Method and system for the identification of compounds in complex biological or environmental samples by receiving (102) a mass spectrum (1) from a mass spectrometry coupled with a separation technique; for each data point (2) of the mass spectrum (1), annotating (106) in an annotation database (12) combinations of formulas and adducts the theoretical mass-to-charge ratio of which (m/z).sup.T corresponds to the mass-to-charge ratio (m/z) measured of the data point (2); for each formula and adduct annotated, detecting (108) regions of interest in a retention time range (RT.sub.0-RT.sub.1) according to characterisation criteria; generating (110) an inclusion list (14) with the retention time ranges (RT.sub.0-RT.sub.1) and the theoretical mass-to-charge ratios (m/z).sup.T of the formulas and adducts associated with the regions of interest; and sending (112) the inclusion list to a mass spectrometer for the identification of compounds in the sample by tandem mass spectrometry.

Techniques for real-time or substantially real-time peak detection are described. In one embodiment, for example, logic coupled to memory may be configured to receive data from at least one analytical instrument and perform processing or analysis on the received data. Moreover, the logic may be configured to determine, via one or more GPUs or CPUs (or both), one or more peaks based on the processing or the analysis of the received data and generate peak detection data based on the detected one or more peaks in real-time or substantially real-time. Other embodiments are described.

Methods, devices, and systems for improving the quality of electrospray ionization mass spectrometer (ESI-MS) data are described, as are methods, devices, and systems for achieving improved correlation between chemical separation data and mass spectrometry data.

The present invention relates to a method for identifying a chemical structure of a wide variety of low molecular weight compounds using mass-to-charge ratio and collision cross section of fragment ions of an analyte compound. The analyte compound is ionized and fragmented, and the fragment ions are measured by a mass spectrometer with an ion mobility spectrometry measurement device. According to the present method, it does not depend on any compound class-specific characteristics or structural features, therefore enabling determinations of any classes of low molecular weight compounds, which does not limit to a specific compound class. The present invention comprises three methods which share a common data structure and s data processing method.

A method of predicting whether an MDS patient has a good or poor prognosis uses a general purpose computer configured as a classifier and mass-spectrometry data obtained from a blood-based sample. The classifier assigns a classification label of either Early or Late (or the equivalent) to the patient's sample. Patients classified as Early are predicted to have a poor prognosis or worse survival whereas those patients classified as Late are predicted to have a relatively better prognosis and longer survival time. The groupings demonstrated a large effect size between groups in Kaplan-Meier analysis of survival. Most importantly, while the classifications generated were correlated with other prognostic factors, such as IPSS score and genetic category, multivariate and subgroup analysis showed that they had significant independent prognostic power complementary to the existing prognostic factors.

A method of performing mass spectrometry includes accumulating, over an accumulation time, ions produced from components eluting from a chromatography column and transferring the accumulated ions to a mass analyzer. During an acquisition, a mass spectrum of detected ions derived from the transferred ions is acquired. An elution profile is obtained from a series of acquired mass spectra including the acquired mass spectrum and a plurality of previously-acquired mass spectra. The elution profile includes a plurality of detection points representing intensity of the detected ions as a function of time. A current signal state of the elution profile is classified based on a subset of detection points included in the plurality of detection points. The accumulation time for a next acquisition of a mass spectrum is set based on the classified current signal state of the elution profile.

Methods and computer systems related to image-based data analysis such as mass spectrometric data analysis. Methods and computer systems herein utilize multiple micro-processes operating concurrently to carry out rapid, efficient, and automated analysis of mass spectrometry data.

A method includes: performing a time-frequency analysis on measurement data to obtain waveform data representing a temporal change in the intensity of each of a plurality of frequency components; dividing the waveform data of each of a plurality of predetermined frequencies into a plurality of segments so that each section where positive values successively occur and each section where negative values successively occur in a time-axis direction are defined as one segment; calculating the area of each of the segments to obtain segment values; creating, for the waveform data of each of the predetermined frequency components, a selected segment group by excluding a segment whose segment value exceeds a predetermined reference value from the segments in the waveform data; and determining a noise level of each of the predetermined frequency components based on the average value of the segment values of the segments included in the selected segment group.

The invention relates to reducing harmonic signals in FT-ICR spectra. Since harmonic signals in quadrupolar 2ω-detection can be more abundant for the same ion motion in the ICR cell as compared to harmonic signals in classical dipolar 1ω-detection, they could hitherto not be reduced to satisfactory levels by any known method, such as gated deflection during ion introduction into, and correcting for an offset electric field axis in the ICR cell. The present disclosure foresees, in addition to other methods carried out for improving the measurement conditions as the case may be, performing the quadrupolar 2ω-detection at least twice, where the phase of the ion excitation radio frequency is turned by 180° in the second measurement. From the sum transient, a Fourier-transformed spectrum is derived. As a result, the broad band spectra of complex substance mixtures like crude oil become cleaner, and misinterpretations of false (harmonic) peaks are minimized.

A method is disclosed for predicting in advance whether a melanoma patient is likely to benefit from high dose IL2 therapy in treatment of the cancer. The method makes use of mass spectrometry data obtained from a blood-based sample of the patient and a computer configured as a classifier and making use of a reference set of mass spectral data obtained from a development set of blood-based samples from other melanoma patients. A variety of classifiers for making this prediction are disclosed, including a classifier developed from a set of blood-based samples obtained from melanoma patients treated with high dose IL2 as well as melanoma patients treated with an anti-PD-1 immunotherapy drug. The classifiers developed from anti-PD-1 and IL2 patient sample cohorts can also be used in combination to guide treatment of a melanoma patient.