retention time window for a specified number of the input data sets, determining that the product ion is related to the precursor having the single retention time. An apparatus for analyzing a sample includes a chromatography module, a mass-spectrometry module in communication with the chromatography module, and control unit in communication with the chromatography module and the mass-spectrometry module.

Method and apparatus for performing retention time matching

Embodiments of the present invention are directed to apparatus and methods for performing mass spectrometry. Data pair information is subjected to an ion audit process in which data pair information that relates to scored compounds is subtracted from the data pair information. The depleted information more readily reveals data pair information for compounds present with smaller signals.

Apparatus and method for performing mass spectroscopy

Techniques are described for performing mass spectrometry. A stream of one or more ions is generated. The stream is transmitted into a collision cell over a period of time. In accordance with a set of criteria including a retention time of one or more precursor ions, a collision energy of the collision cell is selected to generate one or more product ions for said one or more precursor ions in said stream.

Techniques for efficient fragmentation of peptides

A method () for analyzing chemicals includes fractionating a complex sample into at least two sample portions that each includes potions of two polypeptides though in different concentration ratios, digesting and performing LC/MS on each of the sample portions (, and associating precursor ions observed via LC/MS with their corresponding polypeptide in response to LC/MS provided intensity data (). A set of precursor ions that has substantially similar intensity ratios in both sample portions is determined to be associated with the same polypeptide.

Method and apparatus for fractionation-based chemical analyses

Absolute quantitation of protein in a sample is provided by comparing a sum or average of the N highest ionization intensities observed for peptides of a particular protein along with a calibration standard. The calibration standard can be in the form of a table generated by prior protein peptide analysis performed using one or more pre-determined proteins. The comparison is used to determine a corresponding absolute quantity of protein based on the observed sum or average of ionization intensities. A simple conversion factor can be applied to the calibration standard value to determine the absolute quantity of protein in the sample.

System and method for absolute quantitation of proteins

Techniques are described for matching a precursor ion with one or more related product ions. Input data sets are obtained from a plurality of injections. Each of the input data sets includes a same precursor ion and one or more product ions. The input data sets are normalized in accordance with a single retention time for the precursor ion. For each input data set, it is determined which product ions are within a predetermined retention time window with respect to the single retention time for the precursor ion. If a product ion is within the predetermined retention time window in at least one of the input data sets, it is determined that the product ion is related to the precursor ion. An apparatus for analyzing a sample includes a chromatography module, a mass-spectrometry module, and a control unit.

Techniques for performing retention-time matching of precursor and product ions and for constructing precursor and product ion spectra

Methods and apparatus for performing retention-time matching

A method for analyzing chemicals includes fractionating a complex sample into at least two sample portions that each include portions of two polypeptides though in different concentration ratios, digesting and performing LC/MS on each of the sample portions, and associating precursor ions observed via LC/MS with their corresponding polypeptide in response to LC/MS-provided intensity data. A set of precursor-ions that has substantially similar intensity ratios in both sample portions is determined to be associated with the same polypeptide.

Methods and apparatus for fractionation-based chemical analyses

Protein identification in a complex sample begins by selecting a database having proteins likely to be in the sample. In-silico digestion is performed and a target peptide is selected from produced peptides. The masses of the Y- and B-ion fragments of the target peptide are determined. These masses are used to search previously obtained low- and high-energy AMRTs obtained from LC/MS analysis of the complex sample for masses on the list. Any mass observed in the data within a detection threshold are considered a hit. If enough hits accumulate in a given retention time, the target peptide is identified as being in the sample. The list of peptides identified in the complex sample can be used to identify the proteins present in the sample, track the chromatographic retention times of peptides between samples, and quantitate the peptides and proteins present in complex samples.

Method and apparatus for identifying proteins in mixtures

System and method for absolute quantitation of proteins using LC/MS

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Beverly, MA, United States of America

Jeffrey Cruz Silva