PeptideAtlasMichael J. CombNon-small Cell Lung CarcinomaTPP'https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ManageTable.cgi?TABLE_NAME=AT_sample&sample_id=6595'mcomb@cellsignal.comLungPeptideAtlasProteomicsLTQ OrbitrapHomo Sapiens (human)H520; H838; H1437; H1563; H1568; H1792; H1944; H2170; H2172; HCC827; H2228; H2347; A549; H441; H1703; H1373; H358; H1993; Calu-3; H1648; H1975; H1666; H1869; H1650; H1734; H1793; H2023; H661; H2444; H1299; H1693; H226; H1623; H1651; H460; H2122; SKMES-1; HCC78; Cal-12T; HCC366; HCC15; HCC44; LOU-NH91.Data analysis and interpretation remain major logistical challenges when attempting to identify large numbers of protein phosphorylation sites by nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS) (Supplementary Figure 1 online). In this report we address challenges that are often only addressable by laborious manual validation, including data set error, data set sensitivity and phosphorylation site localization. We provide a large-scale phosphorylation data set with a measured error rate as determined by the target-decoy approach, we demonstrate an approach to maximize data set sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs), and we present a probability-based score, the Ascore, that measures the probability of correct phosphorylation site localization based on the presence and intensity of site-determining ions in MS/MS spectra. We applied our methods in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we identified 1,761 nonredundant phosphorylation sites from 491 proteins with a peptide false-positive rate of 1.3%.A probability-based approach for high-throughput protein phosphorylation analysis and site localization.Beausoleil Sean A SA, Villén Judit J, Gerber Scott A SA, Rush John J, Gygi Steven P 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X5Q8NE71Q8NEF9Q8NEJ9Q8NEY8Q8NEY8-3Q8NFC6Q8NFH5Q8NHQ9Q8NHW5Q8NI22Q8NI36Q8TAP8Q8TAQ2Q8TB72Q8TBA6Q8TCJ2Q8TDD1Q8TDD1-2Q8TEA8Q8TEK3Q8WU90Q8WUA2Q8WUY3Q8WUZ0Q8WVC0Q8WWM7Q8WWM7-3Q8WWM7-4Q8WWQ0Q8WWY3Q8WX92Q8WXI9Q8WYP5Q92466Q92504Q92508Q92538Q92538-2Q92552Q92560Q92613Q92614Q92621Q92667Q92685Q92688Q92733Q92769Q92785Q92797Q92804Q92804-2Q92882Q92887Q92890Q92922Q92945Q92974Q93045Q95604Q96A57Q96AE4Q96AQ6Q96B23Q96B36Q96B97Q96B97-2Q96CB8Q96D46Q96E39Q96EV2Q96EZ8Q96FV9Q96GM8Q96GP6Q96HA1Q96HS1Q96JM3Q96JP5Q96K49Q96KC8Q96KR1Q96MU7Q96N67Q96NB3Q96PK6Q96PU5Q96QD9Q96QE2Q96QR8Q96RE7Q96RU3Q96S94Q96ST2Q96ST3Q96T23Q96T37Q96T58Q96T60Q96TA1Q96TC7Q99081Q99442Q99567Q99575Q99666Q99714Q99733Q99733-2Q99848Q9BQE3Q9BQE5Q9BQG0Q9BRD0Q9BRR8Q9BRS2Q9BTC0Q9BTK6Q9BTU6Q9BUA3Q9BUH6Q9BUJ2Q9BUR4Q9BV36Q9BVA1Q9BVC5Q9BVG4Q9BVJ6Q9BVV8Q9BW71Q9BXB4Q9BXK5Q9BXW6Q9BXY0Q9BY44Q9BYG3Q9BYW2Q9BYX7Q9BZL6Q9C004Q9C0B5Q9C0E8Q9C0H2Q9GZR7Q9GZV4Q9GZY8-2Q9H019Q9H0C8Q9H0D6Q9H0E9-2Q9H0G5Q9H0L4Q9H0S4Q9H0U4Q9H1A4Q9H1B7Q9H1E3Q9H2J7Q9H2K8Q9H2P0Q9H2Y7Q9H307Q9H330Q9H3N1Q9H3S7Q9H3Z4Q9H3Z4-2Q9H4L4Q9H4M7Q9H4M7-2Q9H501Q9H6F5Q9H6S0Q9H6Y2Q9H7L9Q9H7N4Q9H8G2Q9H8H0Q9H8M2Q9H8S9Q9H8W4Q9H8Y8Q9H9J4Q9HAN9Q9HAU0Q9HB58Q9HB90Q9HCD5Q9HCG8Q9HCN4Q9NPH3Q9NQ55Q9NQC3Q9NQC3-2Q9NQC3-5Q9NQL2Q9NQQ7Q9NQS7Q9NQZ2Q9NR30Q9NRA2Q9NRX5Q9NRY4Q9NS56Q9NS69Q9NS91Q9NTI5Q9NTJ3Q9NU22Q9NUM4Q9NV56Q9NVM9Q9NVR2Q9NVU7Q9NWH9Q9NWQ8Q9NWS9Q9NWW5Q9NX40Q9NX63Q9NX70Q9NXC5Q9NXG2Q9NY65Q9NYB0Q9NYF8Q9NYF8-3Q9NYF8-4Q9NYM9Q9NYV4Q9NYV4-2Q9NYY8Q9NZ63Q9NZI8Q9NZM3Q9P035Q9P0V3Q9P1Y6Q9P2E9Q9P2I0Q9P2K5Q9UBB9Q9UBC2Q9UBC2-2Q9UER7Q9UEY8Q9UEY8-2Q9UFC0Q9UFW8Q9UGH3Q9UH62Q9UHB6Q9UHB7Q9UHD8Q9UHD8-2Q9UHD8-5Q9UID3Q9UIF9Q9UIG0Q9UII2Q9UK58Q9UK76Q9UK76-2Q9UKA4Q9UKJ3Q9UKL0Q9UKM9Q9UKS6Q9UKV3Q9UKV3-5Q9ULC3Q9ULH0Q9ULH0-4Q9ULL5-3Q9ULM3Q9ULU4Q9ULW0Q9ULX3Q9UN86Q9UN86-2Q9UNE7Q9UNF0Q9UNF0-2Q9UNF1Q9UNX4Q9UPN6Q9UPQ9Q9UPQ9-2Q9UPW0Q9UQ35Q9UQ49Q9UQR1Q9Y232Q9Y232-2Q9Y241Q9Y266Q9Y2F5Q9Y2J2Q9Y2J2-4Q9Y2W1Q9Y2W2Q9Y2X3Q9Y2X7Q9Y2X7-3Q9Y320Q9Y385Q9Y388Q9Y3B9Q9Y3D3Q9Y3L3Q9Y3T9Q9Y485Q9Y487Q9Y4E1Q9Y4F1Q9Y4H2Q9Y4I1Q9Y4I1-3Q9Y4W2Q9Y520Q9Y5B6Q9Y5B9Q9Y5J1Q9Y5Q9Q9Y606Q9Y608Q9Y618Q9Y666Q9Y6D5Q9Y6G9Q9Y6M1S4R359-HSPA1B;HSPA1ATUBB2816041385788147817679481718626693519606