← Back
Home › Systems › Biotech and life sciences

proteomics-ms

mass-spectrometry proteomics identification and quantification

MaxQuant, DIA-NN, Spectronaut

SystemTechniques · 4Primitives · 24 proteomics-ms Isotope pattern deconvolutionphysics · medium: Fit isotopic envelopes to mass spectrum peaks to assign charge and monoisotopic mass and collapse peaks to neutral massesPeptide spectrum matchingphysics · medium: Score observed MS/MS spectra against theoretical fragment spectra of digested database peptides to pick the best peptide matchDynamic time warpingsignal-processing · medium: DTW alignment of time series and trajectories of different speedInverted indexstorage · medium: Map each term to a sorted, compressed list of the documents containing it; the core of full-text search and other fast set queries.›Robust statisticsstatistics · low: Location and scale estimates (median, MAD, trimmed mean, Huber M-estimator) that stay correct when a minority of the data is garbage.›Deflatecompression · low: DEFLATE/gzip: LZ77 + Huffman, the format behind HTTP gzip, zip and PNGUnion-findgraphs · low: Disjoint-set forest with union by size and path compression; merges sets and answers same-set queries in effectively constant time.›Linear and logistic regressionmachine-learning · low: Fit a weighted sum of features to a number (least squares) or a probability (logistic); the baseline every model must beat.›Recurrent networksmachine-learning · low: GRU and LSTM cells for streaming sequence modelsFast Fourier transformnumerics · low: Computes the DFT in O(n log n) by recursively splitting into even and odd halves; the basis of fast convolution and spectral methods.›Spline interpolationnumerics · low: Linear, bilinear/trilinear and cubic spline interpolation on grids and tablesMolecular fingerprints similarityphysics · low: Circular (ECFP/Morgan) bit fingerprints and Tanimoto similarity with popcountTop-k selectionsearch-sort · low: Keep the k best of n items without sorting all n - bounded min-heap for streams, quickselect for arrays, threshold pruning to skip most items.›Peak detectionsignal-processing · low: Robust peak and event detection in noisy signals with adaptive thresholds and refractory periodsTarget decoy fdrstatistics · low: Estimate false discovery rate by searching a decoy database alongside targets and thresholding scores by decoy fraction (q-values)XML Streaming Parserstorage · low: Tokenize XML into start, text and end events in constant memory, so a few fields can be extracted from huge, broken or hostile documents.›SIMD programminghardware-os · low: Process 4-16 lanes per instruction with AVX2, AVX-512 or NEON via Rust std::arch, with runtime dispatch and a portable fallback.›Bit packing and PFORcompression · low: Store blocks of integers with exactly b bits each and patch rare outliers separately (PFOR); the fastest integer codec family, billions of values per second.›Delta encodingcompression · low: Store differences between consecutive values instead of the values, turning sorted IDs, timestamps and counters into small numbers that pack into few bits.›Varint (LEB128)compression · low: Variable-length integers in 7-bit groups with a continuation bit; small numbers take 1 byte, the wire format of Protobuf, WebAssembly and DWARF.›+ 8 more primitives